Development and characterization of genomic simple sequence repeat markers in eggplant and their application to the study of diversity and relationships in a collection of different cultivar types and origins

Abstract

The eggplant (Solanum melongena L.) genome is the least investigated among the economically most important solanaceous crops. Extensive use of molecular markers will improve eggplant germplasm enhancement and breeding. Microsatellites, or simple sequence repeats, have proved to be very useful for eggplant germplasm management and breeding, but there is limited availability of these polymorphic, codominant, and highly repeatable markers in eggplant. We developed a genomic DNA library enriched with AG/CT, which allowed the identification of 55 new genomic microsatellites. Variation parameters of microsatellite loci analyzed showed high average values. The potential of these markers for fingerprinting was assessed in a collection of 24 accessions, of which 22 correspond to S. melongena from different types (landraces, heirlooms, modern F1 hybrids, and obsolete cultivars) and origins, and two to each of the cultivated relatives S. aethiopicum and S. macrocarpon. The multivariate (cluster and PCoA) analyses clearly differentiated four main clusters: (a) two outgroups formed by S. aethiopicum and S. macrocarpon accessions, (b) S. melongena accessions derived mostly from the Mediterranean basin, Central Europe, Africa, and America (‘occidental’ eggplants), and (c) S. melongena accessions derived mostly from Eastern and Southeastern Asia (‘oriental’ eggplants). However, no apparent association pattern was found for accessions of the different types. Observed heterozygosity (Ho) values were low, although hybrid cultivars had higher values (Ho = 0.12) than non-hybrid materials (Ho = 0.02). The new set of eggplant microsatellite markers has proved highly informative and useful for studying the diversity, relationships, and genetic characteristics of an eggplant collection. These markers will be useful for germplasm management and breeding in eggplant.