Patent application title: MAIZE EVENT DP-004114-3 AND METHODS FOR DETECTION THEREOF
Inventors:
IPC8 Class: AC12N1582FI
USPC Class:
1 1
Class name:
Publication date: 2020-12-10
Patent application number: 20200385749
Abstract:
The invention provides DNA compositions that relate to transgenic insect
resistant maize plants. Also provided are assays for detecting the
presence of the maize DP-004114-3 event based on the DNA sequence of the
recombinant construct inserted into the maize genome and the DNA
sequences flanking the insertion site. Kits and conditions useful in
conducting the assays are provided.Claims:
1-9. (canceled)
10. A method of determining zygosity of DNA of a corn plant comprising corn event DP-004114-3 in a biological sample comprising: (a) contacting said sample with a primer pair selected from the group consisting of SEQ ID NOs: 29 and 30, or a primer pair selected from the group consisting of SEQ ID NOs: 33 and 34, such that (1) when used in a nucleic acid amplification reaction comprising corn event DP-004114-3 DNA, produces a first amplicon that is diagnostic for corn event DP-004114-3, and (2) when used in a nucleic acid amplification reaction comprising corn genomic DNA other than DP-004114-3 DNA, produces a second amplicon that is diagnostic for corn genomic DNA other than DP-004114-3 DNA; (b) performing a nucleic acid amplification reaction; and (c) detecting the amplicons so produced, wherein detection of presence of both amplicons indicates that said sample is heterozygous for corn event DP-004114-3 DNA, wherein detection of only the first amplicon indicates that said sample is homozygous for corn event DP-004114-3 DNA.
11. A pair of polynucleotide primers comprising a first polynucleotide primer and a second polynucleotide primer, wherein the first polynucleotide primer comprises the nucleotide sequence of SEQ ID NO: 29 and the complement thereof, and the second polynucleotide primer comprises the nucleotide sequence of SEQ ID NO: 30 and the complement thereof, which function together in the presence of a DP-004114-3 DNA template in a sample to produce an amplicon diagnostic for event DP-004114-3.
12. A kit for detecting nucleic acids that are unique to event DP-004114-3 comprising is a primer pair consisting of SEQ ID NOs: 29 and 30, or SEQ ID NOs: 33 and 34, and the complements thereof, which function as a primer pair in a nucleic acid detection method, and which upon amplification of or hybridization to a target nucleic acid sequence in a sample followed by detection of the amplicon or hybridization to the target sequence, are diagnostic for the presence of nucleic acid sequences unique to event DP-004114-3 in the sample.
Description:
CROSS REFERENCE
[0001] This utility application claims the benefit U.S. Provisional Application No. 61/617,990 filed Mar. 30, 2012, which is incorporated herein by reference in its entirety.
REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY
[0002] The official copy of the sequence listing is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file named "5251USCNT2_SequenceListing.txt" created on Mar. 8, 2013, and having a size of 51 kilobytes and is filed concurrently with the specification. The sequence listing contained in this ASCII formatted document is part of the specification and is herein incorporated by reference in its entirety.
FIELD OF INVENTION
[0003] Embodiments of the present invention relate to the field of plant molecular biology, specifically embodiment of the invention relate to DNA constructs for conferring insect resistance to a plant. Embodiments of the invention more specifically relate to insect resistant corn plant event DP-004114-3 and to assays for detecting the presence of corn event DP-004114-3 in a sample and compositions thereof.
BACKGROUND OF INVENTION
[0004] An embodiment of this invention relates to the insect resistant corn (Zea mays) plant DP-004114-3, also referred to as "maize line DP-004114-3," "maize event DP-004114-3," and "4114 maize," and to the DNA plant expression construct of corn plant DP-004114-3 and the detection of the transgene/flanking insertion region in corn plant DP-004114-3 and progeny thereof.
[0005] Corn is an important crop and is a primary food source in many areas of the world. Damage caused by insect pests is a major factor in the loss of the world's corn crops, despite the use of protective measures such as chemical pesticides. In view of this, insect resistance has been genetically engineered into crops such as corn in order to control insect damage and to reduce the need for traditional chemical pesticides. One group of genes which have been utilized for the production of transgenic insect resistant crops is the delta-endotoxin group from Bacillus thuringiensis (Bt). Delta-endotoxins have been successfully expressed in crop plants such as cotton, potatoes, rice, sunflower, as well as corn, and have proven to provide excellent control over insect pests. (Perlak, F. J et al. (1990) Bio/Technology 8:939-943; Perlak, F. J. et al. (1993) Plant Mol. Biol. 22:313-321; Fujimoto, H. et al. (1993) Bio/Technology 11:1151-1155; Tu et al. (2000) Nature Biotechnology 18:1101-1104; PCT publication WO 01/13731; and Bing, J. W. et al. (2000) Efficacy of Cry1F Transgenic Maize, 14.sup.th Biennial International Plant Resistance to Insects Workshop, Fort Collins, Colo.).
[0006] The expression of foreign genes in plants is known to be influenced by their location in the plant genome, perhaps due to chromatin structure (e.g., heterochromatin) or the proximity of transcriptional regulatory elements (e.g., enhancers) close to the integration site (Weising et al. (1988) Ann. Rev. Genet. 22:421-477). At the same time the presence of the transgene at different locations in the genome will influence the overall phenotype of the plant in different ways. For this reason, it is often necessary to screen a large number of events in order to identify an event characterized by optimal expression of an introduced gene of interest. For example, it has been observed in plants and in other organisms that there may be a wide variation in levels of expression of an introduced gene among events. There may also be differences in spatial or temporal patterns of expression, for example, differences in the relative expression of a transgene in various plant tissues, that may not correspond to the patterns expected from transcriptional regulatory elements present in the introduced gene construct. For this reason, it is common to produce hundreds to thousands of different events and screen those events for a single event that has desired transgene expression levels and patterns for commercial purposes. An event that has desired levels or patterns of transgene expression is useful for introgressing the transgene into other genetic backgrounds by sexual outcrossing using conventional breeding methods. Progeny of such crosses maintain the transgene expression characteristics of the original transformant. This strategy is used to ensure reliable gene expression in a number of varieties that are well adapted to local growing conditions.
[0007] It would be advantageous to be able to detect the presence of a particular event in order to determine whether progeny of a sexual cross contain a transgene of interest. In addition, a method for detecting a particular event would be helpful for complying with regulations requiring the pre-market approval and labeling of foods derived from recombinant crop plants, for example, or for use in environmental monitoring, monitoring traits in crops in the field, or monitoring products derived from a crop harvest, as well as for use in ensuring compliance of parties subject to regulatory or contractual terms.
[0008] It is possible to detect the presence of a transgene by any nucleic acid detection method known in the art including, but not limited to, the polymerase chain reaction (PCR) or DNA hybridization using nucleic acid probes. These detection methods generally focus on frequently used genetic elements, such as promoters, terminators, marker genes, etc., because for many DNA constructs, the coding region is interchangeable. As a result, such methods may not be useful for discriminating between different events, particularly those produced using the same DNA construct or very similar constructs unless the DNA sequence of the flanking DNA adjacent to the inserted heterologous DNA is known. For example, an event-specific PCR assay is described in U.S. Pat. No. 6,395,485 for the detection of elite event GAT-ZM1. Accordingly, it would be desirable to have a simple and discriminative method for the identification of event DP-004114-3.
SUMMARY OF INVENTION
[0009] Embodiments of this invention relate to methods for producing and selecting an insect resistant monocot crop plant. More specifically, a DNA construct is provided that when expressed in plant cells and plants confers resistance to insects. According to one aspect of the invention, a DNA construct, capable of introduction into and replication in a host cell, is provided that when expressed in plant cells and plants confers insect resistance to the plant cells and plants. Maize event DP-004114-3 was produced by Agrobacterium-mediated transformation with plasmid PHP27118. This event contains the cry1F, cry34Ab1, cry35Ab1, and pat gene cassettes, which confer resistance to certain lepidopteran and coleopteran pests, as well as tolerance to phosphinothricin.
[0010] Specifically, the first cassette contains a truncated version of the cry1F gene from Bacillus thuringiensis var. aizawai. The insertion of the cry1F gene confers resistance to damage by lepidopteran pests. The Cry1F protein (SEQ ID NO: 1) is comprised of 605 amino acids and has a molecular weight of approximately 68 kDa. The expression of the cry1F gene is controlled by the maize polyubiquitin promoter (Christensen et al. (1992) Plant Mol. Biol. 118(4):675-89), providing constitutive expression of the Cry1F protein in maize. This region also includes the 5' untranslated region (UTR) and intron associated with the native polyubiquitin promoter. The terminator for the cry1F gene is the poly(A) addition signal from Open Reading Frame 25 (ORF 25) of the Agrobacterium tumefaciens Ti plasmid pTi15955 (Barker et al. (1983) Plant Mol. Biol. 2:335-350).
[0011] The second cassette contains the cry34Ab1 gene isolated from Bacillus thuringiensis strain PS149B1 (U.S. Pat. Nos. 6,127,180; 6,624,145 and 6,340,593). The Cry34Ab1 protein (SEQ ID NO: 2) is 123 amino acid residues in length and has a molecular weight of approximately 14 kDa. The expression of the cry34Ab1 gene is controlled by a second copy of the maize polyubiquitin promoter with 5' UTR and intron (Christensen et al., 1992, supra). The terminator for the cry34Ab1 gene is the pinII terminator (Keil et al. (1986) Nucleic Acids Res. 14:5641-5650; An et al. (1989) Plant Cell 1:115-22).
[0012] The third gene cassette contains the cry35Ab1 gene, also isolated from Bacillus thuringiensis strain PS149B1 (U.S. Pat. Nos. 6,083,499; 6,548,291 and 6,340,593). The Cry35Ab1 protein (SEQ ID NO: 3) has a length of 383 amino acids and a molecular weight of approximately 44 kDa. Simultaneous expression of the Cry34Ab1 and Cry35Ab1 proteins in the plant confers resistance to coleopteran insects. The expression of the cry35Ab1 gene is controlled by the Triticum aestivum (wheat) peroxidase promoter and leader sequence (Hertig et al. (1991) Plant Mol. Biol. 16:171-174). The terminator for the cry35Ab1 gene is a second copy of the pinII terminator (Keil et al., 1986, supra; An et al., 1989, supra).
[0013] The fourth and final gene cassette contains a version of the phosphinothricin acetyl transferase gene from Streptomyces viridochromogenes (pat) that has been optimized for expression in maize. The pat gene expresses the phosphinothricin acetyl transferase enzyme (PAT) that confers tolerance to phosphinothricin. The PAT protein (SEQ ID NO: 4) is 183 amino acids residues in length and has a molecular weight of approximately 21 kDa. Expression of the pat gene is controlled by the promoter and terminator regions from the CaMV 35S transcript (Franck et al. (1980) Cell 21:285-294; Odell et al. (1985) Nature 313:810-812; Pietrzak, et al. (1986) Nucleic Acids Res. 14(14):5857-5868). Plants containing the DNA constructs are also provided.
[0014] According to another embodiment of the invention, compositions and methods are provided for identifying a novel corn plant designated DP-004114-3. The methods are based on primers or probes which specifically recognize the 5' and/or 3' flanking sequence of DP-004114-3. DNA molecules are provided that comprise primer sequences that when utilized in a PCR reaction will produce amplicons unique to the transgenic event DP-004114-3. The corn plant and seed comprising these molecules is an embodiment of this invention. Further, kits utilizing these primer sequences for the identification of the DP-004114-3 event are provided.
[0015] An additional embodiment of the invention relates to the specific flanking sequence of DP-004114-3 described herein, which can be used to develop specific identification methods for DP-004114-3 in biological samples. More particularly, the invention relates to the 5' and/or 3' flanking regions of DP-004114-3 which can be used for the development of specific primers and probes. A further embodiment of the invention relates to identification methods for the presence of DP-004114-3 in biological samples based on the use of such specific primers or probes.
[0016] According to another embodiment of the invention, methods of detecting the presence of DNA corresponding to the corn event DP-004114-3 in a sample are provided. Such methods comprise: (a) contacting the sample comprising DNA with a DNA primer set, that when used in a nucleic acid amplification reaction with genomic DNA extracted from corn event DP-004114-3 produces an amplicon that is diagnostic for corn event DP-004114-3; (b) performing a nucleic acid amplification reaction, thereby producing the amplicon; and (c) detecting the amplicon.
[0017] According to another embodiment of the invention, methods of detecting the presence of a DNA molecule corresponding to the DP-004114-3 event in a sample, such methods comprising: (a) contacting the sample comprising DNA extracted from a corn plant with a DNA probe molecule that hybridizes under stringent hybridization conditions with DNA extracted from corn event DP-004114-3 and does not hybridize under the stringent hybridization conditions with a control corn plant DNA; (b) subjecting the sample and probe to stringent hybridization conditions; and (c) detecting hybridization of the probe to the DNA. More specifically, a method for detecting the presence of a DNA molecule corresponding to the DP-004114-3 event in a sample, such methods, consisting of (a) contacting the sample comprising DNA extracted from a corn plant with a DNA probe molecule that consists of sequences that are unique to the event, e.g. junction sequences, wherein said DNA probe molecule hybridizes under stringent hybridization conditions with DNA extracted from corn event DP-004114-3 and does not hybridize under the stringent hybridization conditions with a control corn plant DNA; (b) subjecting the sample and probe to stringent hybridization conditions; and (c) detecting hybridization of the probe to the DNA.
[0018] In addition, a kit and methods for identifying event DP-004114-3 in a biological sample which detects a DP-004114-3 specific region are provided.
[0019] DNA molecules are provided that comprise at least one junction sequence of DP-004114-3; wherein a junction sequence spans the junction between heterologous DNA inserted into the genome and the DNA from the corn cell flanking the insertion site, i.e. flanking DNA, and is diagnostic for the DP-004114-3 event.
[0020] According to another embodiment of the invention, methods of producing an insect resistant corn plant that comprise the steps of: (a) sexually crossing a first parental corn line comprising the expression cassettes of the invention, which confers resistance to insects, and a second parental corn line that lacks insect resistance, thereby producing a plurality of progeny plants; and (b) selecting a progeny plant that is insect resistant. Such methods may optionally comprise the further step of back-crossing the progeny plant to the second parental corn line to producing a true-breeding corn plant that is insect resistant.
[0021] A further embodiment of the invention provides a method of producing a corn plant that is resistant to insects comprising transforming a corn cell with the DNA construct PHP27118, growing the transformed corn cell into a corn plant, selecting the corn plant that shows resistance to insects, and further growing the corn plant into a fertile corn plant. The fertile corn plant can be self pollinated or crossed with compatible corn varieties to produce insect resistant progeny.
[0022] Another embodiment of the invention further relates to a DNA detection kit for identifying maize event DP-004114-3 in biological samples. The kit comprises a first primer which specifically recognizes the 5' or 3' flanking region of DP-004114-3, and a second primer which specifically recognizes a sequence within the foreign DNA of DP-004114-3, or within the flanking DNA, for use in a PCR identification protocol. A further embodiment of the invention relates to a kit for identifying event DP-004114-3 in biological samples, which kit comprises a specific probe having a sequence which corresponds or is complementary to, a sequence having between 80% and 100% sequence identity with a specific region of event DP-004114-3. The sequence of the probe corresponds to a specific region comprising part of the 5' or 3' flanking region of event DP-004114-3.
[0023] The methods and kits encompassed by the embodiments of the present invention can be used for different purposes such as, but not limited to the following: to identify event DP-004114-3 in plants, plant material or in products such as, but not limited to, food or feed products (fresh or processed) comprising, or derived from plant material; additionally or alternatively, the methods and kits can be used to identify transgenic plant material for purposes of segregation between transgenic and non-transgenic material; additionally or alternatively, the methods and kits can be used to determine the quality of plant material comprising maize event DP-004114-3. The kits may also contain the reagents and materials necessary for the performance of the detection method.
[0024] A further embodiment of this invention relates to the DP-004114-3 corn plant or its parts, including, but not limited to, pollen, ovules, vegetative cells, the nuclei of pollen cells, and the nuclei of egg cells of the corn plant DP-004114-3 and the progeny derived thereof. The corn plant and seed of DP-004114-3 from which the DNA primer molecules provide a specific amplicon product is an embodiment of the invention.
[0025] The foregoing and other aspects of the invention will become more apparent from the following detailed description and accompanying drawing.
BRIEF DESCRIPTION OF THE DRAWINGS
[0026] FIG. 1. Schematic diagram of plasmid PHP27118 with genetic elements indicated and Hind III restriction enzyme sites. Plasmid size is 54910 bp.
[0027] FIG. 2. Schematic diagram of the T-DNA indicating the cry1F, cry34Ab1, cry35Ab1, and pat genes (arrows) along with their respective regulatory elements. Hind III restriction enzyme sites within the T-DNA are indicated. The size of the T-DNA is 11978 bp.
[0028] FIG. 3. Schematic Diagram of the Transformation and Development of DP-004114-3.
[0029] FIG. 4. Western corn rootworm (WCRW) larvae developmental effects in the sub-lethal seedling assay employing maize hybrid seedlings in the same genetic background: DP-004114-3 maize with an isoline as a negative control. Results are based on three replicates. Graphic profiles show the percent of larvae in each of three instars at 17 days post egg hatch. A shift towards instar 3 indicates a decrease in efficacy.
[0030] FIG. 5. Schematic representation of the insert and genomic border regions sequenced in 4114 maize. The diagram indicates the PCR fragments generated from 4114 maize genomic DNA that were cloned and sequenced: fragments A through F. The vertical dash line represents the genomic border/insert junctions. Fragment G and H represent the 5' and 3' genomic border regions, respectively. Figure is not drawn to scale.
DETAILED DESCRIPTION
[0031] The following definitions and methods are provided to better define the present invention and to guide those of ordinary skill in the art in the practice of the present invention. Unless otherwise noted, terms are to be understood according to conventional usage by those of ordinary skill in the relevant art. Definitions of common terms in molecular biology may also be found in Rieger et al., Glossary of Genetics: Classical and Molecular, 5.sup.th edition, Springer-Verlag; New York, 1991; and Lewin, Genes V, Oxford University Press: New York, 1994. The nomenclature for DNA bases as set forth at 37CFR .sctn. 1.822 is used.
[0032] The following table sets forth abbreviations used throughout this document, and in particular in the Examples section.
TABLE-US-00001 Table of Abbreviations 4114 maize Maize containing event DP-004114-3 bp Base pair Bt Bacillus thuringiensis CaMV Cauliflower mosaic virus cry1F cty1F gene from Bacillus thuringiensis var. aizawai Cry1F Protein from cry1F gene cry34Ab1 cry34Ab1 gene from Bacillus thuringiensis strain PS149B1 Cry34Ab1 Protein from cry34Ab1 cry35Ab1 cry35Ab1 gene from Bacillus thuringiensis strain PS149B1 Cry35Ab1 Protein from cry35Ab1 gene kb Kilobase pair kDa KiloDalton LB Left T-DNA border pat phosphinothricin acetyl transferase gene PAT Protein from phosphinothricin acetyl transferase gene PCR Polymerase chain reaction pinII Proteinase inhibitor II gene from Solanum tuberosum RB Right T-DNA border T-DNA The transfer DNA portion of the Agrobacterium transformation plasmid between the Left and Right Borders that is expected to be transferred to the plant genome UTR Untranslated region ECB European corn borer (Ostrinia nubilalis) FAW Fall armyworm (Spodoptera frugiperda) WCRW western corn rootworm (Diabrotica virgifera virgifera)
[0033] Compositions of this disclosure include seed deposited as Patent Deposit No. PTA-11506 and plants, plant cells, and seed derived therefrom. Applicant(s) have made a deposit of at least 2500 seeds of maize event DP-004114-3 with the American Type Culture Collection (ATCC), Manassas, Va. 20110-2209 USA, on Nov. 24, 2010 and the deposits were assigned ATCC Deposit No. PTA-11506. These deposits will be maintained under the terms of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure. These deposits were made merely as a convenience for those of skill in the art and are not an admission that a deposit is required under 35 U.S.C. .sctn. 112. The seeds deposited with the ATCC on Nov. 24, 2010 were taken from the deposit maintained by Pioneer Hi-Bred International, Inc., 7250 NW 62.sup.nd Avenue, Johnston, Iowa 50131-1000. Access to this deposit will be available during the pendency of the application to the Commissioner of Patents and Trademarks and persons determined by the Commissioner to be entitled thereto upon request. Upon allowance of any claims in the application, the Applicant(s) will make available to the public, pursuant to 37 C.F.R. .sctn. 1.808, sample(s) of the deposit of at least 2500 seeds of hybrid maize with the American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, Va. 20110-2209. This deposit of seed of maize event DP-004114-3 will be maintained in the ATCC depository, which is a public depository, for a period of 30 years, or 5 years after the most recent request, or for the enforceable life of the patent, whichever is longer, and will be replaced if it becomes nonviable during that period. Additionally, Applicant(s) have satisfied all the requirements of 37 C.F.R. .sctn..sctn. 1.801-1.809, including providing an indication of the viability of the sample upon deposit. Applicant(s) have no authority to waive any restrictions imposed by law on the transfer of biological material or its transportation in commerce. Applicant(s) do not waive any infringement of their rights granted under this patent or rights applicable to event DP-004114-3 under the Plant Variety Protection Act (7 USC 2321 et seq.). Unauthorized seed multiplication prohibited. The seed may be regulated.
[0034] As used herein, the term "comprising" means "including but not limited to."
[0035] As used herein, the term "corn" means Zea mays or maize and includes all plant varieties that can be bred with corn, including wild maize species.
[0036] As used herein, the term "DP-004114-3 specific" refers to a nucleotide sequence which is suitable for discriminatively identifying event DP-004114-3 in plants, plant material, or in products such as, but not limited to, food or feed products (fresh or processed) comprising, or derived from plant material.
[0037] As used herein, the terms "insect resistant" and "impacting insect pests" refers to effecting changes in insect feeding, growth, and/or behavior at any stage of development, including but not limited to: killing the insect; retarding growth; preventing reproductive capability; inhibiting feeding; and the like.
[0038] As used herein, the terms "pesticidal activity" and "insecticidal activity" are used synonymously to refer to activity of an organism or a substance (such as, for example, a protein) that can be measured by numerous parameters including, but not limited to, pest mortality, pest weight loss, pest attraction, pest repellency, and other behavioral and physical changes of a pest after feeding on and/or exposure to the organism or substance for an appropriate length of time. For example "pesticidal proteins" are proteins that display pesticidal activity by themselves or in combination with other proteins.
[0039] "Coding sequence" refers to a nucleotide sequence that codes for a specific amino acid sequence. As used herein, the terms "encoding" or "encoded" when used in the context of a specified nucleic acid mean that the nucleic acid comprises the requisite information to guide translation of the nucleotide sequence into a specified protein. The information by which a protein is encoded is specified by the use of codons. A nucleic acid encoding a protein may comprise non-translated sequences (e.g., introns) within translated regions of the nucleic acid or may lack such intervening non-translated sequences (e.g., as in cDNA).
[0040] "Gene" refers to a nucleic acid fragment that expresses a specific protein, including regulatory sequences preceding (5' non-coding sequences) and following (3' non-coding sequences) the coding sequence. "Native gene" refers to a gene as found in nature with its own regulatory sequences. "Chimeric gene" refers any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. "Endogenous gene" refers to a native gene in its natural location in the genome of an organism. "Foreign" refers to material not normally found in the location of interest. Thus "foreign DNA" may comprise both recombinant DNA as well as newly introduced, rearranged DNA of the plant. A "foreign" gene refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes. A "transgene" is a gene that has been introduced into the genome by a transformation procedure. The site in the plant genome where a recombinant DNA has been inserted may be referred to as the "insertion site" or "target site".
[0041] As used herein, "insert DNA" refers to the heterologous DNA within the expression cassettes used to transform the plant material while "flanking DNA" can exist of either genomic DNA naturally present in an organism such as a plant, or foreign (heterologous) DNA introduced via the transformation process which is extraneous to the original insert DNA molecule, e.g. fragments associated with the transformation event. A "flanking region" or "flanking sequence" as used herein refers to a sequence of at least 20 bp, preferably at least 50 bp, and up to 5000 bp, which is located either immediately upstream of and contiguous with or immediately downstream of and contiguous with the original foreign insert DNA molecule. Transformation procedures leading to random integration of the foreign DNA will result in transformants containing different flanking regions characteristic and unique for each transformant. When recombinant DNA is introduced into a plant through traditional crossing, its flanking regions will generally not be changed. Transformants will also contain unique junctions between a piece of heterologous insert DNA and genomic DNA, or two (2) pieces of genomic DNA, or two (2) pieces of heterologous DNA. A "junction" is a point where two (2) specific DNA fragments join. For example, a junction exists where insert DNA joins flanking DNA. A junction point also exists in a transformed organism where two (2) DNA fragments join together in a manner that is modified from that found in the native organism. "Junction DNA" refers to DNA that comprises a junction point. Two junction sequences set forth in this disclosure are the junction point between the maize genomic DNA and the 5' end of the insert as set forth in SEQ ID NO: 27, and the junction point between the 3' end of the insert and maize genomic DNA as set forth in SEQ ID NO: 28.
