Development of EST-SSR markers to study genetic diversity in hyacinth bean (Lablab purpureus L.)

The development of expressed sequence tags (ESTs) has provided a useful source for the mining of simple sequence repeat (SSR) markers. The hyacinth bean (Lablab purpureus L.) is one of the most ancient and important legume crops in the world, and is widely distributed in tropical and sub-tropical regions, but currently only limited molecular markers are available. The aim of the present study is to develop EST-SSRs for hyacinth beans to investigate the genetic structure and diversity of different populations originating from China and Africa. A total of 459 hyacinth bean ESTs from the National Center for Biotechnology Information (NCBI) database were downloaded and analyzed to search for SSRs with a minimum of 12 repeating nucleotides Finally, 22 microsatellites were identified in 420 unigenes, indicating that merely 4.79% of the sequences contained SSRs. EST-SSR loci were subsequently screened on 24 hyacinth bean accessions collected from both China and Africa. Among 22 EST-SSRs, 11 loci showed polymorphism and revealed two to four alleles per locus. Tri-nucleotide motifs were the most common type of repeats, accounting for 54.55% of the total, followed by di-nucleotide repeats. The polymorphic information content (PIC) values ranged from 0.0767 to 0.4864, with a mean of 0.286. Furthermore, both principal coordinate analysis (PCA) and phylogenetic tree analysis indicated that all accessions were clustered into two main groups, and that all 19 Chinese accessions were clustered into the single group. These results suggest that there is a narrow genetic basis for Chinese hyacinth bean accessions. In summary, the results of this study suggest that the data mining of EST databases is a feasible method for generating EST-SSR markers for hyacinth bean, and these newly developed EST-SSR markers will be useful for further taxonomy, molecular breeding and comparative mapping studies.