Development of a Database (BARCPvSSR_1.0) Containing Candidate Polymorphic Simple Sequence Repeat (SSR) Markers in Common Bean

SSR or microsatellite genetic markers are characterized by simplicity of use and transferability among laboratories and are useful for QTL mapping, map-based cloning and for marker assisted selection in plant breeding.  The availability of the whole genome sequence facilitates the identification of SSRs.  We screened SSRs based on the whole genome sequence of the Phaseolus vulgaris v1.0 assembly and identified a total of 85,646 SSRs with di-, tri- or tetra-nucleotide repeats of five or more.  Among these, 16,225, 2597 and 97 SSRs contained repeat units of di-(≥10), tri-(≥8), and tetra-nucleotide (≥7), respectively.  As in soybean, (AT)n, (ATT)n and (AAAT)n are the most abundant motifs among di-, tri- and tetra-nucleotide SSRs, respectively.  After screening for a number of factors including locus-specificity using e-PCR a common bean SSR database (BARCPvSSR_1.0) containing genome position, primer sequences and motif types of 13,700 SSRs was created.  To examine the likelihood that primers in the database would function to amplify locus-specific polymorphic products, 1152 primer sets were evaluated by amplifying DNAs of 16 diverse common bean accessions from market classes: dark red kidney, light red kidney, black, navy, pinto, and great northern.  A total of 1064 (92.4%) of the primer sets amplified a single polymerase chain reaction (PCR) product and 759 (65.9%) amplified polymorphic amplicons as determined by 3.5% agarose gel electrophoresis.