[0042] As used herein, "heterologous" in reference to a nucleic acid is a nucleic acid that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention. For example, a promoter operably linked to a heterologous nucleotide sequence can be from a species different from that from which the nucleotide sequence was derived, or, if from the same species, the promoter is not naturally found operably linked to the nucleotide sequence. A heterologous protein may originate from a foreign species, or, if from the same species, is substantially modified from its original form by deliberate human intervention.
[0043] "Regulatory sequences" refer to nucleotide sequences located upstream (5' non-coding sequences), within, or downstream (3' non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, and polyadenylation recognition sequences.
[0044] "Promoter" refers to a nucleotide sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3' to a promoter sequence. The promoter sequence consists of proximal and more distal upstream elements, the latter elements are often referred to as enhancers. Accordingly, an "enhancer" is a nucleotide sequence that can stimulate promoter activity and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue-specificity of a promoter. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic nucleotide segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions. Promoters that cause a nucleic acid fragment to be expressed in most cell types at most times are commonly referred to as "constitutive promoters". New promoters of various types useful in plant cells are constantly being discovered; numerous examples may be found in the compilation by Okamuro and Goldberg (1989) Biochemistry of Plants 15:1-82. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, nucleic acid fragments of different lengths may have identical promoter activity.
[0045] The "translation leader sequence" refers to a nucleotide sequence located between the promoter sequence of a gene and the coding sequence. The translation leader sequence is present in the fully processed mRNA upstream of the translation start sequence. The translation leader sequence may affect numerous parameters including, processing of the primary transcript to mRNA, mRNA stability and/or translation efficiency. Examples of translation leader sequences have been described (Turner and Foster (1995) Mol. Biotechnol. 3:225-236).
[0046] The "3' non-coding sequences" refer to nucleotide sequences located downstream of a coding sequence and include polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3' end of the mRNA precursor. The use of different 3' non-coding sequences is exemplified by Ingelbrecht et al. (1989) Plant Cell 1:671-680.
[0047] A "protein" or "polypeptide" is a chain of amino acids arranged in a specific order determined by the coding sequence in a polynucleotide encoding the polypeptide.
[0048] A DNA construct is an assembly of DNA molecules linked together that provide one or more expression cassettes. The DNA construct may be a plasmid that is enabled for self replication in a bacterial cell and contains various endonuclease enzyme restriction sites that are useful for introducing DNA molecules that provide functional genetic elements, i.e., promoters, introns, leaders, coding sequences, 3' termination regions, among others; or a DNA construct may be a linear assembly of DNA molecules, such as an expression cassette. The expression cassette contained within a DNA construct comprises the necessary genetic elements to provide transcription of a messenger RNA. The expression cassette can be designed to express in prokaryote cells or eukaryotic cells. Expression cassettes of the embodiments of the present invention are designed to express in plant cells.
[0049] The DNA molecules of embodiments of the invention are provided in expression cassettes for expression in an organism of interest. The cassette will include 5' and 3' regulatory sequences operably linked to a coding sequence. "Operably linked" means that the nucleic acid sequences being linked are contiguous and, where necessary to join two protein coding regions, contiguous and in the same reading frame. Operably linked is intended to indicate a functional linkage between a promoter and a second sequence, wherein the promoter sequence initiates and mediates transcription of the DNA sequence corresponding to the second sequence. The cassette may additionally contain at least one additional gene to be co-transformed into the organism. Alternatively, the additional gene(s) can be provided on multiple expression cassettes or multiple DNA constructs.
[0050] The expression cassette will include in the 5' to 3' direction of transcription: a transcriptional and translational initiation region, a coding region, and a transcriptional and translational termination region functional in the organism serving as a host. The transcriptional initiation region (i.e., the promoter) may be native or analogous, or foreign or heterologous to the host organism. Additionally, the promoter may be the natural sequence or alternatively a synthetic sequence. The expression cassettes may additionally contain 5' leader sequences in the expression cassette construct. Such leader sequences can act to enhance translation.
[0051] It is to be understood that as used herein the term "transgenic" includes any cell, cell line, callus, tissue, plant part, or plant, the genotype of which has been altered by the presence of a heterologous nucleic acid including those transgenics initially so altered as well as those created by sexual crosses or asexual propagation from the initial transgenic. The term "transgenic" as used herein does not encompass the alteration of the genome (chromosomal or extra-chromosomal) by conventional plant breeding methods or by naturally occurring events such as random cross-fertilization, non-recombinant viral infection, non-recombinant bacterial transformation, non-recombinant transposition, or spontaneous mutation.
[0052] A transgenic "event" is produced by transformation of plant cells with a heterologous DNA construct(s), including a nucleic acid expression cassette that comprises a transgene of interest, the regeneration of a population of plants resulting from the insertion of the transgene into the genome of the plant, and selection of a particular plant characterized by insertion into a particular genome location. An event is characterized phenotypically by the expression of the transgene. At the genetic level, an event is part of the genetic makeup of a plant. The term "event" also refers to progeny produced by a sexual outcross between the transformant and another variety that include the heterologous DNA. Even after repeated back-crossing to a recurrent parent, the inserted DNA and flanking DNA from the transformed parent is present in the progeny of the cross at the same chromosomal location. The term "event" also refers to DNA from the original transformant comprising the inserted DNA and flanking sequence immediately adjacent to the inserted DNA that would be expected to be transferred to a progeny that receives inserted DNA including the transgene of interest as the result of a sexual cross of one parental line that includes the inserted DNA (e.g., the original transformant and progeny resulting from selfing) and a parental line that does not contain the inserted DNA.
[0053] An insect resistant DP-004114-3 corn plant can be bred by first sexually crossing a first parental corn plant consisting of a corn plant grown from the transgenic DP-004114-3 corn plant and progeny thereof derived from transformation with the expression cassettes of the embodiments of the present invention that confers insect resistance, and a second parental corn plant that lacks insect resistance, thereby producing a plurality of first progeny plants; and then selecting a first progeny plant that is resistant to insects; and selfing the first progeny plant, thereby producing a plurality of second progeny plants; and then selecting from the second progeny plants an insect resistant plant. These steps can further include the back-crossing of the first insect resistant progeny plant or the second insect resistant progeny plant to the second parental corn plant or a third parental corn plant, thereby producing a corn plant that is resistant to insects.
[0054] As used herein, the term "plant" includes reference to whole plants, plant organs (e.g., leaves, stems, roots, etc.), seeds, plant cells, and progeny of same. Parts of transgenic plants understood to be within the scope of the invention comprise, for example, plant cells, protoplasts, tissues, callus, embryos as well as flowers, stems, fruits, leaves, and roots originating in transgenic plants or their progeny previously transformed with a DNA molecule of the invention and therefore consisting at least in part of transgenic cells, are also an embodiment of the present invention.
[0055] As used herein, the term "plant cell" includes, without limitation, seeds, suspension cultures, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen, and microspores. The class of plants that can be used in the methods of the invention is generally as broad as the class of higher plants amenable to transformation techniques, including both monocotyledonous and dicotyledonous plants.
[0056] "Transformation" refers to the transfer of a nucleic acid fragment into the genome of a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as "transgenic" organisms. Examples of methods of plant transformation include Agrobacterium-mediated transformation (De Blaere et al. (1987) Meth. Enzymol. 143:277) and particle-accelerated or "gene gun" transformation technology (Klein et al. (1987) Nature (London) 327:70-73; U.S. Pat. No. 4,945,050, incorporated herein by reference). Additional transformation methods are disclosed below.
[0057] Thus, isolated polynucleotides of the invention can be incorporated into recombinant constructs, typically DNA constructs, which are capable of introduction into and replication in a host cell. Such a construct can be a vector that includes a replication system and sequences that are capable of transcription and translation of a polypeptide-encoding sequence in a given host cell. A number of vectors suitable for stable transfection of plant cells or for the establishment of transgenic plants have been described in, e.g., Pouwels et al., (1985; Supp. 1987) Cloning Vectors: A Laboratory Manual, Weissbach and Weissbach (1989) Methods for Plant Molecular Biology, (Academic Press, New York); and Flevin et al., (1990) Plant Molecular Biology Manual, (Kluwer Academic Publishers). Typically, plant expression vectors include, for example, one or more cloned plant genes under the transcriptional control of 5' and 3' regulatory sequences and a dominant selectable marker. Such plant expression vectors also can contain a promoter regulatory region (e.g., a regulatory region controlling inducible or constitutive, environmentally- or developmentally-regulated, or cell- or tissue-specific expression), a transcription initiation start site, a ribosome binding site, an RNA processing signal, a transcription termination site, and/or a polyadenylation signal.
[0058] It is also to be understood that two different transgenic plants can also be mated to produce offspring that contain two independently segregating added, exogenous genes. Selfing of appropriate progeny can produce plants that are homozygous for both added, exogenous genes. Back-crossing to a parental plant and out-crossing with a non-transgenic plant are also contemplated, as is vegetative propagation. Descriptions of other breeding methods that are commonly used for different traits and crops can be found in one of several references, e.g., Fehr, in Breeding Methods for Cultivar Development, Wilcos J. ed., American Society of Agronomy, Madison Ws. (1987).
[0059] A "probe" is an isolated nucleic acid to which is attached a conventional detectable label or reporter molecule, e.g., a radioactive isotope, ligand, chemiluminescent agent, or enzyme. Such a probe is complementary to a strand of a target nucleic acid, in the case of the present invention, to a strand of isolated DNA from corn event DP-004114-3 whether from a corn plant or from a sample that includes DNA from the event. Probes according to the present invention include not only deoxyribonucleic or ribonucleic acids but also polyamides and other probe materials that bind specifically to a target DNA sequence and can be used to detect the presence of that target DNA sequence.
[0060] "Primers" are isolated nucleic acids that are annealed to a complementary target DNA strand by nucleic acid hybridization to form a hybrid between the primer and the target DNA strand, then extended along the target DNA strand by a polymerase, e.g., a DNA polymerase. Primer pairs of the invention refer to their use for amplification of a target nucleic acid sequence, e.g., by PCR or other conventional nucleic-acid amplification methods. "PCR" or "polymerase chain reaction" is a technique used for the amplification of specific DNA segments (see, U.S. Pat. Nos. 4,683,195 and 4,800,159; herein incorporated by reference).
[0061] Probes and primers are of sufficient nucleotide length to bind to the target DNA sequence specifically in the hybridization conditions or reaction conditions determined by the operator. This length may be of any length that is of sufficient length to be useful in a detection method of choice. Generally, 11 nucleotides or more in length, 18 nucleotides or more, and 22 nucleotides or more, are used. Such probes and primers hybridize specifically to a target sequence under high stringency hybridization conditions. Probes and primers according to embodiments of the present invention may have complete DNA sequence similarity of contiguous nucleotides with the target sequence, although probes differing from the target DNA sequence and that retain the ability to hybridize to target DNA sequences may be designed by conventional methods. Probes can be used as primers, but are generally designed to bind to the target DNA or RNA and are not used in an amplification process.
[0062] Specific primers can be used to amplify an integration fragment to produce an amplicon that can be used as a "specific probe" for identifying event DP-004114-3 in biological samples. When the probe is hybridized with the nucleic acids of a biological sample under conditions which allow for the binding of the probe to the sample, this binding can be detected and thus allow for an indication of the presence of event DP-004114-3 in the biological sample. Such identification of a bound probe has been described in the art. In an embodiment of the invention the specific probe is a sequence which, under optimized conditions, hybridizes specifically to a region within the 5' or 3' flanking region of the event and also comprises a part of the foreign DNA contiguous therewith. The specific probe may comprise a sequence of at least 80%, between 80 and 85%, between 85 and 90%, between 90 and 95%, and between 95 and 100% identical (or complementary) to a specific region of the event.
[0063] Methods for preparing and using probes and primers are described, for example, in Sambrook et al., Molecular Cloning: A Laboratory Manual, 2.sup.nd ed., vol. 1-3, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. 1989 (hereinafter, "Sambrook et al., 1989"); Ausubel et al. eds., Current Protocols in Molecular Biology, Greene Publishing and Wiley-Interscience, New York, 1995 (with periodic updates) (hereinafter, "Ausubel et al., 1995"); and Innis et al., PCR Protocols: A Guide to Methods and Applications, Academic Press: San Diego, 1990. PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as the PCR primer analysis tool in Vector NTI version 6 (Informax Inc., Bethesda Md.); PrimerSelect (DNASTAR Inc., Madison, Wis.); and Primer (Version 0.5.COPYRGT., 1991, Whitehead Institute for Biomedical Research, Cambridge, Mass.). Additionally, the sequence can be visually scanned and primers manually identified using guidelines known to one of skill in the art.
[0064] A "kit" as used herein refers to a set of reagents for the purpose of performing the method embodiments of the invention, more particularly, the identification of event DP-004114-3 in biological samples. The kit of the invention can be used, and its components can be specifically adjusted, for purposes of quality control (e.g. purity of seed lots), detection of event DP-004114-3 in plant material, or material comprising or derived from plant material, such as but not limited to food or feed products. "Plant material" as used herein refers to material which is obtained or derived from a plant.
[0065] Primers and probes based on the flanking DNA and insert sequences disclosed herein can be used to confirm (and, if necessary, to correct) the disclosed sequences by conventional methods, e.g., by re-cloning and sequencing such sequences. The nucleic acid probes and primers of the present invention hybridize under stringent conditions to a target DNA sequence. Any conventional nucleic acid hybridization or amplification method can be used to identify the presence of DNA from a transgenic event in a sample. Nucleic acid molecules or fragments thereof are capable of specifically hybridizing to other nucleic acid molecules under certain circumstances. As used herein, two nucleic acid molecules are said to be capable of specifically hybridizing to one another if the two molecules are capable of forming an anti-parallel, double-stranded nucleic acid structure.
[0066] A nucleic acid molecule is said to be the "complement" of another nucleic acid molecule if they exhibit complete complementarity. As used herein, molecules are said to exhibit "complete complementarity" when every nucleotide of one of the molecules is complementary to a nucleotide of the other. Two molecules are said to be "minimally complementary" if they can hybridize to one another with sufficient stability to permit them to remain annealed to one another under at least conventional "low-stringency" conditions. Similarly, the molecules are said to be "complementary" if they can hybridize to one another with sufficient stability to permit them to remain annealed to one another under conventional "high-stringency" conditions. Conventional stringency conditions are described by Sambrook et al., 1989, and by Haymes et al., In: Nucleic Acid Hybridization, a Practical Approach, IRL Press, Washington, D.C. (1985), departures from complete complementarity are therefore permissible, as long as such departures do not completely preclude the capacity of the molecules to form a double-stranded structure. In order for a nucleic acid molecule to serve as a primer or probe it need only be sufficiently complementary in sequence to be able to form a stable double-stranded structure under the particular solvent and salt concentrations employed.
[0067] In hybridization reactions, specificity is typically the function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. The thermal melting point (T.sub.m) is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. For DNA-DNA hybrids, the T.sub.m can be approximated from the equation of Meinkoth and Wahl (1984) Anal. Biochem. 138:267-284: T.sub.m=81.5.degree. C.+16.6 (log M)+0.41 (% GC)-0.61 (% form)-500/L; where M is the molarity of monovalent cations, % GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. T.sub.m is reduced by about 1.degree. C. for each 1% of mismatching; thus, T.sub.m, hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with >90% identity are sought, the T.sub.m can be decreased 10.degree. C. Generally, stringent conditions are selected to be about 5.degree. C. lower than the T.sub.m for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4.degree. C. lower than the T.sub.m; moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10.degree. C. lower than the T.sub.m; low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20.degree. C. lower than the T.sub.m.
[0068] Using the equation, hybridization and wash compositions, and desired T.sub.m, those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. If the desired degree of mismatching results in a T.sub.m of less than 45.degree. C. (aqueous solution) or 32.degree. C. (formamide solution), it is preferred to increase the SSC concentration so that a higher temperature can be used. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes, Part I, Chapter 2 (Elsevier, New York); and Ausubel et al., eds. (1995) and Sambrook et al. (1989).
[0069] As used herein, a substantially homologous sequence is a nucleic acid molecule that will specifically hybridize to the complement of the nucleic acid molecule to which it is being compared under high stringency conditions. Appropriate stringency conditions which promote DNA hybridization, for example, 6.times. sodium chloride/sodium citrate (SSC) at about 45.degree. C., followed by a wash of 2.times.SSC at 50.degree. C., are known to those skilled in the art or can be found in Ausubel et al. (1995), 6.3.1-6.3.6. Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30.degree. C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60.degree. C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of a destabilizing agent such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37.degree. C., and a wash in 1.times. to 2.times.SSC (20.times.SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55.degree. C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1 M NaCl, 1% SDS at 37.degree. C., and a wash in 0.5.times. to 1.times.SSC at 55 to 60.degree. C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37.degree. C., and a wash in 0.1.times.SSC at 60 to 65.degree. C. A nucleic acid of the invention may specifically hybridize to one or more of the nucleic acid molecules unique to the DP-004114-3 event or complements thereof or fragments of either under moderately stringent conditions.
[0070] Methods of alignment of sequences for comparison are well known in the art. Thus, the determination of percent identity between any two sequences can be accomplished using a mathematical algorithm. Non-limiting examples of such mathematical algorithms are the algorithm of Myers and Miller (1988) CABIOS 4:11-17; the local homology algorithm of Smith et al. (1981) Adv. Appl. Math. 2:482; the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443-453; the search-for-similarity-method of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. 85:2444-2448; the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877.
[0071] Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity. Such implementations include, but are not limited to: CLUSTAL in the PC/Gene program (available from Intelligenetics, Mountain View, Calif.); the ALIGN program (Version 2.0); the ALIGN PLUS program (version 3.0, copyright 1997); and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Version 10 (available from Accelrys, 9685 Scranton Road, San Diego, Calif. 92121, USA). Alignments using these programs can be performed using the default parameters.
[0072] The CLUSTAL program is well described by Higgins and Sharp, Gene 73: 237-244 (1988); Higgins and Sharp, CABIOS 5: 151-153 (1989); Corpet, et al., Nucleic Acids Research 16: 10881-90 (1988); Huang, et al., Computer Applications in the Biosciences 8: 155-65 (1992), and Pearson, et al., Methods in Molecular Biology 24: 307-331 (1994). The ALIGN and the ALIGN PLUS programs are based on the algorithm of Myers and Miller (1988) supra. The BLAST programs of Altschul et al. (1990) J. Mol. Biol. 215:403 are based on the algorithm of Karlin and Altschul (1990) supra. The BLAST family of programs which can be used for database similarity searches includes: BLASTN for nucleotide query sequences against nucleotide database sequences; BLASTX for nucleotide query sequences against protein database sequences; BLASTP for protein query sequences against protein database sequences; TBLASTN for protein query sequences against nucleotide database sequences; and TBLASTX for nucleotide query sequences against nucleotide database sequences. See, Ausubel, et al., (1995). Alignment may also be performed manually by visual inspection.
[0073] To obtain gapped alignments for comparison purposes, Gapped BLAST (in BLAST 2.0) can be utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25:3389. Alternatively, PSI-BLAST (in BLAST 2.0) can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra. When utilizing BLAST, Gapped BLAST, PSI-BLAST, the default parameters of the respective programs (e.g., BLASTN for nucleotide sequences, BLASTX for proteins) can be used.
[0074] As used herein, "sequence identity" or "identity" in the context of two nucleic acid or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window. When percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. When sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Sequences that differ by such conservative substitutions are said to have "sequence similarity" or "similarity." Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, Calif.).
[0075] As used herein, "percentage of sequence identity" means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity.
[0076] Regarding the amplification of a target nucleic acid sequence (e.g., by PCR) using a particular amplification primer pair, "stringent conditions" are conditions that permit the primer pair to hybridize only to the target nucleic-acid sequence to which a primer having the corresponding wild-type sequence (or its complement) would bind and preferably to produce a unique amplification product, the amplicon, in a DNA thermal amplification reaction.
[0077] The term "specific for (a target sequence)" indicates that a probe or primer hybridizes under stringent hybridization conditions only to the target sequence in a sample comprising the target sequence.
[0078] As used herein, "amplified DNA" or "amplicon" refers to the product of nucleic acid amplification of a target nucleic acid sequence that is part of a nucleic acid template. For example, to determine whether a corn plant resulting from a sexual cross contains transgenic event genomic DNA from the corn plant of the invention, DNA extracted from the corn plant tissue sample may be subjected to a nucleic acid amplification method using a DNA primer pair that includes a first primer derived from flanking sequence adjacent to the insertion site of inserted heterologous DNA, and a second primer derived from the inserted heterologous DNA to produce an amplicon that is diagnostic for the presence of the event DNA. Alternatively, the second primer may be derived from the flanking sequence. The amplicon is of a length and has a sequence that is also diagnostic for the event. The amplicon may range in length from the combined length of the primer pairs plus one nucleotide base pair to any length of amplicon producible by a DNA amplification protocol. Alternatively, primer pairs can be derived from flanking sequence on both sides of the inserted DNA so as to produce an amplicon that includes the entire insert nucleotide sequence of the PHP27118 expression construct as well as the sequence flanking the transgenic insert. A member of a primer pair derived from the flanking sequence may be located a distance from the inserted DNA sequence, this distance can range from one nucleotide base pair up to the limits of the amplification reaction, or about 20,000 bp. The use of the term "amplicon" specifically excludes primer dimers that may be formed in the DNA thermal amplification reaction.
[0079] Nucleic acid amplification can be accomplished by any of the various nucleic acid amplification methods known in the art, including PCR. A variety of amplification methods are known in the art and are described, inter alia, in U.S. Pat. Nos. 4,683,195 and 4,683,202 and in Innis et al., (1990) supra. PCR amplification methods have been developed to amplify up to 22 Kb of genomic DNA and up to 42 Kb of bacteriophage DNA (Cheng et al., Proc. Natl. Acad. Sci. USA 91:5695-5699, 1994). These methods as well as other methods known in the art of DNA amplification may be used in the practice of the embodiments of the present invention. It is understood that a number of parameters in a specific PCR protocol may need to be adjusted to specific laboratory conditions and may be slightly modified and yet allow for the collection of similar results. These adjustments will be apparent to a person skilled in the art.
[0080] The amplicon produced by these methods may be detected by a plurality of techniques, including, but not limited to, Genetic Bit Analysis (Nikiforov, et al. Nucleic Acid Res. 22:4167-4175, 1994) where a DNA oligonucleotide is designed which overlaps both the adjacent flanking DNA sequence and the inserted DNA sequence. The oligonucleotide is immobilized in wells of a microwell plate. Following PCR of the region of interest (using one primer in the inserted sequence and one in the adjacent flanking sequence) a single-stranded PCR product can be hybridized to the immobilized oligonucleotide and serve as a template for a single base extension reaction using a DNA polymerase and labeled ddNTPs specific for the expected next base. Readout may be fluorescent or ELISA-based. A signal indicates presence of the insert/flanking sequence due to successful amplification, hybridization, and single base extension.
[0081] Another detection method is the pyrosequencing technique as described by Winge (2000) Innov. Pharma. Tech. 00:18-24. In this method an oligonucleotide is designed that overlaps the adjacent DNA and insert DNA junction. The oligonucleotide is hybridized to a single-stranded PCR product from the region of interest (one primer in the inserted sequence and one in the flanking sequence) and incubated in the presence of a DNA polymerase, ATP, sulfurylase, luciferase, apyrase, adenosine 5' phosphosulfate and luciferin. dNTPs are added individually and the incorporation results in a light signal which is measured. A light signal indicates the presence of the transgene insert/flanking sequence due to successful amplification, hybridization, and single or multi-base extension.
[0082] Fluorescence polarization as described by Chen et al., (1999) Genome Res. 9:492-498 is also a method that can be used to detect an amplicon of the invention. Using this method an oligonucleotide is designed which overlaps the flanking and inserted DNA junction. The oligonucleotide is hybridized to a single-stranded PCR product from the region of interest (one primer in the inserted DNA and one in the flanking DNA sequence) and incubated in the presence of a DNA polymerase and a fluorescent-labeled ddNTP. Single base extension results in incorporation of the ddNTP. Incorporation can be measured as a change in polarization using a fluorometer. A change in polarization indicates the presence of the transgene insert/flanking sequence due to successful amplification, hybridization, and single base extension.
[0083] Taqman.RTM. (PE Applied Biosystems, Foster City, Calif.) is described as a method of detecting and quantifying the presence of a DNA sequence and is fully understood in the instructions provided by the manufacturer. Briefly, a FRET oligonucleotide probe is designed which overlaps the flanking and insert DNA junction. The FRET probe and PCR primers (one primer in the insert DNA sequence and one in the flanking genomic sequence) are cycled in the presence of a thermostable polymerase and dNTPs. Hybridization of the FRET probe results in cleavage and release of the fluorescent moiety away from the quenching moiety on the FRET probe. A fluorescent signal indicates the presence of the flanking/transgene insert sequence due to successful amplification and hybridization.
