The design of Capsicum spp. SSR assays via analysis of in silico DNA sequence, and their potential utility for genetic mapping

Various types of molecular marker have been used to conduct phylogenetic and mapping studies in pepper (Capsicum annuum), among which microsatellites (SSRs) have been shown to be particularly valuable because of their co-dominant and multi-allelic nature. Of the approximately 180 pepper SSRs available in public domain, only a few have been either inter-and/or intraspecifically mapped so far. This paper reports the development of a set of new EST-based SSR assays. This class of SSRs is more transferable between species than those based on genomic sequence, and so can provide anchor markers in cross-species comparative mapping. A search of >8000 Capsicum ESTs, corresponding to approximately 4.1 Mbp of DNA, yielded 1325 SSRs present in 899 sequences. A cluster analysis was employed to obtain non-redundant SSR-containing sequences, leading to the definition of 576 non-redundant sequences containing 783 SSRs. Primer pairs were designed to amplify 348 SSRs, and a subset of 204 was used to screen for polymorphism within a parental set of four C. annuum inbred lines and one C. frutescens accession, used as parents of three mapping populations. The resulting 49 polymorphic SSRs provided the basis for assessing genetic diversity within an extended Capsicum spp. genotype set.