Using SSR markers to map genetic diversity and population structure of Solanum pimpinellifolium for development of a core collection

The present study was undertaken to examine the population structure of the Solanum pimpinellifolium collection maintained by AVRDC - The World Vegetable Center - and to construct a core set of this collection. Out of the entire collection of 322 accessions, a diverse subset of 190 accessions was chosen representing 14 countries of origin. Data on 32 qualitative and 22 quantitative phenotypic traits (IPGRI-AVRDC descriptor traits) and 48 simple sequence repeat markers evenly distributed over the genome were used to develop the core set. A total of 377 alleles were detected with 7.85 alleles per locus, on average. Of these, 52 alleles at 28 loci were extremely rare-frequency alleles. The 190 accessions clustered into two main populations and an admixture group. Population I (PopI) included 99 accessions, 93 of which originated from Peru. Population II (PopII) contained 49 accessions, the majority of which originated from Ecuador and Mexico. The remaining 42 accessions were classified as admixture group. The two main populations were further subdivided into five subgroups. Values of F-st among the five sub-populations were significant (average pairwise F-st of 0.296), suggesting a real difference between these populations. A clear differentiation was observed among and within populations based on geography. Peruvian accessions were genetically more diverse than accessions originating in Ecuador and Mexico. Within the Peruvian group, a gradual increase in genetic diversity was observed from southern to northern Peru. The constructed core collection consists of 75 accessions representing 23.4% of AVRDC's entire S. pimpinellifolium collection and 39.5% of the subset used in this study. It is a well-balanced core with a good representation of the different populations (31 accessions from PopI, 22 from PopII and 22 from the Admixture group) and geographic origins (40 accessions from Peru, 17 from Ecuador, 14 from Mexico and four from other countries).