[0084] Molecular beacons have been described for use in sequence detection as described in Tyangi et al. (1996) Nature Biotech. 14:303-308. Briefly, a FRET oligonucleotide probe is designed that overlaps the flanking and insert DNA junction. The unique structure of the FRET probe results in it containing secondary structure that keeps the fluorescent and quenching moieties in close proximity. The FRET probe and PCR primers (one primer in the insert DNA sequence and one in the flanking sequence) are cycled in the presence of a thermostable polymerase and dNTPs. Following successful PCR amplification, hybridization of the FRET probe to the target sequence results in the removal of the probe secondary structure and spatial separation of the fluorescent and quenching moieties. A fluorescent signal results. A fluorescent signal indicates the presence of the flanking/transgene insert sequence due to successful amplification and hybridization.
[0085] A hybridization reaction using a probe specific to a sequence found within the amplicon is yet another method used to detect the amplicon produced by a PCR reaction.
[0086] Maize event DP-004114-3 is effective against insect pests including insects selected from the orders Coleoptera, Diptera, Hymenoptera, Lepidoptera, Mallophaga, Homoptera, Hemiptera, Orthoptera, Thysanoptera, Dermaptera, Isoptera, Anoplura, Siphonaptera, Trichoptera, etc., particularly Coleoptera and Lepidoptera.
[0087] Insects of the order Lepidoptera include, but are not limited to, armyworms, cutworms, loopers, and heliothines in the family Noctuidae: Agrotis ipsilon Hufnagel (black cutworm); A. orthogonia Morrison (western cutworm); A. segetum Denis & Schiffermuller (turnip moth); A. subterranea Fabricius (granulate cutworm); Alabama argillacea Hubner (cotton leaf worm); Anticarsia gemmatalis Hubner (velvetbean caterpillar); Athetis mindara Barnes and McDunnough (rough skinned cutworm); Earias insulana Boisduval (spiny bollworm); E. vittella Fabricius (spotted bollworm); Egira (Xylomyges) curialis Grote (citrus cutworm); Euxoa messoria Harris (darksided cutworm); Helicoverpa armigera Hubner (American bollworm); H. zea Boddie (corn earworm or cotton bollworm); Heliothis virescens Fabricius (tobacco budworm); Hypena scabra Fabricius (green cloverworm); Hyponeuma taltula Schaus; (Mamestra configurata Walker (bertha armyworm); M. brassicae Linnaeus (cabbage moth); Melanchra picta Harris (zebra caterpillar); Mocis latipes Guenee (small mocis moth); Pseudaletia unipuncta Haworth (armyworm); Pseudoplusia includens Walker (soybean looper); Richia albicosta Smith (Western bean cutworm); Spodoptera frugiperda JE Smith (fall armyworm); S. exigua Hubner (beet armyworm); S. litura Fabricius (tobacco cutworm, cluster caterpillar); Trichoplusia ni Hubner (cabbage looper); borers, casebearers, webworms, coneworms, and skeletonizers from the families Pyralidae and Crambidae such as Achroia grisella Fabricius (lesser wax moth); Amyelois transitella Walker (naval orangeworm); Anagasta kuehniella Zeller (Mediterranean flour moth); Cadra cautella Walker (almond moth); Chilo partellus Swinhoe (spotted stalk borer); C. suppressalis Walker (striped stem/rice borer); C. terrenellus Pagenstecher (sugarcane stem borer); Corcyra cephalonica Stainton (rice moth); Crambus caliginosellus Clemens (corn root webworm); C. teterrellus Zincken (bluegrass webworm); Cnaphalocrocis medinalis Guenee (rice leaf roller); Desmia funeralis Hubner (grape leaffolder); Diaphania hyalinata Linnaeus (melon worm); D. nitidalis Stoll (pickleworm); Diatraea flavipennella Box; D. grandiosella Dyar (southwestern corn borer), D. saccharalis Fabricius (surgarcane borer); Elasmopalpus lignosellus Zeller (lesser cornstalk borer); Eoreuma loftini Dyar (Mexican rice borer); Ephestia elutella Hubner (tobacco (cacao) moth); Galleria mellonella Linnaeus (greater wax moth); Hedylepta accepta Butler (sugarcane leafroller); Herpetogramma licarsisalis Walker (sod webworm); Homoeosoma electellum Hulst (sunflower moth); Loxostege sticticalis Linnaeus (beet webworm); Maruca testulalis Geyer (bean pod borer); Orthaga thyrisalis Walker (tea tree web moth); Ostrinia nubilalis Hubner (European corn borer); Plodia interpunctella Hubner (Indian meal moth); Scirpophaga incertulas Walker (yellow stem borer); Udea rubigalis Hubner (celery leaftier); and leafrollers, budworms, seed worms, and fruit worms in the family Tortricidae Acleris gloverana Walsingham (Western blackheaded budworm); A. variana Fernald (Eastern blackheaded budworm); Adoxophyes orana Fischer von Rosslerstamm (summer fruit tortrix moth); Archips spp. including A. argyrospila Walker (fruit tree leaf roller) and A. rosana Linnaeus (European leaf roller); Argyrotaenia spp.; Bonagota salubricola Meyrick (Brazilian apple leafroller); Choristoneura spp.; Cochylis hospes Walsingham (banded sunflower moth); Cydia latiferreana Walsingham (filbertworm); C. pomonella Linnaeus (codling moth); Endopiza viteana Clemens (grape berry moth); Eupoecilia ambiguella Hubner (vine moth); Grapholita molesta Busck (oriental fruit moth); Lobesia botrana Denis & Schiffermuller (European grape vine moth); Platynota flavedana Clemens (variegated leafroller); P. stultana Walsingham (omnivorous leafroller); Spilonota ocellana Denis & Schiffermuller (eyespotted bud moth); and Suleima helianthana Riley (sunflower bud moth).
[0088] Selected other agronomic pests in the order Lepidoptera include, but are not limited to, Alsophila pometaria Harris (fall cankerworm); Anarsia lineatella Zeller (peach twig borer); Anisota senatoria J. E. Smith (orange striped oakworm); Antheraea pernyi Guerin-Meneville (Chinese Oak Silkmoth); Bombyx mori Linnaeus (Silkworm); Bucculatrix thurberiella Busck (cotton leaf perforator); Colias eurytheme Boisduval (alfalfa caterpillar); Datana integerrima Grote & Robinson (walnut caterpillar); Dendrolimus sibiricus Tschetwerikov (Siberian silk moth), Ennomos subsignaria Hubner (elm spanworm); Erannis tiliaria Harris (linden looper); Erechthias flavistriata Walsingham (sugarcane bud moth); Euproctis chrysorrhoea Linnaeus (browntail moth); Harrisina americana Guerin-Meneville (grapeleaf skeletonizer); Heliothis subflexa Hubner; Hemileuca oliviae Cockrell (range caterpillar); Hyphantria cunea Drury (fall webworm); Keiferia lycopersicella Walsingham (tomato pinworm); Lambdina fiscellaria fiscellaria Hulst (Eastern hemlock looper); L. fiscellaria lugubrosa Hulst (Western hemlock looper); Leucoma salicis Linnaeus (satin moth); Lymantria dispar Linnaeus (gypsy moth); Malacosoma spp.; Manduca quinquemaculata Haworth (five spotted hawk moth, tomato hornworm); M. sexta Haworth (tomato hornworm, tobacco hornworm); Operophtera brumata Linnaeus (winter moth); Orgyia spp.; Paleacrita vernata Peck (spring cankerworm); Papilio cresphontes Cramer (giant swallowtail, orange dog); Phryganidia californica Packard (California oakworm); Phyllocnistis citrella Stainton (citrus leafminer); Phyllonorycter blancardella Fabricius (spotted tentiform leafminer); Pieris brassicae Linnaeus (large white butterfly); P. rapae Linnaeus (small white butterfly); P. napi Linnaeus (green veined white butterfly); Platyptilia carduidactyla Riley (artichoke plume moth); Plutella xylostella Linnaeus (diamondback moth); Pectinophora gossypiella Saunders (pink bollworm); Pontia protodice Boisduval & Leconte (Southern cabbageworm); Sabulodes aegrotata Hubner (omnivorous looper); Schizura concinna J. E. Smith (red humped caterpillar); Sitotroga cerealella Olivier (Angoumois grain moth); Telchin licus Drury (giant sugarcane borer); Thaumetopoea pityocampa Schiffermuller (pine processionary caterpillar); Tineola bisselliella Hummel (webbing clothesmoth); Tuta absoluta Meyrick (tomato leafminer) and Yponomeuta padella Linnaeus (ermine moth).
[0089] Of interest are larvae and adults of the order Coleoptera including weevils from the families Anthribidae, Bruchidae, and Curculionidae including, but not limited to: Anthonomus grandis Boheman (boll weevil); Cylindrocopturus adspersus LeConte (sunflower stem weevil); Diaprepes abbreviatus Linnaeus (Diaprepes root weevil); Hypera punctata Fabricius (clover leaf weevil); Lissorhoptrus oryzophilus Kuschel (rice water weevil); Metamasius hemipterus hemipterus Linnaeus (West Indian cane weevil); M. hemipterus sericeus Olivier (silky cane weevil); Sitophilus granarius Linnaeus (granary weevil); S. oryzae Linnaeus (rice weevil); Smicronyx fulvus LeConte (red sunflower seed weevil); S. sordidus LeConte (gray sunflower seed weevil); Sphenophorus maidis Chittenden (maize billbug); S. livis Vaurie (sugarcane weevil); Rhabdoscelus obscurus Boisduval (New Guinea sugarcane weevil); flea beetles, cucumber beetles, rootworms, leaf beetles, potato beetles, and leafminers in the family Chrysomelidae including, but not limited to: Chaetocnema ectypa Horn (desert corn flea beetle); C. pulicaria Melsheimer (corn flea beetle); Colaspis brunnea Fabricius (grape colaspis); Diabrotica barberi Smith & Lawrence (northern corn rootworm); D. undecimpunctata howardi Barber (southern corn rootworm); D. virgifera virgifera LeConte (western corn rootworm); Leptinotarsa decemlineata Say (Colorado potato beetle); Oulema melanopus Linnaeus (cereal leaf beetle); Phyllotreta cruciferae Goeze (corn flea beetle); Zygogramma exclamationis Fabricius (sunflower beetle); beetles from the family Coccinellidae including, but not limited to: Epilachna varivestis Mulsant (Mexican bean beetle); chafers and other beetles from the family Scarabaeidae including, but not limited to: Antitrogus parvulus Britton (Childers cane grub); Cyclocephala borealis Arrow (northern masked chafer, white grub); C. immaculata Olivier (southern masked chafer, white grub); Dermolepida albohirtum Waterhouse (Greyback cane beetle); Euetheola humilis rugiceps LeConte (sugarcane beetle); Lepidiota frenchi Blackburn (French's cane grub); Tomarus gibbosus De Geer (carrot beetle); T. subtropicus Blatchley (sugarcane grub); Phyllophaga crinita Burmeister (white grub); P. latifrons LeConte (June beetle); Popillia japonica Newman (Japanese beetle); Rhizotrogus majalis Razoumowsky (European chafer); carpet beetles from the family Dermestidae; wireworms from the family Elateridae, Eleodes spp., Melanotus spp. including M. communis Gyllenhal (wireworm); Conoderus spp.; Limonius spp.; Agriotes spp.; Ctenicera spp.; Aeolus spp.; bark beetles from the family Scolytidae; beetles from the family Tenebrionidae; beetles from the family Cerambycidae such as, but not limited to, Migdolus fryanus Westwood (longhorn beetle); and beetles from the Buprestidae family including, but not limited to, Aphanisticus cochinchinae seminulum Obenberger (leaf-mining buprestid beetle).
[0090] Adults and immatures of the order Diptera are of interest, including leafminers Agromyza parvicornis Loew (corn blotch leafminer); midges including, but not limited to: Contarinia sorghicola Coquillett (sorghum midge); Mayetiola destructor Say (Hessian fly); Neolasioptera murtfeldtiana Felt, (sunflower seed midge); Sitodiplosis mosellana Gehin (wheat midge); fruit flies (Tephritidae), Oscinella frit Linnaeus (frit flies); maggots including, but not limited to: Delia spp. including Delia platura Meigen (seedcorn maggot); D. coarctata Fallen (wheat bulb fly); Fannia canicularis Linnaeus, F. femoralis Stein (lesser house flies); Meromyza americana Fitch (wheat stem maggot); Musca domestica Linnaeus (house flies); Stomoxys calcitrans Linnaeus (stable flies)); face flies, horn flies, blow flies, Chrysomya spp.; Phormia spp.; and other muscoid fly pests, horse flies Tabanus spp.; bot flies Gastrophilus spp.; Oestrus spp.; cattle grubs Hypoderma spp.; deer flies Chrysops spp.; Melophagus ovinus Linnaeus (keds); and other Brachycera, mosquitoes Aedes spp.; Anopheles spp.; Culex spp.; black flies Prosimulium spp.; Simulium spp.; biting midges, sand flies, sciarids, and other Nematocera.
[0091] Included as insects of interest are those of the order Hemiptera such as, but not limited to, the following families: Adelgidae, Aleyrodidae, Aphididae, Asterolecaniidae, Cercopidae, Cicadellidae, Cicadidae, Cixiidae, Coccidae, Coreidae, Dactylopiidae, Delphacidae, Diaspididae, Eriococcidae, Flatidae, Fulgoridae, Issidae, Lygaeidae, Margarodidae, Membracidae, Miridae, Ortheziidae, Pentatomidae, Phoenicococcidae, Phylloxeridae, Pseudococcidae, Psyllidae, Pyrrhocoridae and Tingidae.
[0092] Agronomically important members from the order Hemiptera include, but are not limited to: Acrosternum hilare Say (green stink bug); Acyrthisiphon pisum Harris (pea aphid); Adelges spp. (adelgids); Adelphocoris rapidus Say (rapid plant bug); Anasa tristis De Geer (squash bug); Aphis craccivora Koch (cowpea aphid); A. fabae Scopoli (black bean aphid); A. gossypii Glover (cotton aphid, melon aphid); A. maidiradicis Forbes (corn root aphid); A. pomi De Geer (apple aphid); A. spiraecola Patch (spirea aphid); Aulacaspis tegalensis Zehntner (sugarcane scale); Aulacorthum solani Kaltenbach (foxglove aphid); Bemisia tabaci Gennadius (tobacco whitefly, sweetpotato whitefly); B. argentifolii Bellows & Perring (silverleaf whitefly); Blissus leucopterus leucopterus Say (chinch bug); Blostomatidae spp.; Brevicoryne brassicae Linnaeus (cabbage aphid); Cacopsylla pyricola Foerster (pear psylla); Calocoris norvegicus Gmelin (potato capsid bug); Chaetosiphon fragaefolii Cockerell (strawberry aphid); Cimicidae spp.; Coreidae spp.; Corythuca gossypii Fabricius (cotton lace bug); Cyrtopeltis modesta Distant (tomato bug); C. notatus Distant (suckfly); Deois flavopicta Stal (spittlebug); Dialeurodes citri Ashmead (citrus whitefly); Diaphnocoris chlorionis Say (honeylocust plant bug); Diuraphis noxia Kurdjumov/Mordvilko (Russian wheat aphid); Duplachionaspis divergens Green (armored scale); Dysaphis plantaginea Paaserini (rosy apple aphid); Dysdercus suturellus Herrich-Schaffer (cotton stainer); Dysmicoccus boninsis Kuwana (gray sugarcane mealybug); Empoasca fabae Harris (potato leafhopper); Eriosoma lanigerum Hausmann (woolly apple aphid); Erythroneoura spp. (grape leafhoppers); Eumetopina flavipes Muir (Island sugarcane planthopper); Eurygaster spp.; Euschistus servus Say (brown stink bug); E. variolarius Palisot de Beauvois (one-spotted stink bug); Graptostethus spp. (complex of seed bugs); and Hyalopterus pruni Geoffroy (mealy plum aphid); Icerya purchasi Maskell (cottony cushion scale); Labopidicola allii Knight (onion plant bug); Laodelphax striatellus Fallen (smaller brown planthopper); Leptoglossus corculus Say (leaf-footed pine seed bug); Leptodictya tabida Herrich-Schaeffer (sugarcane lace bug); Lipaphis erysimi Kaltenbach (turnip aphid); Lygocoris pabulinus Linnaeus (common green capsid); Lygus lineolaris Palisot de Beauvois (tarnished plant bug); L. Hesperus Knight (Western tarnished plant bug); L. pratensis Linnaeus (common meadow bug); L. rugulipennis Poppius (European tarnished plant bug); Macrosiphum euphorbiae Thomas (potato aphid); Macrosteles quadrilineatus Forbes (aster leafhopper); Magicicada septendecim Linnaeus (periodical cicada); Mahanarva fimbriolata Stal (sugarcane spittlebug); M. posticata Stal (little cicada of sugarcane); Melanaphis sacchari Zehntner (sugarcane aphid); Melanaspis glomerata Green (black scale); Metopolophium dirhodum Walker (rose grain aphid); Myzus persicae Sulzer (peach-potato aphid, green peach aphid); Nasonovia ribisnigri Mosley (lettuce aphid); Nephotettix cinticeps Uhler (green leafhopper); N. nigropictus Stal (rice leafhopper); Nezara viridula Linnaeus (southern green stink bug); Nilaparvata lugens Stal (brown planthopper); Nysius ericae Schilling (false chinch bug); Nysius raphanus Howard (false chinch bug); Oebalus pugnax Fabricius (rice stink bug); Oncopeltus fasciatus Dallas (large milkweed bug); Orthops campestris Linnaeus; Pemphigus spp. (root aphids and gall aphids); Peregrinus maidis Ashmead (corn planthopper); Perkinsiella saccharicida Kirkaldy (sugarcane delphacid); Phylloxera devastatrix Pergande (pecan phylloxera); Planococcus citri Risso (citrus mealybug); Plesiocoris rugicollis Fallen (apple capsid); Poecilocapsus lineatus Fabricius (four-lined plant bug); Pseudatomoscelis seriatus Reuter (cotton fleahopper); Pseudococcus spp. (other mealybug complex); Pulvinaria elongata Newstead (cottony grass scale); Pyrilla perpusilla Walker (sugarcane leafhopper); Pyrrhocoridae spp.; Quadraspidiotus perniciosus Comstock (San Jose scale); Reduviidae spp.; Rhopalosiphum maidis Fitch (corn leaf aphid); R. padi Linnaeus (bird cherry-oat aphid); Saccharicoccus sacchari Cockerell (pink sugarcane mealybug); Scaptocoris castanea Perty (brown root stink bug); Schizaphis graminum Rondani (greenbug); Sipha flava Forbes (yellow sugarcane aphid); Sitobion avenae Fabricius (English grain aphid); Sogatella furcifera Horvath (white-backed planthopper); Sogatodes oryzicola Muir (rice delphacid); Spanagonicus albofasciatus Reuter (whitemarked fleahopper); Therioaphis maculata Buckton (spotted alfalfa aphid); Tinidae spp.; Toxoptera aurantil Boyer de Fonscolombe (black citrus aphid); and T. citricida Kirkaldy (brown citrus aphid); Trialeurodes abutiloneus (bandedwinged whitefly) and T. vaporariorum Westwood (greenhouse whitefly); Trioza diospyri Ashmead (persimmon psylla); and Typhlocyba pomaria McAtee (white apple leafhopper).
[0093] Also included are adults and larvae of the order Acari (mites) such as Aceria tosichella Keifer (wheat curl mite); Panonychus ulmi Koch (European red mite); Petrobia latens Muller (brown wheat mite); Steneotarsonemus bancrofti Michael (sugarcane stalk mite); spider mites and red mites in the family Tetranychidae, Oligonychus grypus Baker & Pritchard, O. indicus Hirst (sugarcane leaf mite), O. pratensis Banks (Banks grass mite), O. stickneyi McGregor (sugarcane spider mite); Tetranychus urticae Koch (two spotted spider mite); T. mcdanieli McGregor (McDaniel mite); T. cinnabarinus Boisduval (carmine spider mite); T. turkestani Ugarov & Nikolski (strawberry spider mite), flat mites in the family Tenuipalpidae, Brevipalpus lewisi McGregor (citrus flat mite); rust and bud mites in the family Eriophyidae and other foliar feeding mites and mites important in human and animal health, i.e. dust mites in the family Epidermoptidae, follicle mites in the family Demodicidae, grain mites in the family Glycyphagidae, ticks in the order Ixodidae. Ixodes scapularis Say (deer tick); I. holocyclus Neumann (Australian paralysis tick); Dermacentor variabilis Say (American dog tick); Amblyomma americanum Linnaeus (lone star tick); and scab and itch mites in the families Psoroptidae, Pyemotidae, and Sarcoptidae.
[0094] Insect pests of the order Thysanura are of interest, such as Lepisma saccharina Linnaeus (silverfish); Thermobia domestica Packard (firebrat).
[0095] Additional arthropod pests covered include: spiders in the order Araneae such as Loxosceles reclusa Gertsch & Mulaik (brown recluse spider); and the Latrodectus mactans Fabricius (black widow spider); and centipedes in the order Scutigeromorpha such as Scutigera coleoptrata Linnaeus (house centipede). In addition, insect pests of the order Isoptera are of interest, including those of the termitidae family, such as, but not limited to, Cornitermes cumulans Kollar, Cylindrotermes nordenskioeldi Holmgren and Pseudacanthotermes militaris Hagen (sugarcane termite); as well as those in the Rhinotermitidae family including, but not limited to Heterotermes tenuis Hagen. Insects of the order Thysanoptera are also of interest, including but not limited to thrips, such as Stenchaetothrips minutus van Deventer (sugarcane thrips).
[0096] Embodiments of the present invention are further defined in the following Examples. It should be understood that these Examples are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the embodiments of the invention to adapt it to various usages and conditions. Thus, various modifications of the embodiments of the invention, in addition to those shown and described herein, will be apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims.
[0097] The disclosure of each reference set forth herein is incorporated herein by reference in its entirety.
EXAMPLES
Example 1. Transformation of Maize by Agrobacterium Transformation and Regeneration of Transgenic Plants Containing the Cry1F, Cry34Ab1, Cry35Ab1 (Cry34/35Ab1) and Pat Genes
[0098] 4114 maize was produced by Agrobacterium-mediated transformation with plasmid PHP27118. This event contains the cry1F, cry34Ab1, cry35Ab1, and pat gene cassettes, which confer resistance to certain lepidopteran and coleopteran pests.
[0099] Specifically, the first cassette contains a truncated version of the cry1F gene from Bt var. aizawai. The insertion of the cry1F gene confers resistance to damage by lepidopteran pests, including ECB and FAW. The Cry1F protein (SEQ ID NO: 1) is comprised of 605 amino acids and has a molecular weight of approximately 68 kDa. The expression of the cry1F gene is controlled by the maize polyubiquitin promoter (Christensen et al., 1992, supra), providing constitutive expression of Cry1F protein in maize. This region also includes the 5' UTR and intron associated with the native polyubiquitin promoter. The terminator for the cry1F gene is the poly(A) addition signal from open reading frame 25 (ORF 25) of the Agrobacterium tumefaciens (A. tumefaciens) Ti plasmid pTi15955 (Barker et al., 1983, supra).
[0100] The second cassette contains the cry34Ab1 gene isolated from Bt strain PS149B1 (U.S. Pat. Nos. 6,127,180; 6,624,145 and 6,340,593). The Cry34Ab1 protein (SEQ ID NO: 2) is 123 amino acid residues in length and has a molecular weight of approximately 14 kDa. The expression of the cry34Ab1 gene is controlled by a second copy of the maize polyubiquitin promoter with 5' UTR and intron (Christensen et al., 1992, supra). The terminator for the cry34Ab1 gene is the pinII terminator (Keil et al., 1986, supra; An et al., 1989, supra).
[0101] The third gene cassette contains the cry35Ab1 gene, also isolated from Bt strain PS149B1 (U.S. Pat. Nos. 6,083,499; 6,548,291 and 6,340,593). The Cry35Ab1 protein (SEQ ID NO: 3) has a length of 383 amino acids and a molecular weight of approximately 44 kDa. Simultaneous expression of the Cry34Ab1 and Cry35Ab1 proteins in the plant confers resistance to coleopteran insects, including WCRW. The expression of the cry35Ab1 gene is controlled by the Triticum aestivum (wheat) peroxidase promoter and leader sequence (Hertig et al. 1991, supra). The terminator for the cry35Ab1 gene is a second copy of the pinII terminator (Keil et al. 1986, supra; An et al. 1989, supra).
[0102] The fourth and final gene cassette contains a version of pat from Streptomyces viridochromogenes that has been optimized for expression in maize. The pat gene expresses PAT, which confers tolerance to phosphinothricin (glufosinate-ammonium). The PAT protein (SEQ ID NO: 4) is 183 amino acids residues in length and has a molecular weight of approximately 21 kDa. Expression of the pat gene is controlled by the promoter and terminator regions from the CaMV 35S transcript (Franck et al., 1980, supra; Odell et al., 1985, supra; Pietrzak, et al., 1986, supra). Plants containing the DNA constructs are also provided. A description of the genetic elements in the PHP27118 T-DNA (set forth in SEQ ID NO: 5) and their sources are described further in Table 1.
