Plant & Animal Genomes XVI Conference

January 12-16, 2008
Town & Country Convention Center
San Diego, CA

Single Nucleotide Polymorphisms Between Coding Sequences Of The Brassica A And C Genomes

J. Erron Haggard¹ , Alexander Kozik² , Carlos F. Quiros¹

¹  Department of Plant Sciences, University of California, Davis; One Shields Ave. Davis, CA 95616

²  The Genome Center, University of California, Davis; Davis, CA 95616

Our interest in the characterization and exploitation of complete sets of Brassica oleracea / B. rapa and B. rapa / B. oleracea addition lines necessitates the development of suitable molecular markers. Single-nucleotide polymorphisms (SNPs) based on known single-copy genes in Arabidopsis thaliana were selected as ideal molecular markers, based on the availability of sequence information for Brassica spp. and our ability to select specific genes of interest to target for genotyping. To achieve this goal, we downloaded expressed sequence tag (EST) sequences from the NCBI GenBank database for the three species which contain these genomes (B. rapa-A, B. oleracea-C, B. napus-A & C). Next, we selected ESTs homologous to known A. thaliana proteins and extracted their coding regions (CDS). The CDS for the three species were then assembled using CAP3, resulting in 13,501 contigs. These contigs were visualized using Python Contig Viewer to highlight SNPs and locate approximate intron/exon boundaries based on A. thaliana sequences, with the objective of designing oligonucleotide primers for use with Illumina® bead-array genotyping technology. Here, we report the results of our marker selection. All EST, assembly, and SNP data as well as scripts and additional information are available at http://informatics.plantsciences.ucdavis.edu/haggard/brassica.html.