Abundance and characterization of simple-sequence repeats (SSRs) isolated from a size-fractionated genomic library of Brassica napus L. (rapeseed)

A size-fractionated library of Brassica napus L. (rapeseed), composed of 15000 clones, was screened for the presence of GA-, CA-, and GATA-simple-sequence repeats (SSRs). GA-SSRs were four- and five-fold more abundant than CA- and GATA-SSRs, respectively, and present at a frequency of approximately one SSR for every 100 kb of DNA. Following the sequencing of 124 positive clones, primer pairs were designed and evaluated for seven selected SSRs. Products were amplified in an array of individuals of B. napus, B. oleracea and B. rapa, demonstrating that the seven SSRs were conserved among species. Two SSRs were polymorphic. Among 11 accessions, the dinucleotide (GA)-repeat, B.n.9A, yielded 12 fragments, while the tetranucleotide-repeat (GATA), B.n.6A2, revealed two fragments. Automated, fluorescence-based detection of polyacrylamide gels has been employed to simultaneously increase throughput, reduce unit cost, improve analytical resolution, and expedite data acquisition of SSR analysis. Though initial financial investment and technical capabilities may prevent some from directly employing our documented approach, SSR analysis warrants further investigation as a tool in genetic studies for enhancing both the conservation and utilization of genetic resources.