TABLE-US-00002 TABLE 1 Genetic Elements in the T-DNA Region of Plasmid PHP27118 Location on T-DNA Genetic Size (bp position) Element (bp) Description 1 to 25 Right 25 T-DNA RB region from Ti plasmid of Border A. tumefaciens 26 to 76 Ti Plasmid 51 Non-functional sequence from Ti plasmid of Region A. tumefaciens 77 to 114 Polylinker 38 Region required for cloning genetic elements Region 115 to 1014 ubiZM1 900 Promoter region from Zea mays polyubiquitin gene Promoter (Christensen et al., 1992, supra) 1015 to 1097 ubiZM1 5' 83 5' UTR from Zea mays polyubiquitin gene. Id. UTR 1098 to 2107 ubiZM1 1010 Intron region from Zea mays polyubiquitin gene. Id. Intron 2108 to 2129 Polylinker 22 Region required for cloning genetic elements Region 2130 to 3947 cty1F Gene 1818 Truncated version of cry1F from Bt var. aizawai 3948 to 3992 Polylinker 45 Region required for cloning genetic elements Region 3993 to 4706 ORF 25 714 Terminator sequence from A. tumefaciens Terminator pTi15955 ORF 25 (Barker et al., 1983, supra) 4707 to 4765 Polylinker 59 Region required for cloning genetic elements Region 4766 to 5665 ubiZM1 900 Promoter region from Zea mays polyubiquitin gene Promoter (Christensen et al., 1992, supra) 5666 to 5748 ubiZM1 5' 83 5' UTR from Zea mays polyubiquitin gene. Id. UTR 5749 to 6758 ubiZM1 1010 Intron region from Zea mays polyubiquitin gene. Id. Intron 6759 to 6786 Polylinker 28 Region required for cloning genetic elements Region 6787 to 7158 cry34Ab1 372 Synthetic version of cry34Ab1 encoding 14 kDa Gene delta-endotoxin parasporal crystal protein from the nonmotile strain PS149B1 of Bt (Moellenbeck et al. (2001) Nature Biotech. 19:668-672; Ellis et al. (2002) Appl. Env. Microbiol. 68(3): 1137-1145; Herman et al. (2002) Environ. Entomol. 31(2): 208-214.) 7159 to 7182 Polylinker 24 Region required for cloning genetic elements Region 7183 to 7492 pinII 310 Terminator region from Solanum tuberosum Terminator proteinase inhibitor II gene (Keil et al. 1986, supra; An et al. 1989, supra) 7493 to 7522 Polylinker 30 Region required for cloning genetic elements Region 7523 to 8820 TA 1298 Promoter from Triticum aestivum peroxidase Peroxidase including leader sequence (Hertig et al. 1991, supra) Promoter 8821 to 8836 Polylinker 16 Region required for cloning genetic elements Region 8837 to 9988 cry35Ab1 1152 Synthetic version of cry35Ab1 encoding a 44 kDa delta-endotoxin parasporal crystal protein from the nonmotile strain PS149B1 of Bt (Moellenbeck et al. 2001, supra; Ellis et al. 2002, supra; Herman et al. 2002, supra) 9989 to Polylinker 24 Region required for cloning genetic elements 10012 Region 10013 to pinll 310 Terminator region from Solanum tuberosum 10322 Terminator proteinase inhibitor II gene (Keil et al. 1986, supra; An et al. 1989, supra) 10323 to Polylinker 45 Region required for cloning genetic elements 10367 Region 10368 to CaMV 530 35S promoter from CaMV (Franck etal., 1980, 10897 35S supra; Odell et al., 1985, supra; Pietrzak, et al., Promoter 1986, supra) 10898 to Polylinker 19 Region required for cloning genetic elements 10916 Region 10917 to pat Gene 552 Synthetic, plant-optimized phosphinothricin 11468 acetyltransferase coding sequence from Streptomyces viridochromogenes. 11469 to Polylinker 20 Region required for cloning genetic elements 11488 Region 11489 to CaMV35S 192 35S terminator from CaMV (Franck et al., 1980, 11680 Terminator supra; Pietrzak, et al., 1986, supra) 11681 to Polylinker 76 Region required for cloning genetic elements 11756 Region 11757 to Ti Plasmid 197 Non-functional sequence from Ti plasmid of A. 11953 Region tumefaciens 11954 to Left Border 25 T-DNA LB region from Ti plasmid of A. tumefaciens 11978
[0103] Immature embryos of maize (Zea mays L.) were aseptically removed from the developing caryopsis nine to eleven days after pollination and inoculated with A. tumefaciens strain LBA4404 containing plasmid PHP27118 (FIG. 1), essentially as described in Zhao (U.S. Pat. No. 5,981,840, the contents of which are hereby incorporated by reference). The T-DNA region of PHP27118 is shown in FIG. 2. After three to six days of embryo and Agrobacterium co-cultivation on solid culture medium with no selection, the embryos were then transferred to a medium without herbicide selection but containing carbenicillin. After three to five days on this medium, embryos were then transferred to selective medium that was stimulatory to maize somatic embryogenesis and contained bialaphos for selection of cells expressing the pat transgene. The medium also contained carbenicillin to kill any remaining Agrobacterium. After six to eight weeks on the selective medium, healthy, growing calli that demonstrated resistance to bialaphos were identified. The putative transgenic calli were subsequently regenerated to produce T0 plantlets.
[0104] Samples were taken from the T0 plantlets for PCR analysis to verify the presence and copy number of the inserted cry1F, cry35Ab1, cry34Ab1, and/or pat genes. Maize event DP-004114-3 was confirmed to contain a single copy of the T-DNA (See Examples 2 and 3). In addition to this analysis, the T0 plantlets were analyzed for the presence of certain Agrobacterium binary vector backbone sequences by PCR (data not shown). Plants that were determined to be single copy for the inserted genes and negative for Agrobacterium backbone sequences were selected for further greenhouse propagation. These selected T0 plants were screened for trait efficacy and protein expression by conducting numerous bioassays (See Example 5). The T0 plants meeting all criteria were advanced and crossed to inbred lines to produce seed for further testing. A schematic overview of the transformation and event development is presented in FIG. 3.
Example 2. Characterization of Maize Event DP-004114-3
[0105] Genomic DNA from leaf tissue of test seed from 4114 maize and a control substance (seed from a non-genetically modified maize with a genetic background representative of the event background) was isolated and subjected to qualitative PCR amplification using a construct-specific primer pair. The PCR products were separated on an agarose gel to confirm the presence of the inserted construct in the genomic DNA isolated from the test seed, and the absence of the inserted construct in the genomic DNA isolated from the control seed. A reference standard (Low DNA Mass Ladder; Invitrogen Corporation Catalog #10380-012) was used to determine the PCR product size. The reliability of the construct-specific PCR method was assessed by repeating the experiment three times. The sensitivity of the PCR amplification was evaluated by various dilutions of the genomic DNA from 4114 maize.
[0106] Test and control leaf samples (V5-V7 leaf stage) were harvested from plants grown at the DuPont Experimental Station (Wilmington, Del.) from seed obtained from Pioneer Hi-Bred (Johnston, Iowa). Genomic DNA extractions from the test and control leaf tissues were performed using a standard urea extraction protocol.
[0107] Genomic DNA was quantified using the NanoDrop 1000 Spectrophotometer using ND-1000 V3.6 Software (ThermoScientific, Wilmington, Del.) and the Quant-iT PicoGreen.RTM. reagent (Invitrogen, Carslbad, Calif.). DNA samples were visualized on an agarose gel to confirm quantitation values and to determine the DNA quality.
[0108] Genomic DNA samples isolated from leaf tissue of 4114 maize and control samples were subjected to PCR amplification (Roche High Fidelity PCR Master Kit, Roche Catalog #12140314001) utilizing a construct-specific primer pair (SEQ ID NOs: 7 and 8) which spans the maize ORF 25 terminator and the ubiquitin promoter (See FIG. 2), and allows for the unique identification of the inserted T-DNA in 4114 maize. A second primer set (SEQ ID NOs: 9 and 10) was used to amplify the endogenous maize invertase gene (GenBank accession number AF171874.1) as a positive control for PCR amplification. The PCR target site and size of the expected PCR product for each primer set are shown in Table 2. PCR reagents and reaction conditions are shown in Table 3. In this study, 50 ng of leaf genomic DNA was used in all PCR reactions.
TABLE-US-00003 TABLE 2 PCR Genomic DNA Target Site and Expected Size of PCR Products Expected Size of Primer Set Target Site PCR Product (bp) SEQ ID NO: 7 & 8 Construct Specific T-DNA: 287 ORF 25 terminator and ubiquitin promoter SEQ ID NO: 9 & 10 Endogenous maize 225 invertase gene
TABLE-US-00004 TABLE 3 PCR Reagents and Reaction Conditions PCR Reagents PCR Reaction Conditions Volume Cycle Temp Time # Reagent (.mu.L) Element (.degree. C.) (sec) Cycles Template DNA 2 Initial 94 120 1 (25 ng/.mu.L) Denaturation Primer 1 (10 .mu.M) 2 Denaturation 94 10 35 Primer 2 (10 .mu.M) 2 Annealing 65 15 PCR Master Mix* 25 Elongation 68 60 ddH.sub.2O 19 Final Elongation 68 420 1 -- -- Hold Cycle 4 Until -- analysis ddH.sub.2O: double-distilled water *Roche High Fidelity Master Mix
[0109] A PCR product of approximately 300 bp in size amplified by the construct-specific primer set (SEQ ID NOs: 7 and 8) was observed in PCR reactions using plasmid PHP27118 (10 ng) as a template and all 4114 maize DNA samples, but absent in all control maize samples and the no-template control. This experiment was repeated three times, and similar results were obtained. Results observed for DNA extracts from five 4114 maize plants and five control maize plants corresponded closely with the expected PCR product size (287 bp) for samples containing 4114 maize genomic DNA. A PCR product approximately 220 bp in size was observed for both 4114 maize and control maize samples following PCR reaction with the primer set (SEQ ID NOs: 9 and 10) for detection of the endogenous maize invertase gene. These results corresponded closely with the expected PCR product size (225 bp) for genomic DNA samples containing the maize endogenous invertase gene. The endogenous target band was not observed in the no-template control.
[0110] In order to assess the sensitivity of the PCR amplification, various concentrations of a single DNA sample from 4114 maize were diluted in non-genetically modified control DNA, resulting in 4114 maize DNA amounts ranging from 500 fg, 5 pg, 10 pg, 50 pg, 100 pg, 500 pg, 5 ng, and 50 ng (the total amount of genomic DNA in all PCR samples was 50 ng). Each dilution was subjected to PCR amplification as previously conducted. Based on this analysis, the limit of detection (LOD) was determined to be approximately 100 pg of 4114 maize DNA in 50 ng of total DNA, or 0.2% 4114 maize DNA.
[0111] In conclusion, qualitative PCR analysis utilizing a construct-specific primer set for 4114 maize confirmed that the test plants contained the inserted T-DNA from plasmid PHP27118, as evident by the presence of the construct-specific target band in all test plant samples analyzed, and the absence in the non-genetically modified control plants. This result was reproducible. Test and control plants both contained the endogenous maize invertase gene. The sensitivity of the analysis under the conditions described is approximately 100 pg of 4114 maize genomic DNA in 50 ng of total genomic DNA or 0.2% 4114 maize genomic DNA.
Example 3. Southern Blot Analysis of DP-004114-3 Maize for Integrity and Copy Number
[0112] Southern blot analysis was used to confirm the integrity and copy number of the inserted T-DNA from PHP27118 and to confirm the presence of the cry1F, cry34Ab1, cry35Ab1, and pat gene cassettes in 4114 maize.
[0113] Five individual plants from the T1 generation of 4114 maize were selected for Southern blot analysis. Young leaf material was harvested from the 4114 maize (test) and non-transgenic maize (control) plants and was immediately placed on dry ice. The frozen samples were lyophilized and genomic DNA was extracted from the test and control tissues using a CTAB extraction method.
[0114] Following restriction enzyme digestions as detailed below, the DNA fragments were separated on agarose gels, depurinated, denatured, and neutralized in situ, and transferred to a nylon membrane in 20.times.SSC buffer using the method as described for TURBOBLOTTER.TM. Rapid Downward Transfer System (Schleicher & Schuell). Following transfer to the membrane, the DNA was bound to the membrane by ultraviolet light crosslinking.
Integrity
[0115] The restriction enzyme Hind III was selected for Southern analysis of integrity, as there are three sites located within the T-DNA (FIG. 2). Approximately 1-3 .mu.g of genomic DNA was digested with Hind III and separated by size on an agarose gel. As a positive control, approximately 15 pg of plasmid containing the PHP27118 T-DNA was spiked into a control plant DNA sample, digested and included on the agarose gel. A negative control was also included to verify background hybridization of the probe to the maize genome.
[0116] Four probes homologous to the cry1F, cry34Ab1, cry35Ab1, and pat genes on the PHP27118 T-DNA (for gene elements, see FIG. 2) were used for hybridization to confirm the presence of the genes. In order to develop the probes, fragments homologous to the cry1F, cry34Ab1, cry35Ab1, and pat genes were generated by PCR from plasmid containing the PHP27118 T-DNA, size separated on an agarose gel, and purified using a QIAquick.RTM. gel extraction kit (Qiagen). All DNA probes were subsequently generated from the fragments using the Rediprime.TM. II DNA Labeling System (Amersham) which performs random prime labeling with [.sup.32P]dCTP.
[0117] The labeled probes were hybridized to the target DNA on the nylon membranes for detection of the specific fragments using the MiracleHyb.RTM. Hybridization Solution essentially as described by the manufacturer (Stratagene). Washes after hybridization were carried out at high stringency. Blots were exposed to X-ray film at -80.degree. C. for one or more time points to detect hybridizing fragments.
[0118] Because the Hind III enzyme sites were known within the T-DNA, exact expected band sizes were determined for each of the probes (Table 4, FIG. 2). For an intact copy of the T-DNA, the cry1F probe was expected to hybridize to a fragment of 3891 bp. The cry34Ab1, cry35Ab1, and pat gene probes were expected to hybridize to a fragment of 7769 bp. Fragments from the test samples matching the expected sizes, as well as matching the bands in the plasmid control sample, would confirm the integrity of the inserted T-DNA and the presence of each gene.
[0119] The results of the Southern blot analysis with Hind III and the cry1F, cry34Ab1, cry35Ab1, and pat gene probes confirmed the expected fragment sizes and, thus, confirmed that the T-DNA inserted intact into each of the events and that each of the genes was present.
[0120] A band of approximately 4 kb was observed with the cry1F probe which is consistent with the expected fragment size. A similar fragment of approximately 4 kb was observed in the plasmid positive control lane, which was presumed to be the expected band of 3891 bp. Based on equivalent migration of the hybridizing band in the events to the band in the plasmid positive control, it was confirmed that the portion of the T-DNA containing cry1F had inserted intact in 4114 maize.
[0121] In the hybridization with the cry34Ab1 probe, a band of approximately 8 kb was observed in the event and also in the plasmid positive control. The hybridizing band in the plasmid positive control lane was presumed to be the expected band of 7769 bp. Because the hybridizing band in the event had migrated equivalently with this band, it was confirmed that this portion of the T-DNA containing cry34Ab1 was inserted intact.
[0122] Similarly, hybridizations with cry35Ab1 and pat hybridized to the same 7769 bp fragment in the plant and plasmid positive control as expected. These results confirmed that the portion of the T-DNA containing the cry35Ab1 and pat genes had inserted intact.
[0123] This Southern blot analysis confirms that 4114 maize contains an intact copy of the T-DNA from PHP27118 containing the cry1F, cry34Ab1, cry35Ab1, and pat genes.
TABLE-US-00005 TABLE 4 Summary of Expected and Observed Hybridization Fragments on Southern Blots for 4114 Maize DNA digested with Hind III Expected Fragment Size from Observed Fragment Probe PHP27118 T-DNA (bp).sup.1 Size (kb) .sup.2 cry1F 3891 ~4 cry34Ab1 7769 ~8 cry35Ab1 7769 ~8 pat 7769 ~8 .sup.1Expected fragment sizes based on map of PHP27118 T-DNA (FIG 2). .sup.2 All observed fragments migrated equivalently with the plasmid positive control and, therefore, were confirmed to represent the intact portion of the PHP27118 T-DNA.
Copy Number
[0124] The cry1F and pat probes were used in Southern blot hybridizations to evaluate the copy number of the insertions in 4114 maize.
[0125] The restriction enzyme Bcl I was selected for Southern analysis of copy number, as there is a single site located within the T-DNA (FIG. 2). Approximately 3 g of genomic DNA from individual plants of the T1 generation of event 4114 was digested with Bcl I and separated by size on an agarose gel. A plasmid containing the PHP27118 T-DNA was spiked into a control plant DNA sample, digested and included on the agarose gel to serve as a positive hybridization control. Negative control maize DNA was also included to verify background hybridization of the probe to the maize genome. DNA Molecular Weight Marker VII, digoxigenin (DIG) labeled (Roche, Indianapolis, Ind.), was included on BclI blots as a size standard for hybridizing fragments.
[0126] Probes for the cry1F and pat genes were also labeled by a PCR reaction incorporating a digoxigenin (DIG) labeled nucleotide, [DIG-11]-dUTP, into the fragment. PCR labeling of isolated fragments was carried out according to the procedures supplied in the PCR DIG Probe Synthesis Kit (Roche).
[0127] The DIG-labeled probes were hybridized to the Bcl I Southern blots of the T1 generation of the 4114 event. Probes were hybridized to the target DNA for detection of the specific fragments using DIG Easy Hyb solution (Roche) essentially as described by manufacturer. Post-hybridization washes were carried out at high stringency. DIG-labeled probes hybridized to the bound fragments were detected using the CDP-Star Chemiluminescent Nucleic Acid Detection System (Roche). Blots were exposed to X-ray film at room temperature for one or more time points to detect hybridizing fragments. Membranes were stripped of hybridized probe following the manufacturer's recommendation prior to hybridization with additional probes.
[0128] The restriction enzyme Bcl I, having a single restriction site within the T-DNA (FIG. 2), was selected to confirm the presence of a single PHP27118 T-DNA insertion in 4114 maize. The site for Bcl I is located at bp 2546 of the T-DNA (FIG. 2) and will yield fragments of greater than about 2500 bp and 9400 bp for a single inserted T-DNA. Hybridization with the pat probe would indicate the number of copies of this element found in the event based on the number of hybridizing bands (e.g., one hybridizing band indicates one copy of the element). The pat probe would hybridize to the fragment of greater than 9400 bp. Because the Bcl I restriction enzyme site is within the cry1F gene, the cry1F probe is expected to hybridize to both fragments and result in two bands for a single T-DNA insertion (FIG. 2).
[0129] The results of the Southern blot analysis with Bcl I and the cry1F and pat gene probes for 4114 maize are summarized in Table 5.
TABLE-US-00006 TABLE 5 Summary of Expected and Observed Hybridization Fragments on Southern Blots for Bcl I digests of 4114 Maize Observed Enzyme Expected Fragment Size from Fragment Size Probe Digest PHP27118 T-DNA (bp).sup.1 (kb).sup.2 cry1F Bcl I >2500.sup.3 ~3.1 >9400 >8.6 pat Bcl I >9400 >8.6 .sup.1Expected fragment sizes based on map of PHP27118 T-DNA (Figure 2). .sup.2All observed fragment sizes are approximated based on the migration of the DIG VII molecular weight marker. .sup.3Two fragments are expected with the cry1F probe due to the location of the Bcl I restriction site within the cry1F gene.
[0130] The results of the Southern blot analysis of 4114 maize with Bcl I digestion and the cry1F probe showed two bands as expected, one band of greater than 8.6 kb and a second band of approximately 3.1 kb. Two bands are expected for a single insertion due to the location of the Bcl I site within the cry1F gene, so these results indicate that there is a single copy of cry1F in 4114 maize. The results of the Southern blot analysis of 4114 maize with BclI digestion and the pat probe showed a single band of greater than 8.6 kb that matched the size of the larger cry1F band as expected. These results indicate that there is also a single insertion of the pat gene in maize event 4114.
[0131] As the cry34Ab1 and cry35Ab1 genes are located on the same fragment as the pat gene and part of the cry1F gene, and between the cry1F and pat genes on the T-DNA, by extension this also demonstrates that this event is likely to contain a single copy of each of these genes.
Example 4. Sequencing Characterization of Insert and Genomic Border Regions of Maize Event DP-004114-3
[0132] The sequence of the insert and genomic border regions was determined to confirm the integrity of the inserted DNA and to characterize the genomic sequence flanking the insertion site present in 4114 maize. In total, 16,752 bp of 4114 maize genomic sequence was confirmed, comprising 2,422 bp of the 5' genomic border sequence, 2,405 bp of the 3' genomic border sequence, and 11,925 bp of inserted T-DNA from PHP27118. The inserted T-DNA in 4114 maize was found to have a 29 bp deletion on the Right Border (RB) end and a 24 bp deletion on the Left Border (LB) end. All remaining sequence is intact and identical to that of plasmid PHP27118. The 5' and 3' genomic border regions of 4114 maize were verified to be of maize origin by PCR amplification and sequencing of the genomic border regions from both 4114 maize and control maize plants.
[0133] Seed containing event DP-004114-3 was obtained from a T1S2 generation of 4114 maize. Control seed was obtained from a maize line that has a similar genetic background to 4114 maize but does not contain the cry1F, cry34Ab1, cry35Ab1, and pat gene cassettes. All seeds were obtained from Pioneer Hi-Bred International, Inc. (Johnston, Iowa). The Low DNA Mass Ladder (Invitrogen Corp., Carlsbad, Calif.) and the High DNA Mass Ladder (Invitrogen Corp.) were used for gel electrophoresis to estimate DNA fragment sizes on agarose gels.
[0134] The 4114 maize seed and the control seed were planted in growth chambers at the DuPont Experimental Station (Wilmington, Del.) to produce plant tissues used for this study. One seed was planted per pot, and the pot was uniquely identified. All plants were grown with light, temperature, and water regulated for healthy plant growth. Leaf samples were collected from the control and 4114 maize plants. For each individual plant, leaf material was collected in a pre-labeled bag, placed on dry ice, and then transferred to an ultra low freezer (<-55.degree. C.) following collection. All samples were maintained frozen until tissue processing.
Genotype Confirmation Via Event-Specific PCR Analysis
[0135] A leaf sample was taken from all test and control plants for event-specific PCR analysis. DNA was extracted from each leaf sample using the Extract-N-Amp.TM. Plant PCR kit following the described procedure (Sigma-Aldrich, St. Louis, Mo.) for real-time PCR analysis.
[0136] Real-time PCR was performed on each DNA sample utilizing an ABI PRISM.RTM. 7500HT Sequence Detection System (Applied Biosystems, Inc., Foster City, Calif.). TaqMan.RTM. probe (Applied Biosystems, Inc.) and primer sets (Integrated DNA Technologies, Coralville, Iowa) were designed to detect a target sequence from 4114 maize. In addition, a second TaqMan.RTM. probe and primer set for a reference maize endogenous gene was used to confirm the presence of amplifiable DNA in each reaction. The analysis consisted of real-time PCR determination of qualitative positive/negative calls. The extracted DNA was assayed using TaqMan.RTM. Universal PCR Master Mix, No AmpErase.RTM. UNG (Applied Biosystems, Inc.).
[0137] Positive or negative determination for 4114 maize was based on comparison of the CT (threshold cycle) of the event-specific target PCR to that of the maize endogenous reference target. If the event and endogenous PCR targets amplified above CT threshold, then the plant was scored as positive for that event. If the endogenous target amplified and the event target did not, then the plant was scored as negative. If neither target amplified for a particular sample, then it was determined to be a poor quality DNA sample or failed run and the assay was repeated.
[0138] All 4114 maize plants were positive for the event-specific PCR and the PAT, Cry1F, and Cry34Ab1 proteins, whereas all the control maize plants were negative. The results are summarized in Table 6.
TABLE-US-00007 TABLE 6 Summary of Event-Specific PCR Analysis and Cry1F, Cry34Ab1, and PAT Protein Expression in 4114 Maize and Control Maize Plants Event-Specific PCR.sup.1 Cry1F.sup.2 Cry34Ab1.sup.2 PAT.sup.2 4114 Maize Plant ID T-F-08-233C-1 + + + + T-F-08-233C-2 + + + + T-F-08-233C-3 + + + + T-F-08-233C-4 + + + + Control Maize Plant ID C-F-08-246C-1 - - - - C-F-08-246C-2 - - - - .sup.1.Summary of event-specific real time PCR assay for 4114 maize. Positive (+) indicates the presence of 4114 maize event. Negative (-) indicates the absence of 4114 maize event. .sup.2.Summary of Cry1F, Cry34Ab1, and PAT protein expression in 4114 maize and control maize plants using lateral flow devices. Positive (+) indicates the presence of the protein. Negative (-) indicates the absence of the protein.
DNA Sequencing
[0139] DNA fragments were cloned and submitted for sequencing at the Pioneer Crop Genetics Research sequencing facility (Wilmington, Del.). Sequencher.TM. software from Gene Codes Corporation (Ann Arbor, Mich.) was used to assemble the sequences. Sequence annotation was performed using Vector NTI 9.1.0 (Invitrogen Corp) by comparing the T-DNA insert sequences generated from 4114 maize with the sequences from the T-DNA region of plasmid PHP27118 (used for transformation to produce 4114 maize).
