The potential for cross-taxa simple-sequence repeat (SSR) amplification between Arabidopsis thaliana L. and crop brassicas

Abstract

Simple-sequence repeats (SSRs) may prove to be valuable descriptors of plant genetic variation, but developing markers for each of many taxa is costly. The applicability of SSR markers may be increased if they can be amplified across taxa. In this study, we examined whether 30 primer pairs designed to amplify single-locus SSRs in Arabidopsis thaliana could be used to amplify marker loci in six Brassica crop species. Most of the pairs amplified multiple fragments in Brassica. In initial assays, 17 pairs generated products that were identified as likely to contain SSRs. Most of these products were similar in size to A. thaliana SSRs; many were variable for product length, and many of the variants were species- or genome-specific. In subsequent hybridization assays, however, not all of the identified Brassica products hybridized to SSR probes. A Brassica product’s length variation and its size similarity to A. thaliana SSRs were not good predictors of whether the product contained repeats. In addition, some products of two-primer reactions hybridized to SSR probes but were the same size as single-primer reaction products, so they may have been amplified by only one primer. In summary, Brassica products amplified by A. thaliana SSR primer pairs may be useful as markers, but additional tests (hybridization, DNA sequencing, and single-primer assays) are necessary in order to determine whether the products contain SSRs and whether they are amplified by one or two primers. The results of this study are consistent with conservation, duplication, and rearrangement between Arabidopsis and Brassica genomes.