DOI: 10.5061/dryad.p8cz8w9sg
title: Targeted sequencing of T-DNA borders in OCP1xOGC transgenic lines of Camelina

description: Background: Genetic engineering of crop plants has been successful in
 transferring traits into elite lines beyond what can be achieved with
 breeding techniques. Introduction of transgenes originating from other
 species has conferred resistance to biotic and abiotic stresses, increased
 efficiency, and modified developmental programs. The next challenge is now
 to combine multiple transgenes into elite varieties via gene stacking to
 combine traits. Generating stable homozygous lines with multiple
 transgenes requires selection of segregating generations which is time
 consuming and labor intensive, especially if the crop is polyploid.
 Insertion site effects and transgene copy number are important metrics for
 commercialization and trait efficiency. Results: We have developed a
 simple method to identify the sites of transgene insertions using
 T-DNA-specific primers and high-throughput sequencing that enables
 identification of multiple insertion sites in the T1 generation
 of any crop transformed via Agrobacterium. We present an example
 using the allohexaploid oil-seed plant Camelina
 sativa to determine insertion site location of two transgenes.
 Conclusion: This new methodology enables the early selection of desirable
 transgene location and copy number to generate homozygous lines within two
 generations.
description: Data are unprocessed, PEx150bp FASTQ reads generated from the
 sequencing run. FASTQ files were demultiplexed from the original base call
 files using Illumina's FASTQ generator analysis pipeline within Local
 Run Manager.
description: Line1415_LB includes all data for Camelina transgenic line #1415
 using a left-border-specific primer. Sample identifiers represent the
 genome-walking primer used in the PCR, as indicated in the README
 file. Line1415_RB includes all data for Camelina
 transgenic line #1415 using a right-border-specific primer. Sample
 identifiers represent the genome-walking primer used in the PCR, as
 indicated in the README file. Line1416_LB includes all
 data for Camelina transgenic line #1416 using a left-border-specific
 primer. Sample identifiers represent the genome-walking primer used in the
 PCR, as indicated in the README file. Line1416_RB
 includes all data for Camelina transgenic line #1416 using a
 right-border-specific primer. Sample identifiers represent the
 genome-walking primer used in the PCR, as indicated in the README
 file. At_LB includes all data for the Arabidopsis T-DNA
 insertion mutant (GK-269g12) using a left-border-specific primer. Sample identifiers represent the genome-walking primer used in the PCR, as indicated in the README file. At_RB includes all data for the Arabidopsis T-DNA insertion mutant (GK-269g12) using a right-border-specific primer. Sample identifiers represent the genome-walking primer used in the PCR, as indicated in the README file. Cs_LB includes all data for wildtype Camelina using a left-border-specific primer. Sample identifiers represent the genome-walking primer used in the PCR, as indicated in the README file. Cs_RB includes all data for wildtype Camelina using a right-border-specific primer. Sample identifiers represent the genome-walking primer used in the PCR, as indicated in the README file.