[0140] The T-DNA region of plasmid PHP27118, used to create 4114 maize, was sequenced and compared with the inserted T-DNA sequence in 4114 maize.
[0141] The sequence of the T-DNA region of plasmid PHP27118 was used to design primer pairs to characterize the inserted T-DNA in 4114 maize. Six overlapping PCR products were generated using genomic DNA from four different 4114 maize plants as template. These PCR products were cloned and sequenced.
Sequencing of 5' and 3' Flanking Genomic Border Regions
[0142] Preliminary sequence characterization of the 5' and 3' flanking genomic border regions were carried out using several rounds of inverse PCR, (Silver and Keerikatte (1989) J. Virol. 63: 1924; Ochman et al. (1988) Genetics 120:621-623; Triglia et al., (1988) Nucl. Acids Res. 16:8186) with primers anchored within various regions of the inserted T-DNA. Sequence information obtained from inverse PCR was subjected to BLASTn analysis and showed a match to the maize BAC clone AC211214 from the NCBI (National Center for Biotechnology Information) GenBank nucleotide database. This sequence was then used to design primers that spanned the 5' and 3' insert/genomic junctions in 4114 maize. The PCR products generated from four 4114 maize plants were cloned and sequenced to verify the 5' and 3' insert/genomic junctions and the genomic border regions.
[0143] In addition, to demonstrate that the identified 5' and 3' genomic border regions were of maize origin, PCR was performed on 4114 maize and control maize plants within the genomic regions. Each PCR fragment was directly sequenced to verify its identity of maize origin.
[0144] The T-DNA sequence information of plasmid PHP27118 was used to design primers to verify the inserted sequence in 4114 maize (Tables 7 and 8).
TABLE-US-00008 TABLE 7 PCR Primers Used to Characterize the Genomic Border Regions and Inserted T-DNA in 4114 Maize PCR Primer Fragment Primer Pair SEQ ID NOs: Size (bp) Amplified Region A 09-0-3030/09-0-2787 11/12 2511 5` Genomic border region and insert B 09-0-3036/09-0-3046 13/14 3622 Insert C 09-0-2980/09-0-3045 16/15 4146 Insert D 08-0-2463/08-0-2759 17/18 2713 Insert E 09-0-2775/09-0-3083 19/20 3062 Insert F 09-0-2799/09-0-3005 21/22 2612 3` Genomic border region and insert G 09-0-3230/09-0-3229 23/24 257 5` Genomic border region H 09-0-3231/09-0-3084 25/26 283 3` Genomic border region
TABLE-US-00009 TABLE 8 Sequence and Location of Primers Used For PCR Reactions Target Primer Sequence PCR (SEQ ID Location Fragment NO:) Primer Sequence (5'-3') (bp to bp).sup.1 A 09-0-3030 GAGCATATCCAGCACCAGCTGGTACCAAG 1-29 (SID: 11) 09-0-2787 GCAGGCATGCCCGCGGATA 2,511-2,493 (SID: 12) B 09-0-3036 TGGTCTACCCGATGATGTGATTGGCC 1,994-2,019 (SID: 13) 09-0-3046 CGAAGACAGGATCTGACAAGGTCCGATAG 5,615-5,587 (SID: 14) C 09-0-3045 GACTTCATGAACTCTTTGTTTGTGAC 5,414-5,414 (SID: 15) TGCAGAGAC 09-0-2980 CTCATGACTCAGGACTTGTGGC 9,559-9,538 (SID: 16) D 08-0-2463 ATCAGCCTCTACTTCGAC 9,390-9,407 (SID: 17) 08-0-2759 CTCCATGATCTTCGTCTCATGTG 12,102- (SID: 18) 12,080 E 09-0-2775 CACCAACTCCATCCAGAAGTGGC 11,481- (SID: 19) 11,503 09-0-3083 GCCTTGCATTGGCGCAGTGAGAACCG 14,542- (SID: 20) 14,517 F 09-0-2799 CGGCGCGCCTCTAGTTGAAGACACGTT 14,141- (SID: 21) 14,167 09-0-3005 CACTGGACTGAGCCGCACAGCTAAGGACAC 16,752- (SID: 22) 16,723 G 09-0-3230 GGAACATTCAGACTTGGGAGTCTGGACT 2,086-2,113 (SID: 23) 09-0-3229 GAACAGGGTCCTCGAATCAAGGGCAGC 2,342-2,316 (SID: 24) H 09-0-3231 CGGTTCTCACTGCGCCAATGCAAGGC 14,517- (SID: 25) 14,542 09-0-3084 CATGACGACCATGAAGCAACATC 14, 799- (SID: 26) 14,777 .sup.1Location in sequence of 4114 Maize. Bases 1-2,422 = 5' genomic border region Bases 2,423-14,347 = insert Bases 14,348-16,752 = 3' genomic border region.
[0145] To characterize the inserted T-DNA in 4114 maize, PCR primers were designed to amplify the T-DNA insert in six separate, overlapping PCR products as outlined in Table 7: fragments A through F(Positions indicated in FIG. 5). As expected, the predicted PCR products were generated only from 4114 maize genomic DNA samples, and were not present in the control maize samples. The six PCR products were cloned and sequenced. When comparing the sequence of the inserted T-DNA in 4114 maize to the T-DNA region of plasmid PHP27118 used to create 4114 maize, it was determined that there was a 29 bp deletion on the RB end, and a 24 bp deletion on the LB end. RB and LB termini deletions often occur in Agrobacterium-mediated transformation (Kim et al. (2007) Plant J. 51:779-791). All remaining sequence is intact and identical to that of plasmid PHP27118. The sequence of the insertion is presented in SEQ ID NO: 27.
[0146] To verify the additional 5' genomic border sequence, PCR was performed with a forward primer (SEQ ID NO: 11) in the 5' genomic border region and a reverse primer (SEQ ID NO: 12) within the inserted T-DNA. The resulting 2,511 bp PCR fragment A from 4114 maize genomic DNA samples was cloned and sequenced (FIG. 3). The 2,422 bp of the 5' genomic border region sequence is set forth in nucleotides 1-2,422 of SEQ ID NO: 27.
[0147] To verify the additional 3' genomic border sequence, PCR was performed with a forward primer (SEQ ID NO: 21) within the inserted T-DNA and a reverse primer (SEQ ID NO: 22) in the 3' genomic border region. The resulting 2,612 bp PCR fragment F from 4114 maize genomic DNA samples was cloned and sequenced (FIG. 3). The 2,405 bp of the 3' genomic border region sequence is set forth in nucleotides 14,348 to 16,752 of SEQ ID NO: 27.
[0148] In total, 16,752 bp of sequence from genomic DNA of 4114 maize were confirmed: 2,422 bp of the 5' genomic border sequence, 2,405 bp of the 3' genomic border sequence, and 11,925 bp comprising the inserted T-DNA.
[0149] To demonstrate that the identified 5' and 3' flanking genomic border sequences are of maize origin, PCR was performed within the 5' and 3' genomic border regions (the primer pair set forth in SEQ ID NOs: 23 and 24 and the primer pair set forth in SEQ ID NOs: 25 and 26, respectively) on 4114 maize genomic DNA samples and control maize samples. The expected PCR fragment G (257 bp for the 5' genomic region) and PCR fragment H (283 bp for the 3' genomic region) were generated from both 4114 maize and control maize. These PCR products were cloned and sequenced, and the corresponding products from the 4114 maize and the control maize are identical, thus confirming that the sequences are of maize genomic origin.
Example 5. Insect Efficacy of Maize Event DP-004114-3
[0150] Efficacy data was generated on 4114 maize. Field testing compared 4114 maize in two genetic backgrounds to a negative control (isoline) in the same backgrounds. Efficacy testing included: first generation ECB (ECB1) foliage damage and second generation ECB (ECB2) stalk damage at four locations, WCRW root damage at three locations, and FAW foliar damage at one location. At each location, single-row plots were planted in a randomized complete block with three replications (20 kernels/plot.times.12 entries.times.3 replicates=1 experiment/location). All plants were tissue sampled after emergence to confirm the presence of the event by event-specific PCR. Any negatives were culled and each plot thinned to a target stand of 10-15 evenly spaced plants per plot.
[0151] For trials characterizing ECB1 damage, each plant was manually infested with approximately 100 ECB neonate larvae 3 times (300 larvae total) over approximately one week beginning at approximately the V5 growth stage. Approximately three weeks after the last successful infestation, leaf damage ratings (based on a 9-1 visual rating scale where 9 indicates no damage and 1 indicates maximum damage) were taken on 8 consecutive plants per plot (total of 24 plants per genetic background, per entry) and means were calculated for each treatment. First generation ECB foliar feeding results on 4114 maize are shown in Table 9.
TABLE-US-00010 TABLE 9 Efficacy of DP-004114-3 Maize Against First Generation ECB Larvae Mean ECB1LF Damage Location Maize Line Rating .+-. Standard Error.sup.a,b York, NE 4114 9.0 .+-. 0.05 A 1507 .times. 59122 9.0 .+-. 0.08 A Negative control 4.4 .+-. 0.09 B Johnston, IA 4114 9.0 .+-. 0.00 A 1507 .times. 59122 9.0 .+-. 0.00 A Negative control 4.5 .+-. 0.08 B Mankato, MN 4114 9.0 .+-. 0.02 A 1507 .times. 59122 9.0 .+-. 0.03 A Negative control 4.7 .+-. 0.11 B Princeton, IL 4114 9.0 .+-. 0.00 A 1507 .times. 59122 9.0 .+-. 0.00 A Negative control 5.5 .+-. 0.17 B .sup.aDamage ratings on individual plants were determined using the following visual rating scale: 9. No visible leaf injury or a small amount of pin or fine shot-hole type injury on a few leaves. 8. Small amount of shot-hole type lesions on a few leaves. 7. Shot-hole injury common on several leaves. 6. Several leaves with shot-hole and elongated lesions (Lesions <0.5'' in length). 5. Several leaves with elongated lesions (Lesions 0.5'' to 1.0'' in length). 4. Several leaves with elongated lesions (Lesions >1.0'' in length). 3. Long lesions (>1.0'') common on about one-half the leaves. 2. Long lesions (>1.0'') common on about two-thirds the leaves. 1. Most of the leaves with long lesions. .sup.bWithin a location, means with the same letter are not significantly different (Fisher`s Protected LSD test, P > 0.05).
[0152] For trials characterizing ECB2 damage, the same plants infested above for ECB1 were manually infested again later in the growing season with approximately 100 ECB neonate larvae (300 larvae total) per plant 3 times over approximately one week beginning at the R1 growth stage, when approximately 50% of the plants were shedding pollen. At approximately 50-60 days after the last infestation, stalks of 8 consecutive plants per plot (total of 24 plants per genetic background, per entry) were split from the top of the 4th internode above the primary ear to the base of the plant. The total length of ECB stalk tunneling (ECBXCM) was then measured in centimeters and recorded for each plant. Tunnels 1 cm or less were considered entrance holes (larvae was not able to establish in the stalk) and were not included in the total cm of tunneling. Means (total cm of tunneling) were calculated for each treatment. The ECB2 stalk feeding results for 4114 maize are shown in Table 10.
TABLE-US-00011 TABLE 10 Efficacy of DP-004114-3 Maize Against Second Generation ECB Larvae Mean ECBXCM (tunnel Location Maize Line length, cm) .+-. Standard Error.sup.b York, NE 4114 0.9 .+-. 0.27 B 1507 .times. 59122 0.4 .+-. 0.12 B Negative control 22.6 .+-. 1.83 A Mankato, MN 4114 1.3 .+-. 0.30 B 1507 .times. 59122 0.7 .+-. 0.18 B Negative control 31.3 .+-. 2.19 A Johnston, IA 4114 1.1 .+-. 0.26 B 1507 .times. 59122 0.3 .+-. 0.11 B Negative control 33.0 .+-. 2.51 A Princeton, IL 4114 0.8 .+-. 0.22 B 1507 .times. 59122 0.1 .+-. 0.07 B Negative control 10.0 .+-. 0.94 A .sup.bWithin a location, means with the same letter are not significantly different (Fisher`s Protected LSD test, P > 0.05).
[0153] Root damage caused by WCRW was also investigated. Plants at approximately the V2 growth stage were manually infested with approximately 500 WCRW eggs applied into the soil on each side of the plant (.about.1,000 eggs/plant total). Additionally, plots were planted in fields that had a high probability of containing a natural infestation of WCRW. Plant roots were evaluated at approximately the R2 growth stage. Five consecutive plants per plot (total 45 plants per genetic background, per entry) were removed from the plot and washed with pressurized water. The root damage was rated using the 0-3 node injury scale (CRWNIS) (Oleson, et al. (2005) J. Econ. Entomol. 98(1):1-8) and means were calculated for each treatment. Mean root damage ratings from WCRW feeding are shown in Table 11.
TABLE-US-00012 TABLE 11 Efficacy of DP-004114-3 Maize Against WCR Larvae Maize Mean CRWNIS score .+-. Location Line Standard Error.sup.b,c Johnston, IA 4114 0.1 .+-. 0.01 B 1507 .times. 59122 0.1 .+-. 0.02 B Negative Control 0.5 .+-. 0.09 A Mankato, MN 4114 0.1 .+-. 0.02 B 1507 .times. 59122 0.1 .+-. 0.01 B Negative Control 1.1 .+-. 0.11 A Rochelle, IL 4114 0.3 .+-. 0.04 B 1507 .times. 59122 0.1 .+-. 0.01 B Negative Control 1.3 .+-. 0.18 A .sup.bDamage ratings on individual plant root masses were determined using 0-3 Node Injury Scale (Oleson et al. 2005, supra). .sup.cWithin a location, means with the same letter are not significantly different (Fisher`s Protected LSD test, P > 0.05).
[0154] For the FAW efficacy testing, individual plants were manually infested with approximately 75 neonates at approximately the V5 growth stage. Leaves were scored for damage on 8 consecutive plants per plot (total of 24 plants per genetic background, per entry) (FAWLF based on a 9-1 visual rating scale where 9 indicates no damage and 1 indicates maximum damage approximately two weeks after the last successful inoculation and means were calculated for each treatment. Mean damage ratings characterizing FAW foliar feeding on DP-004114-3 are shown in Table 12.
TABLE-US-00013 TABLE 12 Efficacy of DP-004114-3 Maize Against FAW Larvae Mean FAWLF Damage Location Maize Line Rating .+-. Standard Error.sup.a,b Johnston, IA 4114 8.9 .+-. 0.06 BC 1507 .times. 59122 9.0 .+-. 0.00 A Negative control 2.1 .+-. 0.08 D .sup.aDamage ratings on individual plants were determined using the following visual rating scale: 9. No damage to pinhole lesions present on whorl leaves. 8. Pinholes and small circular lesions present on whorl leaves. 7. Small circular lesions and a few small elongated (rectangular shaped) lesions up to 0.5'' in length present on whorl and furl leaves. 6. Several small elongated lesions 0.5'' to 1'' in length on a few whorl and furl leaves. 5. Several large elongated lesions greater than 1'' in length present on a few whorl and furl leaves and/or a few small to mid-sized uniform to irregular shaped holes (basement membrane consumed) in whorl and furl leaves. 4. Several large elongated lesions present on several whorl and furl leaves and/or several large uniform to irregular shaped holes in whorl and furl leaves. 3. Many elongated lesions of all sizes present on several whorl leaves plus several large uniform to irregular shaped holes in whorl and furl leaves. 2. Many elongated lesions of all sizes present on most whorl and furl leaves plus many mid to large-sized uniform to irregular shaped holes in whorl and furl leaves. 1. Whorl and furl leaves almost totally destroyed. .sup.bWithin a location, means with the same letter are not significantly different (Fisher`s Protected LSD test, P > 0.05).
[0155] In addition to field efficacy studies, 4114 maize was evaluated in the lab-based sub-lethal seedling assay (SSA) (U.S. Publication No. 2006/0104904 the contents of which is hereby incorporated by reference). The SSA allowed for a comparison of the efficacy of 4114 maize to an unprotected control (near isoline) without the confounding effects of the field environment. The SSA technique involves exposing a population of neonate WCRW to maize seedlings containing either one of the 4114 maize events or non-transgenic (negative control) maize seedlings. Larvae were exposed for a period of 17 days from the date of initial egg hatch. The experimental unit for the SSA was a single plastic container with dimensions of 23.times.30.times.10 cm (Pactiv Corp., Lake Forest, IL). Entries were arranged in a randomized complete block with 3 replications per entry. For each entry, SSA setup involved placing 115 kernels into each container with 225 mL of a 1% thiophanate-methyl fungicide solution and 1000 mL of Metro-Mix 200 plant growth media (Scotts-Sierra Horticultural Products Company, Marysville, Ohio). Immediately after adding the Metro-Mix, WCRW eggs were infested onto the surface of each container at a rate of 1,000 eggs per container. WCRW eggs were pre-incubated at 25.degree. C. so that initial egg hatch was timed to occur 5-7 days after container setup. Infested containers were held in a walk-in environmental chamber with settings of 25.degree. C., 65% relative humidity, and 14:10 light:dark cycle. Larvae were extracted from the containers 17 days post-egg hatch using a Burlese funnel system. A random subsample of 30 larvae per container were selected and their head capsules measured under a dissecting microscope to categorize each into 1 of 3 instars. Data collected includes the age structure of the larval population determined from the number of larvae in each of three potential instars. Histograms that graphically displayed the age distribution of larvae for each entry were plotted and visually compared as shown in FIG. 4.
[0156] The pest spectrum for 4114 maize is provided in Table 13.
TABLE-US-00014 TABLE 13 Insect Pests That Are Controlled or Suppressed by DP-004114-3 Maize Expressing Cry1F, Cry34Ab1, and Cry35Ab1 Scientific Name Common Name Insect Order Ostrinia nubilalis European corn borer (ECB) Lepidoptera Helicoverpa zea Corn earworm (CEW) Lepidoptera Spodoptera frugiperda Fall armyworm (FAW) Lepidoptera Diatraea grandiosella Southwestern corn borer (SWCB) Lepidoptera Richia albicosta Western bean cutworm (WBCW) Lepidoptera Agrotis ipsilon Black cutworm (BCW) Lepidoptera Elasmopalpus lignosellus Lesser corn stalk borer (LCSB) Lepidoptera Diatrea crambidoides Southern corn stalk borer (SCSB) Lepidoptera Diabrotica virgifera virgifera Western corn rootworm (WCRW) Coleoptera Diabrotica virgifera zeae Mexican corn rootworm (MCR) Coleoptera Diabrotica berberi Northern corn rootworm (NCR) Coleoptera Diatrea saccharalis Sugarcane borer (SCB) Coleoptera
Example 6. Protein Expression and Concentration
Generation of Plant Material
[0157] 4114 maize from the PHNAR.times.BC3F3 generation was grown in five locations in the United States and Canada. Each site employed a randomized complete block design containing four blocks, with each block separated by a buffer distance of at least 36 inches (0.9 m). Each entry was planted in 2-row plots bordered on each side by 1 row of border seed.
Leaf Tissue Collection and Processing
[0158] One leaf tissue sample was collected in each block at the V9 stage. All samples were collected from impartially selected, healthy, representative plants for each event. Each leaf sample was obtained by selecting the youngest leaf that had emerged at least 8 inches (20 cm, visible tissue) from the whorl. If this leaf was damaged or otherwise unhealthy, the next leaf below it was sampled. The leaf was pruned (cut) from the plant approximately 8 inches (20 cm) from the leaf tip. The leaf sample (including midrib) was cut into .ltoreq.1 inch (2.5 cm) pieces and placed in a 50-ml sample vial. The samples were then placed on dry ice until transferred to a freezer (.ltoreq.-10.degree. C.). Samples were shipped frozen and stored at .ltoreq.-10.degree. C. upon arrival. All tissue samples were lyophilized, under vacuum, until dry. The lyophilized leaf samples were finely homogenized in preparation for analysis. Samples were stored frozen between processing steps.
Protein Concentration Determinations
[0159] Concentrations of the Cry1F, Cry34Ab1, Cry35Ab1, and PAT proteins were determined using specific quantitative ELISA methods.
Protein Extraction
[0160] Aliquots of processed leaf tissue samples were weighed into 1.2 mL tubes at the target weight of 10 mg. Each sample analyzed for Cry1F, Cry34Ab1, Cry35Ab1, and PAT protein concentrations was extracted in 0.6 mL of chilled PBST (Phosphate Buffered Saline plus Tween-20). Following centrifugation, supernatants were removed, diluted, and analyzed.
Determination of Cry1F, Cry34Ab1 and PAT Protein Concentration
[0161] The Cry1F, Cry34Ab1 and PAT ELISA kits employed were obtained from EnviroLogix, Inc. (Portland, Me.), and the Cry35Ab1 ELISA kit employed was obtained from Acadia BioScience, LLC (Portland, Me.). The ELISA method for each of these four proteins utilized a sequential "sandwich" format to determine the concentration of the protein in sample extracts. Standards (analyzed in triplicate wells) and diluted sample extracts (analyzed in duplicate wells) were incubated in plate pre-coated with an antibody specific to a single protein chosen from Cry1F, Cry34Ab1, Cry35Ab1 or PAT. Following incubation, unbound substances were washed from the plate. A different specific antibody for the respective selected protein, conjugated to the enzyme horseradish peroxidase (HRP), was added to the plate and incubated. Then, unbound substances were washed from the plate leaving the bound protein "sandwiched" between the antibody coated on the plate and the antibody-HRP conjugate. Detection of the bound antibody-protein complex was accomplished by the addition of substrate, which generated a colored product in the presence of HRP. The reaction was stopped with an acid solution and the optical density (OD) of each well was determined using plate reader. An average of the results from duplicate wells was used to determine the concentration of the Cry1F, Cry34Ab1, Cry35Ab1 or PAT protein in ng/mg sample dry weight.
Calculations for Determining Protein Concentrations
[0162] SoftMax.RTM. Pro software was used to perform the calculations required to convert the OD values obtained by the plate reader to protein concentrations.
1. Standard Curve
[0163] A standard curve was included on each ELISA plate. The equation for the standard curve was generated by the software, which used a quadratic fit to relate the mean OD values obtained for the standards to the respective standard concentration (ng/mL). The quadratic regression equation was applied as follows:
y=Cx.sup.2+Bx+A
[0164] where x=known standard concentration and y=respective mean absorbance value (OD).
2. Sample Concentration
[0165] Interpolation of the sample concentration (ng/ml) was accomplished by solving for x in the above equation using values for A, B, and C determined by the standard curve.
Sample Concentration ( ng / mL ) = - B + B 2 - 4 C ( A - sampleOD ) 2 C ##EQU00001## e . g . Curve Parameters : A = 0.0476 , B = 0.4556 , C = - 0.01910 , and sample OD = 1.438 ##EQU00001.2## Sample Concentration = - 0.4556 + 0.4556 2 - 4 ( - 0.01910 ) ( 0.0476 - 1.488 ) 2 ( - 0.01910 ) = 3.6 ng / mL ##EQU00001.3##
Sample concentration values were adjusted for the dilution factor expressed as 1:N
[0166] Adjusted Concentration=Sample Concentration.times.Dilution Factor
[0167] e.g. Sample Concentration=3.6 ng/mL and Dilution Factor=1:10
[0168] Adjusted Concentration=3.6 ng/mL.times.10=36 ng/mL
Adjusted sample concentration values were converted from ng/mL to ng/mg sample weight as follows:
[0169] ng/mg Sample Weight=ng/mL.times.Extraction Volume (mL)/Sample Weight (mg)
[0170] e.g. Concentration=36 ng/mL, Extraction Volume=0.60 ml, and
[0171] Sample Weight=10.0 mg
[0172] ng/mg Sample Weight=36 ng/mg.times.0.60 mL/10.0 mg=2.2 ng/mg
3. Lower Limit of Quantitation (LLOQ)
[0173] The LLOQ, in ng/mg sample weight, was calculated as follows:
LLOQ = Reportable Assay LLOQ .times. Extraction Volume Sample Target Weight ##EQU00002## e . g . for PAT in leaf : reportable assay LLOQ = 2.3 ng / mL , extraction volume = 0.6 mL , and sample target weight = 10 mg ##EQU00002.2## LLOQ = 2.3 ng / mL .times. 0.6 mL 10 mg = 0.14 ng / mg sample weight ##EQU00002.3##
Results
[0174] The proteins Cry1F, Cry34Ab1, Cry35Ab1, and PAT were detected in V9 leaf tissue of 4114 maize at the concentrations set forth in Table 14 below.
TABLE-US-00015 TABLE 14 Protein Concentrations in 4114 Maize Protein concentration in ng/mg dry weight* Cry1F Cry34Ab1 Cry35Ab1 PAT Mean .+-. SD 9.7 .+-. 2.5 26 .+-. 3.1 33 .+-. 3.1 9.8 .+-. 3.3 Range 5.3-14 22-31 28-39 4.8-15 * The LLOQ for Cry1F and PAT was 0.14 ng/mg Dry Weight; the LLOQ for Cry34Ab1 and Cry35Ab1 were 0.16 ng/mg Dry Weight
Example 7: An Event-Specific Identification System for DP-004114-3 Maize
[0175] The event-specific system for DP-004114-3 maize was designed at the 5' junction between the DP-004114-3 insert and maize genomic region. The forward primer (08-O-2677, SEQ ID NO: 29) is situated within maize genomic DNA, the reverse primer (08-O-2678, SEQ ID NO: 30) is situated within the inserted DNA, and the binding site of the probe (08-QP74, SEQ ID NO: 31) spans the transition between DP-004114-3 insert and maize genomic DNA (Table 15). The optimum primer and probe concentrations were selected based on PCR efficiency and the ability to quantitate at the low (0.08% GM) and high (5% GM) ends of the dynamic range (Table 16).
TABLE-US-00016 TABLE 15 Primers and probe for DP-004114-3 event-specific PCR system Name Sequence SEQ ID NO. 08-O-2677 5'-CGT TTG TAG CAC TTG 29 CAC GTA GT-3' 08-O-2678 5'-GGT AAC CGC TCT TCC 30 AGT TGA A-3' 08-QP74 5'-AAG CTT CAA CAC AGA TC-3' 31 (probe) DP-004114-3 amplicon sequence (underlined are the primer and probe binding sites): Length: 90 bp CGTTTGTAGCACTTGCACGTAGTTACCCGGACCGAAGCTTCAACA CAGATCTGATAGTTTAAACGCTCTTCAACTGGAAGAGCGGTTACC (SEQ ID NO: 32)
TABLE-US-00017 TABLE 16 Mastermix for DP-004114-3 event-specific PCR system Final Chemicals Concentration Concentration.dagger. .mu.l/reaction Applied Biosystems TaqMan 2 x 1 x 10.0 Universal PCR Master Mix, No AmpErase UNG 08-0-2677 10 .mu.M 500 nM 1.0 08-0-2678 10 .mu.M 900 nM 1.8 08-QP74 10 .mu.M 200 nM 0.4 Sterile water 1.8 Total volume 15.0 .dagger. Total PCR reaction is 20 .mu.l (15 .mu.l mastermix and 5 .mu.l genomic DNA template).
TABLE-US-00018 TABLE 17 Reaction and cycling parameters Format: 15 .mu.l mastermix + 5 .mu.l genomic DNA template = 20 .mu.l per reaction Equipment: Applied Biosystems ViiA7 real time thermal cycler Software: ViiA 7 RUO software version 1.1 Plasticware: MicroAmp .RTM. Optical 96-well Reaction Plates (Applied Biosystems, Inc.); PRISM .TM. 384-well Clear Optical Reaction Plates (Applied Biosystems, Inc.); and MicroAmp .TM. Optical Adhesive Film (Applied Biosystems, Inc.)
TABLE-US-00019 TABLE 18 Cycling parameters Data Step Stage Temp. Time collection Cycles 1 Initial enzyme activation 95.degree. C. 600 s no 1.times. 2 Amplification Denaturation 95.degree. C. 15 s no 40.times. 3 Annealing & Extension 60.degree. C. 60 s Yes
[0176] The assay format used a standard curve having four standard points, each in triplicate. The standards were produced by preparing a solution of 40 ng/.mu.l of total genomic maize DNA with 10% DP-004114-3 maize DNA followed by serial dilutions in 0.1.times.TE buffer containing 10 ng/.mu.l salmon sperm DNA. Negative controls (NTC) were measured in triplicate for each system to verify purity of the reagents. Each sample (unknown) was analyzed at 200 ng genomic maize DNA per reaction in triplicates (six reactions per sample in total for both PCR systems). The relative content of DP-004114-3 maize to total maize DNA was subsequently calculated by determining the mean of the copy numbers based on the standard curves (linear regression of threshold cycle (C.sub.T) value versus log [copy number]) and calculating the ratios of DP-004114-3 maize copy number/total copy number of haploid maize genomes.
[0177] This event-specific quantitative PCR system for detection of DP-004114-3 maize DNA was developed, optimized, and validated on Applied Biosystem's ViiA 7.TM. real-time PCR system. The method can also be applied on a different platform however, with minimal optimization and adaptation.
[0178] The event-specific real-time PCR method described here can be applied to determine the relative content of DP-004114-3 maize DNA in total genomic maize DNA. The method performs in a linear manner with an acceptable level of accuracy and precision over the whole range from 0.08% to 5.0% DP-004114-3 content. The method was developed and validated with genomic DNA extracted from maize seeds. However, the assay can be applied to any matrix from which genomic DNA with sufficient quantity and quality can be purified.
Example 8: Gel-Based PCR Detection Method for the Maize Event DP-004114-3
[0179] This protocol describes a qualitative gel-based PCR assay to detect the presence of DP-004114-3 maize DNA. The PCR detection method is used in conjunction with a DNA extraction method which yields DNA of sufficient quality and quantity.
[0180] A PCR system for DP-004114-3 maize was developed using primers to amplify the 5' border junction between maize genomic DNA and the DP-004114-3 insert. The forward primer is located in the maize genomic region, and the reverse primer is located in the transgene insert.
TABLE-US-00020 Forward Primer (11-O-4127) (SEQ ID NO: 33): 5'-GGA CCC TGT TCA CAA CAC AGG GCT C-3' Reverse Primer (11-O-4128) (SEQ ID NO: 34): 5'-GGC CGA AGC TTC GGT CCG G-3'
Amplicon Sequence (Underlined are the Primer Binding Sites) (SEQ ID NO:35):
TABLE-US-00021
[0181] ggaccctgttcacaacacagggctctggctttggagcctctcgtttgtag cacttgcacgtagttacccggaccgaagcttcaacacagatctgatagtt taaacgctcttcaactggaagagcggttacccggaccgaagcttcggcc
Equipment and Materials Used:
TABLE-US-00022
[0182] Equipment/Plasticware Specification 96-well GeneAmp PCR System 9700 Applied Biosystems, Foster City, Ca; or equivalent Gel Electrophoresis Unit Sub Cell GT, Bio-Rad, Hercules, CA; or equivalent Power supply Power Pac, Bio-Rad, Hercules, CA; or equivalent Gel documentation Bio-Rad Molecular Imager Gel Doc XR + Imager System; or equivalent Quantity One, 2.0 Software; or equivalent Pipettes with adjustable volume Ranin, Woburn, MA; Research: 0.5-10 .mu.l; 2-20 .mu.l, 20-200 .mu.l, 100-1000 .mu.l; or equivalent Filter Tips Appropriate for the pipette models used PCR Reaction tubes and Caps Applied Biosystems, Foster City, CA; or equivalent Reaction tubes 1.5 ml Eppendorf, Hamburg, Germany; or equivalent
Reagents, Buffers and Solutions:
TABLE-US-00023
[0183] Reagent Specification 2 .times. Promega PCR Master Mix (contains 15 mM Promega, Madison, WI; or equivalent MgCl.sub.2 and Taq polymerase) PCR Marker Promega, Madison, WI; or equivalent UltraPure Agarose lnvitrogen, Carlsbad, CA; or equivalent Ethidium bromide EMD, Darmstadt, Germany; or equivalent 6 .times. Promega Blue Orange Loading dye Promega, Madison, WI; or equivalent 10 .times. TBE buffer Mediatech, Herndon, VA; or equivalent Molecular Grade Water Mediatech, Herndon, VA; or equivalent
Procedures
[0184] Reagents were thoroughly mixed before use. A reaction mix consisting of all components of the PCR reaction were prepared, except template DNA, in sufficient quantity for all reactions to be performed. Reagents and the master mix were kept on ice.
Preparation of the Mastermix for the PCR System:
TABLE-US-00024
[0185] Component Concentration Final concentration .mu.l/rxn Promega 2 .times. PCR buffer 2 .times. 1 .times. 12.50 Forward Primer (11-O-4127) 10 .mu.M 200 nM 0.50 Reverse Primer (11-O-4128) 10 .mu.M 200 nM 0.50 Sterile water 6.50 Total volume 20.00
[0186] Components were mixed and 20 .mu.l of the thoroughly mixed mastermix dispensed into reaction tubes. 5 .mu.l of a 20 ng/p template genomic DNA were added.
[0187] No Template Controls: Instead of genomic DNA, 5 .mu.l of the diluent used for diluting the test DNA samples were added to their proper concentration; e.g. water, 0.1.times.TE, etc.
[0188] Positive controls: 5 .mu.l of e.g. 1% DP-004114-3 (20 ng/.mu.l) maize DNA were added.
[0189] After addition of template to mastermix, reaction tubes were capped and immediately placed in pre-heated PCR machine and run was initiated.
Cycling Parameters
[0190] The PCR assay was performed using an Applied Biosystems' 96-well GeneAmp PCR System 9700 with the ramp speed set to `GeneAmp 9600`. The cycling parameters were as follows:
PCR Profile for DP-004114-3 Detection Method
TABLE-US-00025
[0191] Step Cycle element T (.degree. C.) Time (min:sec) Cycles 1 Initial Denaturation 95 2:00 1.times. 2 Amplification Denaturation 95 00:30 3 Annealing 66 00:30 35.times. 4 Extension 72 00:30 5 Final Extension 72 07:00 1.times.
Gel Electrophoresis
[0192] PCR products were mixed with enough 6.times. loading buffer added for a final concentration of 1.times. loading buffer (example: 25 .mu.l PCR product plus 5 .mu.l 6.times. loading buffer). 15 .mu.l PCR products/loading dye mixture were loaded on a 2.5% agarose/1.times.TBE gel. Gel was run with a maximum of 7 V per cm (measured electrode to electrode) until the fragments were separated properly. Gel was run long enough to get clear separation of marker bands in the 50 to 200 bp range. The agarose gel was stained in an ethidium bromide bath (1.5 pg per ml in distilled water or buffer) for approximately 15 min, rinsed with distilled water or 1.times.TBE, and photographed under UV-light with an appropriate gel-documentation system. The PCR product for DP-004114-3 maize was 149 bp in length.
[0193] Having illustrated and described the principles of the present invention, it should be apparent to persons skilled in the art that the invention can be modified in arrangement and detail without departing from such principles. We claim all modifications that are within the spirit and scope of the appended claims.
[0194] All publications and published patent documents cited in this specification are incorporated herein by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
Sequence CWU
1
1
351605PRTBacillus thuringiensisCry1F 1Met Glu Asn Asn Ile Gln Asn Gln Cys
Val Pro Tyr Asn Cys Leu Asn1 5 10
15Asn Pro Glu Val Glu Ile Leu Asn Glu Glu Arg Ser Thr Gly Arg
Leu 20 25 30Pro Leu Asp Ile
Ser Leu Ser Leu Thr Arg Phe Leu Leu Ser Glu Phe 35
40 45Val Pro Gly Val Gly Val Ala Phe Gly Leu Phe Asp
Leu Ile Trp Gly 50 55 60Phe Ile Thr
Pro Ser Asp Trp Ser Leu Phe Leu Leu Gln Ile Glu Gln65 70
75 80Leu Ile Glu Gln Arg Ile Glu Thr
Leu Glu Arg Asn Arg Ala Ile Thr 85 90
95Thr Leu Arg Gly Leu Ala Asp Ser Tyr Glu Ile Tyr Ile Glu
Ala Leu 100 105 110Arg Glu Trp
Glu Ala Asn Pro Asn Asn Ala Gln Leu Arg Glu Asp Val 115
120 125Arg Ile Arg Phe Ala Asn Thr Asp Asp Ala Leu
Ile Thr Ala Ile Asn 130 135 140Asn Phe
Thr Leu Thr Ser Phe Glu Ile Pro Leu Leu Ser Val Tyr Val145
150 155 160Gln Ala Ala Asn Leu His Leu
Ser Leu Leu Arg Asp Ala Val Ser Phe 165
170 175Gly Gln Gly Trp Gly Leu Asp Ile Ala Thr Val Asn
Asn His Tyr Asn 180 185 190Arg
Leu Ile Asn Leu Ile His Arg Tyr Thr Lys His Cys Leu Asp Thr 195
200 205Tyr Asn Gln Gly Leu Glu Asn Leu Arg
Gly Thr Asn Thr Arg Gln Trp 210 215
220Ala Arg Phe Asn Gln Phe Arg Arg Asp Leu Thr Leu Thr Val Leu Asp225
230 235 240Ile Val Ala Leu
Phe Pro Asn Tyr Asp Val Arg Thr Tyr Pro Ile Gln 245
250 255Thr Ser Ser Gln Leu Thr Arg Glu Ile Tyr
Thr Ser Ser Val Ile Glu 260 265
270Asp Ser Pro Val Ser Ala Asn Ile Pro Asn Gly Phe Asn Arg Ala Glu
275 280 285Phe Gly Val Arg Pro Pro His
Leu Met Asp Phe Met Asn Ser Leu Phe 290 295
300Val Thr Ala Glu Thr Val Arg Ser Gln Thr Val Trp Gly Gly His
Leu305 310 315 320Val Ser
Ser Arg Asn Thr Ala Gly Asn Arg Ile Asn Phe Pro Ser Tyr
325 330 335Gly Val Phe Asn Pro Gly Gly
Ala Ile Trp Ile Ala Asp Glu Asp Pro 340 345
350Arg Pro Phe Tyr Arg Thr Leu Ser Asp Pro Val Phe Val Arg
Gly Gly 355 360 365Phe Gly Asn Pro
His Tyr Val Leu Gly Leu Arg Gly Val Ala Phe Gln 370
375 380Gln Thr Gly Thr Asn His Thr Arg Thr Phe Arg Asn
Ser Gly Thr Ile385 390 395
400Asp Ser Leu Asp Glu Ile Pro Pro Gln Asp Asn Ser Gly Ala Pro Trp
405 410 415Asn Asp Tyr Ser His
Val Leu Asn His Val Thr Phe Val Arg Trp Pro 420
425 430Gly Glu Ile Ser Gly Ser Asp Ser Trp Arg Ala Pro
Met Phe Ser Trp 435 440 445Thr His
Arg Ser Ala Thr Pro Thr Asn Thr Ile Asp Pro Glu Arg Ile 450
455 460Thr Gln Ile Pro Leu Val Lys Ala His Thr Leu
Gln Ser Gly Thr Thr465 470 475
480Val Val Arg Gly Pro Gly Phe Thr Gly Gly Asp Ile Leu Arg Arg Thr
485 490 495Ser Gly Gly Pro
Phe Ala Tyr Thr Ile Val Asn Ile Asn Gly Gln Leu 500
505 510Pro Gln Arg Tyr Arg Ala Arg Ile Arg Tyr Ala
Ser Thr Thr Asn Leu 515 520 525Arg
Ile Tyr Val Thr Val Ala Gly Glu Arg Ile Phe Ala Gly Gln Phe 530
535 540Asn Lys Thr Met Asp Thr Gly Asp Pro Leu
Thr Phe Gln Ser Phe Ser545 550 555
560Tyr Ala Thr Ile Asn Thr Ala Phe Thr Phe Pro Met Ser Gln Ser
Ser 565 570 575Phe Thr Val
Gly Ala Asp Thr Phe Ser Ser Gly Asn Glu Val Tyr Ile 580
585 590Asp Arg Phe Glu Leu Ile Pro Val Thr Ala
Thr Leu Glu 595 600
6052123PRTBacillus thuringiensisCry34Ab1 2Met Ser Ala Arg Glu Val His Ile
Asp Val Asn Asn Lys Thr Gly His1 5 10
15Thr Leu Gln Leu Glu Asp Lys Thr Lys Leu Asp Gly Gly Arg
Trp Arg 20 25 30Thr Ser Pro
Thr Asn Val Ala Asn Asp Gln Ile Lys Thr Phe Val Ala 35
40 45Glu Ser Asn Gly Phe Met Thr Gly Thr Glu Gly
Thr Ile Tyr Tyr Ser 50 55 60Ile Asn
Gly Glu Ala Glu Ile Ser Leu Tyr Phe Asp Asn Pro Phe Ala65
70 75 80Gly Ser Asn Lys Tyr Asp Gly
His Ser Asn Lys Ser Gln Tyr Glu Ile 85 90
95Ile Thr Gln Gly Gly Ser Gly Asn Gln Ser His Val Thr
Tyr Thr Ile 100 105 110Gln Thr
Thr Ser Ser Arg Tyr Gly His Lys Ser 115
1203383PRTBacillus thuringiensisCry35Ab1 3Met Leu Asp Thr Asn Lys Val Tyr
Glu Ile Ser Asn His Ala Asn Gly1 5 10
15Leu Tyr Ala Ala Thr Tyr Leu Ser Leu Asp Asp Ser Gly Val
Ser Leu 20 25 30Met Asn Lys
Asn Asp Asp Asp Ile Asp Asp Tyr Asn Leu Lys Trp Phe 35
40 45Leu Phe Pro Ile Asp Asp Asp Gln Tyr Ile Ile
Thr Ser Tyr Ala Ala 50 55 60Asn Asn
Cys Lys Val Trp Asn Val Asn Asn Asp Lys Ile Asn Val Ser65
70 75 80Thr Tyr Ser Ser Thr Asn Ser
Ile Gln Lys Trp Gln Ile Lys Ala Asn 85 90
95Gly Ser Ser Tyr Val Ile Gln Ser Asp Asn Gly Lys Val
Leu Thr Ala 100 105 110Gly Thr
Gly Gln Ala Leu Gly Leu Ile Arg Leu Thr Asp Glu Ser Ser 115
120 125Asn Asn Pro Asn Gln Gln Trp Asn Leu Thr
Ser Val Gln Thr Ile Gln 130 135 140Leu
Pro Gln Lys Pro Ile Ile Asp Thr Lys Leu Lys Asp Tyr Pro Lys145
150 155 160Tyr Ser Pro Thr Gly Asn
Ile Asp Asn Gly Thr Ser Pro Gln Leu Met 165
170 175Gly Trp Thr Leu Val Pro Cys Ile Met Val Asn Asp
Pro Asn Ile Asp 180 185 190Lys
Asn Thr Gln Ile Lys Thr Thr Pro Tyr Tyr Ile Leu Lys Lys Tyr 195
200 205Gln Tyr Trp Gln Arg Ala Val Gly Ser
Asn Val Ala Leu Arg Pro His 210 215
220Glu Lys Lys Ser Tyr Thr Tyr Glu Trp Gly Thr Glu Ile Asp Gln Lys225
230 235 240Thr Thr Ile Ile
Asn Thr Leu Gly Phe Gln Ile Asn Ile Asp Ser Gly 245
250 255Met Lys Phe Asp Ile Pro Glu Val Gly Gly
Gly Thr Asp Glu Ile Lys 260 265
270Thr Gln Leu Asn Glu Glu Leu Lys Ile Glu Tyr Ser His Glu Thr Lys
275 280 285Ile Met Glu Lys Tyr Gln Glu
Gln Ser Glu Ile Asp Asn Pro Thr Asp 290 295
300Gln Ser Met Asn Ser Ile Gly Phe Leu Thr Ile Thr Ser Leu Glu
Leu305 310 315 320Tyr Arg
Tyr Asn Gly Ser Glu Ile Arg Ile Met Gln Ile Gln Thr Ser
325 330 335Asp Asn Asp Thr Tyr Asn Val
Thr Ser Tyr Pro Asn His Gln Gln Ala 340 345
350Leu Leu Leu Leu Thr Asn His Ser Tyr Glu Glu Val Glu Glu
Ile Thr 355 360 365Asn Ile Pro Lys
Ser Thr Leu Lys Lys Leu Lys Lys Tyr Tyr Phe 370 375
3804183PRTStreptomyces viridochromogenesPhosphinothricin
acetyl transferase protein 4Met Ser Pro Glu Arg Arg Pro Val Glu Ile Arg
Pro Ala Thr Ala Ala1 5 10
15Asp Met Ala Ala Val Cys Asp Ile Val Asn His Tyr Ile Glu Thr Ser
20 25 30Thr Val Asn Phe Arg Thr Glu
Pro Gln Thr Pro Gln Glu Trp Ile Asp 35 40
45Asp Leu Glu Arg Leu Gln Asp Arg Tyr Pro Trp Leu Val Ala Glu
Val 50 55 60Glu Gly Val Val Ala Gly
Ile Ala Tyr Ala Gly Pro Trp Lys Ala Arg65 70
75 80Asn Ala Tyr Asp Trp Thr Val Glu Ser Thr Val
Tyr Val Ser His Arg 85 90
95His Gln Arg Leu Gly Leu Gly Ser Thr Leu Tyr Thr His Leu Leu Lys
100 105 110Ser Met Glu Ala Gln Gly
Phe Lys Ser Val Val Ala Val Ile Gly Leu 115 120
125Pro Asn Asp Pro Ser Val Arg Leu His Glu Ala Leu Gly Tyr
Thr Ala 130 135 140Arg Gly Thr Leu Arg
Ala Ala Gly Tyr Lys His Gly Gly Trp His Asp145 150
155 160Val Gly Phe Trp Gln Arg Asp Phe Glu Leu
Pro Ala Pro Pro Arg Pro 165 170
175Val Arg Pro Val Thr Gln Ile 180511978DNAArtificial
SequenceComplete sequence of the T-DNA region of Plasmid PHP27118
5gtttacccgc caatatatcc tgtcaaacac tgatagttta aacgctcttc aactggaaga
60gcggttaccc ggaccgaagc ttcggccggg gcccatcgat atccgcgggc atgcctgcag
120tgcagcgtga cccggtcgtg cccctctcta gagataatga gcattgcatg tctaagttat
180aaaaaattac cacatatttt ttttgtcaca cttgtttgaa gtgcagttta tctatcttta
240tacatatatt taaactttac tctacgaata atataatcta tagtactaca ataatatcag
300tgttttagag aatcatataa atgaacagtt agacatggtc taaaggacaa ttgagtattt
360tgacaacagg actctacagt tttatctttt tagtgtgcat gtgttctcct ttttttttgc
420aaatagcttc acctatataa tacttcatcc attttattag tacatccatt tagggtttag
480ggttaatggt ttttatagac taattttttt agtacatcta ttttattcta ttttagcctc
540taaattaaga aaactaaaac tctattttag tttttttatt taataattta gatataaaat
600agaataaaat aaagtgacta aaaattaaac aaataccctt taagaaatta aaaaaactaa
660ggaaacattt ttcttgtttc gagtagataa tgccagcctg ttaaacgccg tcgacgagtc
720taacggacac caaccagcga accagcagcg tcgcgtcggg ccaagcgaag cagacggcac
780ggcatctctg tcgctgcctc tggacccctc tcgagagttc cgctccaccg ttggacttgc
840tccgctgtcg gcatccagaa attgcgtggc ggagcggcag acgtgagccg gcacggcagg
900cggcctcctc ctcctctcac ggcaccggca gctacggggg attcctttcc caccgctcct
960tcgctttccc ttcctcgccc gccgtaataa atagacaccc cctccacacc ctctttcccc
1020aacctcgtgt tgttcggagc gcacacacac acaaccagat ctcccccaaa tccacccgtc
1080ggcacctccg cttcaaggta cgccgctcgt cctccccccc cccccctctc taccttctct
1140agatcggcgt tccggtccat ggttagggcc cggtagttct acttctgttc atgtttgtgt
1200tagatccgtg tttgtgttag atccgtgctg ctagcgttcg tacacggatg cgacctgtac
1260gtcagacacg ttctgattgc taacttgcca gtgtttctct ttggggaatc ctgggatggc
1320tctagccgtt ccgcagacgg gatcgatttc atgatttttt ttgtttcgtt gcatagggtt
1380tggtttgccc ttttccttta tttcaatata tgccgtgcac ttgtttgtcg ggtcatcttt
1440tcatgctttt ttttgtcttg gttgtgatga tgtggtctgg ttgggcggtc gttctagatc
1500ggagtagaat tctgtttcaa actacctggt ggatttatta attttggatc tgtatgtgtg
1560tgccatacat attcatagtt acgaattgaa gatgatggat ggaaatatcg atctaggata
1620ggtatacatg ttgatgcggg ttttactgat gcatatacag agatgctttt tgttcgcttg
1680gttgtgatga tgtggtgtgg ttgggcggtc gttcattcgt tctagatcgg agtagaatac
1740tgtttcaaac tacctggtgt atttattaat tttggaactg tatgtgtgtg tcatacatct
1800tcatagttac gagtttaaga tggatggaaa tatcgatcta ggataggtat acatgttgat
1860gtgggtttta ctgatgcata tacatgatgg catatgcagc atctattcat atgctctaac
1920cttgagtacc tatctattat aataaacaag tatgttttat aattattttg atcttgatat
1980acttggatga tggcatatgc agcagctata tgtggatttt tttagccctg ccttcatacg
2040ctatttattt gcttggtact gtttcttttg tcgatgctca ccctgttgtt tggtgttact
2100tctgcaggtc gactctagag gatccaacaa tggagaacaa catacagaat cagtgcgtcc
2160cctacaactg cctcaacaat cctgaagtag agattctcaa cgaagagagg tcgactggca
2220gattgccgtt agacatctcc ctgtccctta cacgtttcct gttgtctgag tttgttccag
2280gtgtgggagt tgcgtttggc ctcttcgacc tcatctgggg cttcatcact ccatctgatt
2340ggagcctctt tcttctccag attgaacagt tgattgaaca aaggattgag accttggaaa
2400ggaatcgggc catcactacc cttcgtggct tagcagacag ctatgagatc tacattgaag
2460cactaagaga gtgggaagcc aatcctaaca atgcccaact gagagaagat gtgcgtatac
2520gctttgctaa cacagatgat gctttgatca cagccatcaa caacttcacc cttaccagct
2580tcgagatccc tcttctctcg gtctatgttc aagctgctaa cctgcacttg tcactactgc
2640gcgacgctgt gtcgtttggg caaggttggg gactggacat agctactgtc aacaatcact
2700acaacagact catcaatctg attcatcgat acacgaaaca ttgtttggat acctacaatc
2760agggattgga gaacctgaga ggtactaaca ctcgccaatg ggccaggttc aatcagttca
2820ggagagacct tacacttact gtgttagaca tagttgctct ctttccgaac tacgatgttc
2880gtacctatcc gattcaaacg tcatcccaac ttacaaggga gatctacacc agttcagtca
2940ttgaagactc tccagtttct gcgaacatac ccaatggttt caacagggct gagtttggag
3000tcagaccacc ccatctcatg gacttcatga actctttgtt tgtgactgca gagactgtta
3060gatcccaaac tgtgtgggga ggacacttag ttagctcacg caacacggct ggcaatcgta
3120tcaactttcc tagttacggg gtcttcaatc ccgggggcgc catctggatt gcagatgaag
3180atccacgtcc tttctatcgg accttgtcag atcctgtctt cgtccgagga ggctttggca
3240atcctcacta tgtactcggt cttaggggag tggcctttca acaaactggt acgaatcaca
3300cccgcacatt caggaactcc gggaccattg actctctaga tgagatacca cctcaagaca
3360acagcggcgc accttggaat gactactccc atgtgctgaa tcatgttacc tttgtgcgct
3420ggccaggtga gatctcaggt tccgactcat ggagagcacc aatgttctct tggacgcatc
3480gtagcgctac ccccacaaac accattgatc cagagagaat cactcagatt cccttggtga
3540aggcacacac acttcagtca ggaactacag ttgtaagagg gccggggttc acgggaggag
3600acattcttcg acgcactagt ggaggaccat tcgcgtacac cattgtcaac atcaatgggc
3660aacttcccca aaggtatcgt gccaggatac gctatgcctc tactaccaat ctaagaatct
3720acgttacggt tgcaggtgaa cggatctttg ctggtcagtt caacaagaca atggataccg
3780gtgatccact tacattccaa tctttctcct acgccactat caacaccgcg ttcacctttc
3840caatgagcca gagcagtttc acagtaggtg ctgatacctt cagttcaggc aacgaagtgt
3900acattgacag gtttgagttg attccagtta ctgccacact cgagtaagga tccgtcgacc
3960tgcagccaag ctttcgcgag ctcgagatcc ccgacatatg ccccggtttc gttgcgacta
4020acatgagttc ttggacaaat ttgattggac ctgatgagat gatccaaccc gaggatatag
4080caaagctcgt tcgtgcagca atggaacggc caaaccgtgc ttttgtcccc aagaatgagg
4140tgctatgcat gaaggaatct acccgttgat gtccaacagt ctcagggtta atgtctatgt
4200atcttaaata atgttgtcgg tattttgtaa tctcatatag attttcactg tgcgacgcaa
4260aaatattaaa taaatattat tattatctac gttttgattg agatatcatc aatattataa
4320taaaaatatc cattaaacac gatttgatac aaatgacagt caataatctg atttgaatat
4380ttattaattg taacgaatta cataaagatc gaatagaaaa tactgcactg caaatgaaaa
4440ttaacacata ctaataaatg cgtcaaatat ctttgccaag atcaagcgga gtgagggcct
4500catatccggt ctcagttaca agcacggtat ccccgaagcg cgctccacca atgccctcga
4560catagatgcc gggctcgacg ctgaggacat tgcctacctt gagcatggtc tcagcgccgg
4620ctttaagctc aatcccatcc caatctgaat atcctatccc gcgcccagtc cggtgtaaga
4680acgggtctgt ccatccacct ctgttgggaa ttccggtccg ggtcaccttt gtccaccaag
4740atggaactgc ggccagcttg catgcctgca gtgcagcgtg acccggtcgt gcccctctct
4800agagataatg agcattgcat gtctaagtta taaaaaatta ccacatattt tttttgtcac
4860acttgtttga agtgcagttt atctatcttt atacatatat ttaaacttta ctctacgaat
4920aatataatct atagtactac aataatatca gtgttttaga gaatcatata aatgaacagt
4980tagacatggt ctaaaggaca attgagtatt ttgacaacag gactctacag ttttatcttt
5040ttagtgtgca tgtgttctcc tttttttttg caaatagctt cacctatata atacttcatc
5100cattttatta gtacatccat ttagggttta gggttaatgg tttttataga ctaatttttt
5160tagtacatct attttattct attttagcct ctaaattaag aaaactaaaa ctctatttta
5220gtttttttat ttaataattt agatataaaa tagaataaaa taaagtgact aaaaattaaa
5280caaataccct ttaagaaatt aaaaaaacta aggaaacatt tttcttgttt cgagtagata
5340atgccagcct gttaaacgcc gtcgacgagt ctaacggaca ccaaccagcg aaccagcagc
5400gtcgcgtcgg gccaagcgaa gcagacggca cggcatctct gtcgctgcct ctggacccct
5460ctcgagagtt ccgctccacc gttggacttg ctccgctgtc ggcatccaga aattgcgtgg
5520cggagcggca gacgtgagcc ggcacggcag gcggcctcct cctcctctca cggcaccggc
5580agctacgggg gattcctttc ccaccgctcc ttcgctttcc cttcctcgcc cgccgtaata
5640aatagacacc ccctccacac cctctttccc caacctcgtg ttgttcggag cgcacacaca
5700cacaaccaga tctcccccaa atccacccgt cggcacctcc gcttcaaggt acgccgctcg
5760tcctcccccc ccccccctct ctaccttctc tagatcggcg ttccggtcca tggttagggc
5820ccggtagttc tacttctgtt catgtttgtg ttagatccgt gtttgtgtta gatccgtgct
5880gctagcgttc gtacacggat gcgacctgta cgtcagacac gttctgattg ctaacttgcc
5940agtgtttctc tttggggaat cctgggatgg ctctagccgt tccgcagacg ggatcgattt
6000catgattttt tttgtttcgt tgcatagggt ttggtttgcc cttttccttt atttcaatat
6060atgccgtgca cttgtttgtc gggtcatctt ttcatgcttt tttttgtctt ggttgtgatg
6120atgtggtctg gttgggcggt cgttctagat cggagtagaa ttctgtttca aactacctgg
6180tggatttatt aattttggat ctgtatgtgt gtgccataca tattcatagt tacgaattga
6240agatgatgga tggaaatatc gatctaggat aggtatacat gttgatgcgg gttttactga
6300tgcatataca gagatgcttt ttgttcgctt ggttgtgatg atgtggtgtg gttgggcggt
6360cgttcattcg ttctagatcg gagtagaata ctgtttcaaa ctacctggtg tatttattaa
6420ttttggaact gtatgtgtgt gtcatacatc ttcatagtta cgagtttaag atggatggaa
6480atatcgatct aggataggta tacatgttga tgtgggtttt actgatgcat atacatgatg
6540gcatatgcag catctattca tatgctctaa ccttgagtac ctatctatta taataaacaa
6600gtatgtttta taattatttt gatcttgata tacttggatg atggcatatg cagcagctat
6660atgtggattt ttttagccct gccttcatac gctatttatt tgcttggtac tgtttctttt
6720gtcgatgctc accctgttgt ttggtgttac ttctgcaggt cgactctaga ggatccacac
6780gacaccatgt ccgcccgcga ggtgcacatc gacgtgaaca acaagaccgg ccacaccctc
6840cagctggagg acaagaccaa gctcgacggc ggcaggtggc gcacctcccc gaccaacgtg
6900gccaacgacc agatcaagac cttcgtggcc gaatccaacg gcttcatgac cggcaccgag
6960ggcaccatct actactcaat taatggcgag gccgagatca gcctctactt cgacaacccg
7020ttcgccggct ccaacaaata cgacggccac tccaacaagt cccagtacga gatcatcacc
7080cagggcggct ccggcaacca gtcccacgtg acctacacca tccagaccac ctcctcccgc
7140tacggccaca agtcctgagt catgagtcat gagtcagtta acctagactt gtccatcttc
7200tggattggcc aacttaatta atgtatgaaa taaaaggatg cacacatagt gacatgctaa
7260tcactataat gtgggcatca aagttgtgtg ttatgtgtaa ttactagtta tctgaataaa
7320agagaaagag atcatccata tttcttatcc taaatgaatg tcacgtgtct ttataattct
7380ttgatgaacc agatgcattt cattaaccaa atccatatac atataaatat taatcatata
7440taattaatat caattgggtt agcaaaacaa atctagtcta ggtgtgtttt gcgaatgcgg
7500ccgcggaccg aattggggat ctgcatgaaa gaaactgtcg cactgctgaa ccgcaccttg
7560tcactttcat cgaacacgac ctgtgcccaa gatgacggtg ctgcggtcta agtgaggctg
7620aattgccttg gacagaagcg gactccctac aattagttag gccaaacggt gcatccatgt
7680gtagctccgg gctcgggctg tatcgccatc tgcaatagca tccatggagc tcgttccatg
7740tagttggaga tgaaccaatg atcgggcgtg tggacgtatg ttcctgtgta ctccgatagt
7800agagtacgtg ttagctcttt catggtgcaa gtgaaatttg tgttggttta attaccccta
7860cgttagttgc gggacaggag acacatcatg aatttaaagg cgatgatgtc ctctcctgta
7920atgttattct tttgatgtga tgaatcaaaa tgtcatataa aacatttgtt gctctttagt
7980taggcctgat cgtagaacga aatgctcgtg tagcggggct acgagcctat gacgcaataa
8040cactggtttg ccggcccgga gtcgcttgac aaaaaaaagc atgttaagtt tatttacaat
8100tcaaaaccta acatattata ttccctcaaa gcaggttcac gatcacacct gtacctaaaa
8160aaaacatgaa gaatatatta ctccattatt atgagatgaa ccacttggca agagtggtaa
8220gctatataaa aaaatgaaca ttattacgag atgttatatg ccattatatt gattcgaaga
8280tatatgtttc tttctcccac gggcacctaa cggatacatg ataaggccaa ggcagatcac
8340gggaaattat tcgaatacat gttacgccct attgccggaa aaaaaatgca gggcaggtgt
8400tggccgtagc gatttaagca cttaagctgg aggttgccac acttggatgc aagcgtctga
8460cccttctaaa aaatcggcgg ctttgtccgt atccgtatcc cctatccaac atctagctgg
8520ccacacgacg gggctgggca gatcgtggat gccgggtcga cgtcgatcgt cagccatcat
8580agaccaatcg accatctgtt atggatgctt gctagctaga ctagtcagac ataaaatttg
8640gatactttct cccaactggg agacggggac tgatgtgcag ctgcacgtga gctaaatttt
8700tccctataaa tatgcatgaa atactgcatt atcttgccac agccactgcc acagccagat
8760aacaagtgca gctggtagca cgcaacgcat agctctggac ttgtagctag gtagccaacc
8820ggatccacac gacaccatgc tcgacaccaa caaggtgtac gagatcagca accacgccaa
8880cggcctctac gccgccacct acctctccct cgacgactcc ggcgtgtccc tcatgaacaa
8940gaacgacgac gacatcgacg actacaacct caagtggttc ctcttcccga tcgacgacga
9000ccagtacatc atcacctcct acgccgccaa caactgcaag gtgtggaacg tgaacaacga
9060caagattaat gtgtcaacct actcctccac caactccatc cagaagtggc agatcaaggc
9120caacggctcc tcctacgtga tccagtccga caacggcaag gtgctcaccg ccggcaccgg
9180ccaggccctc ggcctcatcc gcctcaccga cgagtcctcc aacaacccga accagcaatg
9240gaacctgacg tccgtgcaga ccatccagct cccgcagaag ccgatcatcg acaccaagct
9300caaggactac ccgaagtact ccccgaccgg caacatcgac aacggcacct ccccgcagct
9360catgggctgg accctcgtgc cgtgcatcat ggtgaacgac ccgaacatcg acaagaacac
9420ccagatcaag accaccccgt actacatcct caagaagtac cagtactggc agagggccgt
9480gggctccaac gtcgcgctcc gcccgcacga gaagaagtcc tacacctacg agtggggcac
9540cgagatcgac cagaagacca ccatcatcaa caccctcggc ttccagatca acatcgacag
9600cggcatgaag ttcgacatcc cggaggtggg cggcggtacc gacgagatca agacccagct
9660caacgaggag ctcaagatcg agtattcaca tgagacgaag atcatggaga agtaccagga
9720gcagtccgag atcgacaacc cgaccgacca gtccatgaac tccatcggct tcctcaccat
9780cacctccctg gagctctacc gctacaacgg ctccgagatc cgcatcatgc agatccagac
9840ctccgacaac gacacctaca acgtgacctc ctacccgaac caccagcagg ccctgctgct
9900gctgaccaac cactcctacg aggaggtgga ggagatcacc aacatcccga agtccaccct
9960caagaagctc aagaagtact acttctgagt catgagtcat gagtcagtta acctagactt
10020gtccatcttc tggattggcc aacttaatta atgtatgaaa taaaaggatg cacacatagt
10080gacatgctaa tcactataat gtgggcatca aagttgtgtg ttatgtgtaa ttactagtta
10140tctgaataaa agagaaagag atcatccata tttcttatcc taaatgaatg tcacgtgtct
10200ttataattct ttgatgaacc agatgcattt cattaaccaa atccatatac atataaatat
10260taatcatata taattaatat caattgggtt agcaaaacaa atctagtcta ggtgtgtttt
10320gcgaattatc gatgggcccc ggccgaagct ggccgcggac cgaattccca tggagtcaaa
10380gattcaaata gaggacctaa cagaactcgc cgtaaagact ggcgaacagt tcatacagag
10440tctcttacga ctcaatgaca agaagaaaat cttcgtcaac atggtggagc acgacacgct
10500tgtctactcc aaaaatatca aagatacagt ctcagaagac caaagggcaa ttgagacttt
10560tcaacaaagg gtaatatccg gaaacctcct cggattccat tgcccagcta tctgtcactt
10620tattgtgaag atagtggaaa aggaaggtgg ctcctacaaa tgccatcatt gcgataaagg
10680aaaggccatc gttgaagatg cctctgccga cagtggtccc aaagatggac ccccacccac
10740gaggagcatc gtggaaaaag aagacgttcc aaccacgtct tcaaagcaag tggattgatg
10800tgatatctcc actgacgtaa gggatgacgc acaatcccac tatccttcgc aagacccttc
10860ctctatataa ggaagttcat ttcatttgga gaggacaggg tacccgggga tccaccatgt
10920ctccggagag gagaccagtt gagattaggc cagctacagc agctgatatg gccgcggttt
10980gtgatatcgt taaccattac attgagacgt ctacagtgaa ctttaggaca gagccacaaa
11040caccacaaga gtggattgat gatctagaga ggttgcaaga tagataccct tggttggttg
11100ctgaggttga gggtgttgtg gctggtattg cttacgctgg gccctggaag gctaggaacg
11160cttacgattg gacagttgag agtactgttt acgtgtcaca taggcatcaa aggttgggcc
11220taggatccac attgtacaca catttgctta agtctatgga ggcgcaaggt tttaagtctg
11280tggttgctgt tataggcctt ccaaacgatc catctgttag gttgcatgag gctttgggat
11340acacagcccg gggtacattg cgcgcagctg gatacaagca tggtggatgg catgatgttg
11400gtttttggca aagggatttt gagttgccag ctcctccaag gccagttagg ccagttaccc
11460agatctgagt cgacctgcag gcatgcccgc tgaaatcacc agtctctctc tacaaatcta
11520tctctctcta taataatgtg tgagtagttc ccagataagg gaattagggt tcttataggg
11580tttcgctcat gtgttgagca tataagaaac ccttagtatg tatttgtatt tgtaaaatac
11640ttctatcaat aaaatttcta attcctaaaa ccaaaatcca gggcgagctc gaattcgagc
11700tcgagcccgg gtggatcctc tagagtcgac ctgcagaagc ttcggtccgg cgcgcctcta
11760gttgaagaca cgttcatgtc ttcatcgtaa gaagacactc agtagtcttc ggccagaatg
11820gcctaactca aggccatcgt ggcctcttgc tcttcaggat gaagagctat gtttaaacgt
11880gcaagcgcta ctagacaatt cagtacatta aaaacgtccg caatgtgtta ttaagttgtc
11940taagcgtcaa tttgtttaca ccacaatata tcctgcca
11978616752DNAArtificial SequenceThe complete sequence of the insert and
flanking regions of event DP-004114-3 6gagcatatcc agcaccagct
ggtaccaagg tcgggtctct gtgctagtgc tattagctag 60tgtaaggagc gagtaggtca
gttaaggctg gtgcgtcgtg agggctgtct tgtgtgtagc 120tacagcagac ggttcatcag
aaggattatt cgtgcagtat atacagtaca actagacaat 180gatgttgatg attggtctag
agctagaggc ctatagccct atactactgt gtattgtccg 240ccgttttagt tttttggtcc
catcccatca atgcaaccgc cttgttttgc tccaattgtc 300ccgttcctgc gcctcgcttt
tgctctgtcg catcgcatac aaaaaaaaaa acgccgcgcc 360ggctttgaat cgcgcccccc
aactgctcca accaggcaac ggacacggcc accgtccgtg 420tcgcgagcaa aaaaacaaaa
agaggaacgc gtccaggacg aagcagtcca ctgccgctgt 480ggccggcaaa agatctggtt
gagcacatgg agattggaga aggttggttg gttcttctgg 540aaacgccaat gaatgggggc
actgacatgt actcttaaca tgtagtgcaa tccagagatc 600ggatatccag acactggcag
cacgatcgcc tcgcgccgta gatcacgcac gcaaattact 660gaagaccatt cacaaaaaaa
aaaaaacaca caggggctag cgtgccccac accaaaccca 720agtgctgcgt tgcacgcagg
ggagcgaaaa aaaacaataa tgctcactgt cacgtcgcgt 780atccaacccc gcggacgtct
cggctctcag cagcagcaca cggggcacct cacgatgccg 840ttctcgttgc actccgtgca
ccgccggaac ccgccgccgc attcgtcgcc ctcctcctcc 900tcctccgcct cgtcttcgtc
acccacgtac accttgcagc tgcccgagca gacatcgcag 960agcacgaacc gcatgtcccc
gcaggcctcg cacgcgccgg cgtcgccgcc gtgtgggccg 1020gccgtcgacg cagcgctctc
gcacccggcc agcctcggcg cgagctcccc ggcctcgtgc 1080agccgcttca gctcctcggc
gttgcccacg agctccccgt ccacgaagag gctggggagg 1140gcggcgggcg tgccgccggc
ttggccgagc ccgaggccga gaaggccgcg gagctcgtcc 1200cggaacccgc ggtgcatgga
cacgtcgcgc tcgtcgaggc gcacgccgta gcccttgagg 1260atggcgcgcg ccaggcagca
gtcctcgtgc gtggcgcgca cgccgcgcag cgacgtgaag 1320tagagcaccg ccctccgcgg
cggcagcgcc ttcccctccc cgccgctcgt cggggcggcg 1380tcgggccgag gcatcggcat
cggcagcggc gtcaccttgg cggacgccgc gaggtcctgc 1440gcaggcgccg tggcgaccgg
gaacgagaag gagtggcgcc cgaacggcgc gcccagcagc 1500ggggagcggt cctcgaggcc
ggccatgagc gcccacgcgt cgatgtcctc gggctcgttg 1560ggcggcgtca tggtgggcgt
gcgcggcgcc agcctcgtgg gcgcgggctc cggcgcccgc 1620ggcagggcct tgtccagctc
cagggacccg agcgtggacg acgtgagccg caccacgtgg 1680acgccgacgt cgctggggca
ccgagccggg aacgactggc tgcgcggcag cggtgacggg 1740cagtaccgga ggtcgtgacg
ggcctgcctt gaggtggtgc accccatggc accaatgtac 1800acacacggcc aaagcgccaa
gtgggctgca gactgcctgc caatgtgatc aagcagccag 1860gagcagagac ggatctctgg
ggatcggggt ttctggggtt taggatcttt atactactct 1920gtcattgggg atataaaact
aggagtgtgg ttaattagga ctcgatagat aagtttacca 1980caagcgcgtg aaatggtcta
cccgatgatg tgattggcct aaaaagaaca agaagagtat 2040ttggagctac tgaacattct
cttttcctga agataactaa tttttggaac attcagactt 2100gggagtctgg acttttggag
ggaagttcaa attgtggtct gcctctgcca tgtgttgttt 2160tttagtcgga gagtggccct
catttttttt gtcctgttta gctttatagt cgtagcagct 2220agtagcgaaa tttaaccttg
gattatggcc gtgttagtca aacaatcatt gatttatttc 2280ctccctttcg cgctgctttt
cctgtacgca tctccgctgc ccttgattcg aggaccctgt 2340tcacaacaca gggctctggc
tttggagcct ctcgtttgta gcacttgcac gtagttaccc 2400ggaccgaagc ttcaacacag
atctgatagt ttaaacgctc ttcaactgga agagcggtta 2460cccggaccga agcttcggcc
ggggcccatc gatatccgcg ggcatgcctg cagtgcagcg 2520tgacccggtc gtgcccctct
ctagagataa tgagcattgc atgtctaagt tataaaaaat 2580taccacatat tttttttgtc
acacttgttt gaagtgcagt ttatctatct ttatacatat 2640atttaaactt tactctacga
ataatataat ctatagtact acaataatat cagtgtttta 2700gagaatcata taaatgaaca
gttagacatg gtctaaagga caattgagta ttttgacaac 2760aggactctac agttttatct
ttttagtgtg catgtgttct cctttttttt tgcaaatagc 2820ttcacctata taatacttca
tccattttat tagtacatcc atttagggtt tagggttaat 2880ggtttttata gactaatttt
tttagtacat ctattttatt ctattttagc ctctaaatta 2940agaaaactaa aactctattt
tagttttttt atttaataat ttagatataa aatagaataa 3000aataaagtga ctaaaaatta
aacaaatacc ctttaagaaa ttaaaaaaac taaggaaaca 3060tttttcttgt ttcgagtaga
taatgccagc ctgttaaacg ccgtcgacga gtctaacgga 3120caccaaccag cgaaccagca
gcgtcgcgtc gggccaagcg aagcagacgg cacggcatct 3180ctgtcgctgc ctctggaccc
ctctcgagag ttccgctcca ccgttggact tgctccgctg 3240tcggcatcca gaaattgcgt
ggcggagcgg cagacgtgag ccggcacggc aggcggcctc 3300ctcctcctct cacggcaccg
gcagctacgg gggattcctt tcccaccgct ccttcgcttt 3360cccttcctcg cccgccgtaa
taaatagaca ccccctccac accctctttc cccaacctcg 3420tgttgttcgg agcgcacaca
cacacaacca gatctccccc aaatccaccc gtcggcacct 3480ccgcttcaag gtacgccgct
cgtcctcccc ccccccccct ctctaccttc tctagatcgg 3540cgttccggtc catggttagg
gcccggtagt tctacttctg ttcatgtttg tgttagatcc 3600gtgtttgtgt tagatccgtg
ctgctagcgt tcgtacacgg atgcgacctg tacgtcagac 3660acgttctgat tgctaacttg
ccagtgtttc tctttgggga atcctgggat ggctctagcc 3720gttccgcaga cgggatcgat
ttcatgattt tttttgtttc gttgcatagg gtttggtttg 3780cccttttcct ttatttcaat
atatgccgtg cacttgtttg tcgggtcatc ttttcatgct 3840tttttttgtc ttggttgtga
tgatgtggtc tggttgggcg gtcgttctag atcggagtag 3900aattctgttt caaactacct
ggtggattta ttaattttgg atctgtatgt gtgtgccata 3960catattcata gttacgaatt
gaagatgatg gatggaaata tcgatctagg ataggtatac 4020atgttgatgc gggttttact
gatgcatata cagagatgct ttttgttcgc ttggttgtga 4080tgatgtggtg tggttgggcg
gtcgttcatt cgttctagat cggagtagaa tactgtttca 4140aactacctgg tgtatttatt
aattttggaa ctgtatgtgt gtgtcataca tcttcatagt 4200tacgagttta agatggatgg
aaatatcgat ctaggatagg tatacatgtt gatgtgggtt 4260ttactgatgc atatacatga
tggcatatgc agcatctatt catatgctct aaccttgagt 4320acctatctat tataataaac
aagtatgttt tataattatt ttgatcttga tatacttgga 4380tgatggcata tgcagcagct
atatgtggat ttttttagcc ctgccttcat acgctattta 4440tttgcttggt actgtttctt
ttgtcgatgc tcaccctgtt gtttggtgtt acttctgcag 4500gtcgactcta gaggatccaa
caatggagaa caacatacag aatcagtgcg tcccctacaa 4560ctgcctcaac aatcctgaag
tagagattct caacgaagag aggtcgactg gcagattgcc 4620gttagacatc tccctgtccc
ttacacgttt cctgttgtct gagtttgttc caggtgtggg 4680agttgcgttt ggcctcttcg
acctcatctg gggcttcatc actccatctg attggagcct 4740ctttcttctc cagattgaac
agttgattga acaaaggatt gagaccttgg aaaggaatcg 4800ggccatcact acccttcgtg
gcttagcaga cagctatgag atctacattg aagcactaag 4860agagtgggaa gccaatccta
acaatgccca actgagagaa gatgtgcgta tacgctttgc 4920taacacagat gatgctttga
tcacagccat caacaacttc acccttacca gcttcgagat 4980ccctcttctc tcggtctatg
ttcaagctgc taacctgcac ttgtcactac tgcgcgacgc 5040tgtgtcgttt gggcaaggtt
ggggactgga catagctact gtcaacaatc actacaacag 5100actcatcaat ctgattcatc
gatacacgaa acattgtttg gatacctaca atcagggatt 5160ggagaacctg agaggtacta
acactcgcca atgggccagg ttcaatcagt tcaggagaga 5220ccttacactt actgtgttag
acatagttgc tctctttccg aactacgatg ttcgtaccta 5280tccgattcaa acgtcatccc
aacttacaag ggagatctac accagttcag tcattgaaga 5340ctctccagtt tctgcgaaca
tacccaatgg tttcaacagg gctgagtttg gagtcagacc 5400accccatctc atggacttca
tgaactcttt gtttgtgact gcagagactg ttagatccca 5460aactgtgtgg ggaggacact
tagttagctc acgcaacacg gctggcaatc gtatcaactt 5520tcctagttac ggggtcttca
atcccggggg cgccatctgg attgcagatg aagatccacg 5580tcctttctat cggaccttgt
cagatcctgt cttcgtccga ggaggctttg gcaatcctca 5640ctatgtactc ggtcttaggg
gagtggcctt tcaacaaact ggtacgaatc acacccgcac 5700attcaggaac tccgggacca
ttgactctct agatgagata ccacctcaag acaacagcgg 5760cgcaccttgg aatgactact
cccatgtgct gaatcatgtt acctttgtgc gctggccagg 5820tgagatctca ggttccgact
catggagagc accaatgttc tcttggacgc atcgtagcgc 5880tacccccaca aacaccattg
atccagagag aatcactcag attcccttgg tgaaggcaca 5940cacacttcag tcaggaacta
cagttgtaag agggccgggg ttcacgggag gagacattct 6000tcgacgcact agtggaggac
cattcgcgta caccattgtc aacatcaatg ggcaacttcc 6060ccaaaggtat cgtgccagga
tacgctatgc ctctactacc aatctaagaa tctacgttac 6120ggttgcaggt gaacggatct
ttgctggtca gttcaacaag acaatggata ccggtgatcc 6180acttacattc caatctttct
cctacgccac tatcaacacc gcgttcacct ttccaatgag 6240ccagagcagt ttcacagtag
gtgctgatac cttcagttca ggcaacgaag tgtacattga 6300caggtttgag ttgattccag
ttactgccac actcgagtaa ggatccgtcg acctgcagcc 6360aagctttcgc gagctcgaga
tccccgacat atgccccggt ttcgttgcga ctaacatgag 6420ttcttggaca aatttgattg
gacctgatga gatgatccaa cccgaggata tagcaaagct 6480cgttcgtgca gcaatggaac
ggccaaaccg tgcttttgtc cccaagaatg aggtgctatg 6540catgaaggaa tctacccgtt
gatgtccaac agtctcaggg ttaatgtcta tgtatcttaa 6600ataatgttgt cggtattttg
taatctcata tagattttca ctgtgcgacg caaaaatatt 6660aaataaatat tattattatc
tacgttttga ttgagatatc atcaatatta taataaaaat 6720atccattaaa cacgatttga
tacaaatgac agtcaataat ctgatttgaa tatttattaa 6780ttgtaacgaa ttacataaag
atcgaataga aaatactgca ctgcaaatga aaattaacac 6840atactaataa atgcgtcaaa
tatctttgcc aagatcaagc ggagtgaggg cctcatatcc 6900ggtctcagtt acaagcacgg
tatccccgaa gcgcgctcca ccaatgccct cgacatagat 6960gccgggctcg acgctgagga
cattgcctac cttgagcatg gtctcagcgc cggctttaag 7020ctcaatccca tcccaatctg
aatatcctat cccgcgccca gtccggtgta agaacgggtc 7080tgtccatcca cctctgttgg
gaattccggt ccgggtcacc tttgtccacc aagatggaac 7140tgcggccagc ttgcatgcct
gcagtgcagc gtgacccggt cgtgcccctc tctagagata 7200atgagcattg catgtctaag
ttataaaaaa ttaccacata ttttttttgt cacacttgtt 7260tgaagtgcag tttatctatc
tttatacata tatttaaact ttactctacg aataatataa 7320tctatagtac tacaataata
tcagtgtttt agagaatcat ataaatgaac agttagacat 7380ggtctaaagg acaattgagt
attttgacaa caggactcta cagttttatc tttttagtgt 7440gcatgtgttc tccttttttt
ttgcaaatag cttcacctat ataatacttc atccatttta 7500ttagtacatc catttagggt
ttagggttaa tggtttttat agactaattt ttttagtaca 7560tctattttat tctattttag
cctctaaatt aagaaaacta aaactctatt ttagtttttt 7620tatttaataa tttagatata
aaatagaata aaataaagtg actaaaaatt aaacaaatac 7680cctttaagaa attaaaaaaa
ctaaggaaac atttttcttg tttcgagtag ataatgccag 7740cctgttaaac gccgtcgacg
agtctaacgg acaccaacca gcgaaccagc agcgtcgcgt 7800cgggccaagc gaagcagacg
gcacggcatc tctgtcgctg cctctggacc cctctcgaga 7860gttccgctcc accgttggac
ttgctccgct gtcggcatcc agaaattgcg tggcggagcg 7920gcagacgtga gccggcacgg
caggcggcct cctcctcctc tcacggcacc ggcagctacg 7980ggggattcct ttcccaccgc
tccttcgctt tcccttcctc gcccgccgta ataaatagac 8040accccctcca caccctcttt
ccccaacctc gtgttgttcg gagcgcacac acacacaacc 8100agatctcccc caaatccacc
cgtcggcacc tccgcttcaa ggtacgccgc tcgtcctccc 8160cccccccccc tctctacctt
ctctagatcg gcgttccggt ccatggttag ggcccggtag 8220ttctacttct gttcatgttt
gtgttagatc cgtgtttgtg ttagatccgt gctgctagcg 8280ttcgtacacg gatgcgacct
gtacgtcaga cacgttctga ttgctaactt gccagtgttt 8340ctctttgggg aatcctggga
tggctctagc cgttccgcag acgggatcga tttcatgatt 8400ttttttgttt cgttgcatag
ggtttggttt gcccttttcc tttatttcaa tatatgccgt 8460gcacttgttt gtcgggtcat
cttttcatgc ttttttttgt cttggttgtg atgatgtggt 8520ctggttgggc ggtcgttcta
gatcggagta gaattctgtt tcaaactacc tggtggattt 8580attaattttg gatctgtatg
tgtgtgccat acatattcat agttacgaat tgaagatgat 8640ggatggaaat atcgatctag
gataggtata catgttgatg cgggttttac tgatgcatat 8700acagagatgc tttttgttcg
cttggttgtg atgatgtggt gtggttgggc ggtcgttcat 8760tcgttctaga tcggagtaga
atactgtttc aaactacctg gtgtatttat taattttgga 8820actgtatgtg tgtgtcatac
atcttcatag ttacgagttt aagatggatg gaaatatcga 8880tctaggatag gtatacatgt
tgatgtgggt tttactgatg catatacatg atggcatatg 8940cagcatctat tcatatgctc
taaccttgag tacctatcta ttataataaa caagtatgtt 9000ttataattat tttgatcttg
atatacttgg atgatggcat atgcagcagc tatatgtgga 9060tttttttagc cctgccttca
tacgctattt atttgcttgg tactgtttct tttgtcgatg 9120ctcaccctgt tgtttggtgt
tacttctgca ggtcgactct agaggatcca cacgacacca 9180tgtccgcccg cgaggtgcac
atcgacgtga acaacaagac cggccacacc ctccagctgg 9240aggacaagac caagctcgac
ggcggcaggt ggcgcacctc cccgaccaac gtggccaacg 9300accagatcaa gaccttcgtg
gccgaatcca acggcttcat gaccggcacc gagggcacca 9360tctactactc aattaatggc
gaggccgaga tcagcctcta cttcgacaac ccgttcgccg 9420gctccaacaa atacgacggc
cactccaaca agtcccagta cgagatcatc acccagggcg 9480gctccggcaa ccagtcccac
gtgacctaca ccatccagac cacctcctcc cgctacggcc 9540acaagtcctg agtcatgagt
catgagtcag ttaacctaga cttgtccatc ttctggattg 9600gccaacttaa ttaatgtatg
aaataaaagg atgcacacat agtgacatgc taatcactat 9660aatgtgggca tcaaagttgt
gtgttatgtg taattactag ttatctgaat aaaagagaaa 9720gagatcatcc atatttctta
tcctaaatga atgtcacgtg tctttataat tctttgatga 9780accagatgca tttcattaac
caaatccata tacatataaa tattaatcat atataattaa 9840tatcaattgg gttagcaaaa
caaatctagt ctaggtgtgt tttgcgaatg cggccgcgga 9900ccgaattggg gatctgcatg
aaagaaactg tcgcactgct gaaccgcacc ttgtcacttt 9960catcgaacac gacctgtgcc
caagatgacg gtgctgcggt ctaagtgagg ctgaattgcc 10020ttggacagaa gcggactccc
tacaattagt taggccaaac ggtgcatcca tgtgtagctc 10080cgggctcggg ctgtatcgcc
atctgcaata gcatccatgg agctcgttcc atgtagttgg 10140agatgaacca atgatcgggc
gtgtggacgt atgttcctgt gtactccgat agtagagtac 10200gtgttagctc tttcatggtg
caagtgaaat ttgtgttggt ttaattaccc ctacgttagt 10260tgcgggacag gagacacatc
atgaatttaa aggcgatgat gtcctctcct gtaatgttat 10320tcttttgatg tgatgaatca
aaatgtcata taaaacattt gttgctcttt agttaggcct 10380gatcgtagaa cgaaatgctc
gtgtagcggg gctacgagcc tatgacgcaa taacactggt 10440ttgccggccc ggagtcgctt
gacaaaaaaa agcatgttaa gtttatttac aattcaaaac 10500ctaacatatt atattccctc
aaagcaggtt cacgatcaca cctgtaccta aaaaaaacat 10560gaagaatata ttactccatt
attatgagat gaaccacttg gcaagagtgg taagctatat 10620aaaaaaatga acattattac
gagatgttat atgccattat attgattcga agatatatgt 10680ttctttctcc cacgggcacc
taacggatac atgataaggc caaggcagat cacgggaaat 10740tattcgaata catgttacgc
cctattgccg gaaaaaaaat gcagggcagg tgttggccgt 10800agcgatttaa gcacttaagc
tggaggttgc cacacttgga tgcaagcgtc tgacccttct 10860aaaaaatcgg cggctttgtc
cgtatccgta tcccctatcc aacatctagc tggccacacg 10920acggggctgg gcagatcgtg
gatgccgggt cgacgtcgat cgtcagccat catagaccaa 10980tcgaccatct gttatggatg
cttgctagct agactagtca gacataaaat ttggatactt 11040tctcccaact gggagacggg
gactgatgtg cagctgcacg tgagctaaat ttttccctat 11100aaatatgcat gaaatactgc
attatcttgc cacagccact gccacagcca gataacaagt 11160gcagctggta gcacgcaacg
catagctctg gacttgtagc taggtagcca accggatcca 11220cacgacacca tgctcgacac
caacaaggtg tacgagatca gcaaccacgc caacggcctc 11280tacgccgcca cctacctctc
cctcgacgac tccggcgtgt ccctcatgaa caagaacgac 11340gacgacatcg acgactacaa
cctcaagtgg ttcctcttcc cgatcgacga cgaccagtac 11400atcatcacct cctacgccgc
caacaactgc aaggtgtgga acgtgaacaa cgacaagatt 11460aatgtgtcaa cctactcctc
caccaactcc atccagaagt ggcagatcaa ggccaacggc 11520tcctcctacg tgatccagtc
cgacaacggc aaggtgctca ccgccggcac cggccaggcc 11580ctcggcctca tccgcctcac
cgacgagtcc tccaacaacc cgaaccagca atggaacctg 11640acgtccgtgc agaccatcca
gctcccgcag aagccgatca tcgacaccaa gctcaaggac 11700tacccgaagt actccccgac
cggcaacatc gacaacggca cctccccgca gctcatgggc 11760tggaccctcg tgccgtgcat
catggtgaac gacccgaaca tcgacaagaa cacccagatc 11820aagaccaccc cgtactacat
cctcaagaag taccagtact ggcagagggc cgtgggctcc 11880aacgtcgcgc tccgcccgca
cgagaagaag tcctacacct acgagtgggg caccgagatc 11940gaccagaaga ccaccatcat
caacaccctc ggcttccaga tcaacatcga cagcggcatg 12000aagttcgaca tcccggaggt
gggcggcggt accgacgaga tcaagaccca gctcaacgag 12060gagctcaaga tcgagtattc
acatgagacg aagatcatgg agaagtacca ggagcagtcc 12120gagatcgaca acccgaccga
ccagtccatg aactccatcg gcttcctcac catcacctcc 12180ctggagctct accgctacaa
cggctccgag atccgcatca tgcagatcca gacctccgac 12240aacgacacct acaacgtgac
ctcctacccg aaccaccagc aggccctgct gctgctgacc 12300aaccactcct acgaggaggt
ggaggagatc accaacatcc cgaagtccac cctcaagaag 12360ctcaagaagt actacttctg
agtcatgagt catgagtcag ttaacctaga cttgtccatc 12420ttctggattg gccaacttaa
ttaatgtatg aaataaaagg atgcacacat agtgacatgc 12480taatcactat aatgtgggca
tcaaagttgt gtgttatgtg taattactag ttatctgaat 12540aaaagagaaa gagatcatcc
atatttctta tcctaaatga atgtcacgtg tctttataat 12600tctttgatga accagatgca
tttcattaac caaatccata tacatataaa tattaatcat 12660atataattaa tatcaattgg
gttagcaaaa caaatctagt ctaggtgtgt tttgcgaatt 12720atcgatgggc cccggccgaa
gctggccgcg gaccgaattc ccatggagtc aaagattcaa 12780atagaggacc taacagaact
cgccgtaaag actggcgaac agttcataca gagtctctta 12840cgactcaatg acaagaagaa
aatcttcgtc aacatggtgg agcacgacac gcttgtctac 12900tccaaaaata tcaaagatac
agtctcagaa gaccaaaggg caattgagac ttttcaacaa 12960agggtaatat ccggaaacct
cctcggattc cattgcccag ctatctgtca ctttattgtg 13020aagatagtgg aaaaggaagg
tggctcctac aaatgccatc attgcgataa aggaaaggcc 13080atcgttgaag atgcctctgc
cgacagtggt cccaaagatg gacccccacc cacgaggagc 13140atcgtggaaa aagaagacgt
tccaaccacg tcttcaaagc aagtggattg atgtgatatc 13200tccactgacg taagggatga
cgcacaatcc cactatcctt cgcaagaccc ttcctctata 13260taaggaagtt catttcattt
ggagaggaca gggtacccgg ggatccacca tgtctccgga 13320gaggagacca gttgagatta
ggccagctac agcagctgat atggccgcgg tttgtgatat 13380cgttaaccat tacattgaga
cgtctacagt gaactttagg acagagccac aaacaccaca 13440agagtggatt gatgatctag
agaggttgca agatagatac ccttggttgg ttgctgaggt 13500tgagggtgtt gtggctggta
ttgcttacgc tgggccctgg aaggctagga acgcttacga 13560ttggacagtt gagagtactg
tttacgtgtc acataggcat caaaggttgg gcctaggatc 13620cacattgtac acacatttgc
ttaagtctat ggaggcgcaa ggttttaagt ctgtggttgc 13680tgttataggc cttccaaacg
atccatctgt taggttgcat gaggctttgg gatacacagc 13740ccggggtaca ttgcgcgcag
ctggatacaa gcatggtgga tggcatgatg ttggtttttg 13800gcaaagggat tttgagttgc
cagctcctcc aaggccagtt aggccagtta cccagatctg 13860agtcgacctg caggcatgcc
cgctgaaatc accagtctct ctctacaaat ctatctctct 13920ctataataat gtgtgagtag
ttcccagata agggaattag ggttcttata gggtttcgct 13980catgtgttga gcatataaga
aacccttagt atgtatttgt atttgtaaaa tacttctatc 14040aataaaattt ctaattccta
aaaccaaaat ccagggcgag ctcgaattcg agctcgagcc 14100cgggtggatc ctctagagtc
gacctgcaga agcttcggtc cggcgcgcct ctagttgaag 14160acacgttcat gtcttcatcg
taagaagaca ctcagtagtc ttcggccaga atggcctaac 14220tcaaggccat cgtggcctct
tgctcttcag gatgaagagc tatgtttaaa cgtgcaagcg 14280ctactagaca attcagtaca
ttaaaaacgt ccgcaatgtg ttattaagtt gtctaagcgt 14340caatttggaa caagtggcta
tcgccagata taagaacttc gatccgaaat atcgtttcaa 14400aactagaaaa cagcgcggct
ttggctaagc cgcgcactat ataggatttt gggcaccttt 14460tgatggaacg tgaaagcgta
ctgcgcacta gttatttagg ttgaaccttg gatatacggt 14520tctcactgcg ccaatgcaag
gcttgaaact tggttagtaa tacgtactcc ctccgtttct 14580ttttatttgt cgctggatag
tgcaattttg cactatcgag cgacaaataa aaagaaacgg 14640agggagtata tgattgtcag
atgtagatat gtttatttat atatcacata cagatatata 14700aaacagatca ctttttcaga
tatacagttc caatgtcagc cctgatcacc ctgtcataaa 14760ttgcacgttt ctaattgatg
ttgcttcatg gtcgtcatga gaaccttctg aagaaatcga 14820tgaaggttgc caacctttca
aagtttcaga aaccactttg catgtacact aagggctggt 14880ttggcagccc aaaaccagcc
agcgttttcc tggtcttttc tcccgggaga aagcccatgc 14940atagattgtc cctggattat
ttatctgtgt cctttggcta aaaattcgtc ccaatttcct 15000gtaggaaact acctcggcct
tgggaggcca ggcgattctc caccgcctcg tctcgtccat 15060ccttcgatgc tcacgcgtgc
ctcctcggat gctatcctca ggcgattctc cgtcgtctcg 15120tctcatccat cctcacgcgc
gcctcctccg acgctatccc caggcgattc tccaccgtct 15180cgtctcatcc atcctcatgt
acgcctcgtc cgatgctatc cccagacgat tttccgtcgt 15240ctcatctcct tcatgctcgc
gcgcgcctcc tccgacgcta tccccaggcg atttttctgc 15300cgtctcgtct ccttcatgcc
cgcgcgcgcc tcctccgacg ctatccccag gcgattttcc 15360gccgtctcgt ctccttcatg
cccgcgcgtg cctcctccga cgctattccc acgagcgcct 15420ccgccgccgc tatccccaga
cgattttccg ctgtctcgtc tccttcatgc ccgcgcgccc 15480ctcctccgac gctatcccca
cgagcgcctc cgccgccgct ccaccgtctt ccccgccgcc 15540atccccttaa ttcctataga
tctggacccc gctctacttt cgttggcata cttttgcttg 15600gtgtgcgcgg gctggagtgg
aaggttgcgc attcgatcac gggggagaag tggatcttgg 15660gtcttggcag gctagggcgg
ttgccaggac gccgtggtgt gcattcatgg gtcctataaa 15720tctttatcat taccgcctta
ggagctagtt gtagttcaca catcatatcc ttttctgctc 15780gacatcgtct ggggatgccc
taggtgccct accgacccta cggcattgtc ttgacctcta 15840ttagactcta tgtcatctag
agccttcttg ggtggccttt tgaccccaaa gcgaccctat 15900gatcttaccc taacgaggtc
tcccttggtg gggcaagatc cactttgtcc acttaactga 15960agatctgatc ctcatcttga
aatctttaat cccaaggtga ctctacgtcg tatgtggatg 16020ctccgggtaa cctgccaacc
cggatcaccc taagatctct ttcctaaggg gcgagatcta 16080ggttcctacg agaaagaaga
cgaccctgca ccattgcggt ccgtccggtc cagagtgcga 16140acgtccggat gcgacacagg
gaaggagtcg ctcctgcagc gaggtcgcag actgtccaca 16200cagcctcaga aggcaccgcc
agacaataca tgtaataccc actctgtaag aaaaacctaa 16260aaggagaaag tatattcctt
tatctatatg tgtgttatat ttctactcac catcacatgt 16320gaacatctca cttacacaaa
taaataatta acaaaagaca ctcaaataaa ttatgcatca 16380tgctcgacct tattttgtgt
gcattctgtt acaatataaa aataatataa aaaacatata 16440ttaatatcaa aatttggaga
tttaacccta atatgcaaat cggagtttag aggaaagaaa 16500gaaaaatgct atacaaaata
aaggaataaa tatataaata aaggtaaaac tattaatact 16560ggtatattaa tttgaacagt
tgacctaatt atgaatatca caactggttt gaattcaaat 16620atgaaatcca agaatttgga
aataggaaaa atggagataa gaataaagga aaagaattct 16680taactcggat gggcctggga
aacgaatttc ggcccacttc ctgtgtcctt agctgtgcgg 16740ctcagtccag tg
16752726DNAArtificial
SequencePrimer 09-0-2877 7agggcctcat atccggtctc agttac
26829DNAArtificial SequencePrimer 09-0-2880
8cacgctgcac tgcaggcatg caagctggc
29925DNAArtificial SequencePrimer 02-0-197 9ccgctgtatc acaagggctg gtacc
251025DNAArtificial
SequencePrimer 02-0-198 10ggagcccgtg tagagcatga cgatc
251129DNAArtificial SequencePrimer 09-0-3030
11gagcatatcc agcaccagct ggtaccaag
291219DNAArtificial SequencePrimer 09-0-2787 12gcaggcatgc ccgcggata
191326DNAArtificial
SequencePrimer 09-0-3036 13tggtctaccc gatgatgtga ttggcc
261429DNAArtificial SequencePrimer 09-0-3046
14cgaagacagg atctgacaag gtccgatag
291535DNAArtificial SequencePrimer 09-0-3045 15gacttcatga actctttgtt
tgtgactgca gagac 351622DNAArtificial
SequencePrimer 09-0-2980 16ctcatgactc aggacttgtg gc
221718DNAArtificial SequencePrimer 08-0-2463
17atcagcctct acttcgac
181823DNAArtificial SequencePrimer 08-0-2759 18ctccatgatc ttcgtctcat gtg
231923DNAArtificial
SequencePrimer 09-0-2775 19caccaactcc atccagaagt ggc
232026DNAArtificial SequencePrimer 09-0-3083
20gccttgcatt ggcgcagtga gaaccg
262127DNAArtificial SequencePrimer 09-0-2799 21cggcgcgcct ctagttgaag
acacgtt 272230DNAArtificial
SequencePrimer 09-0-3005 22cactggactg agccgcacag ctaaggacac
302328DNAArtificial SequencePrimer 09-0-3230
23ggaacattca gacttgggag tctggact
282427DNAArtificial SequencePrimer 09-0-3229 24gaacagggtc ctcgaatcaa
gggcagc 272526DNAArtificial
SequencePrimer 09-0-3231 25cggttctcac tgcgccaatg caaggc
262623DNAArtificial SequencePrimer 09-0-3084
26catgacgacc atgaagcaac atc
232720DNAArtificial Sequence5' Junction Sequence 27caacacagat ctgatagttt
202820DNAArtificial
Sequence3' Junction Sequence 28cgtcaatttg gaacaagtgg
202923DNAArtificial SequencePrimer 08-O-2677
29cgtttgtagc acttgcacgt agt
233022DNAArtificial SequencePrimer 08-O-2678 30ggtaaccgct cttccagttg aa
223117DNAArtificial
SequenceProbe 08-QP74 31aagcttcaac acagatc
173290DNAArtificial SequenceAmplicon 32cgtttgtagc
acttgcacgt agttacccgg accgaagctt caacacagat ctgatagttt 60aaacgctctt
caactggaag agcggttacc
903324DNAArtificial SequenceForward primer 11-O-4127 33ggaccctgtt
cacaacacag ggct
243419DNAArtificial SequenceReverse primer 11-O-4128 34ggccgaagct
tcggtccgg
1935149DNAArtificial SequenceAmplicon 35ggaccctgtt cacaacacag ggctctggct
ttggagcctc tcgtttgtag cacttgcacg 60tagttacccg gaccgaagct tcaacacaga
tctgatagtt taaacgctct tcaactggaa 120gagcggttac ccggaccgaa gcttcggcc
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