Microsatellite Diversity, Population Structure, and Core Collection Formation in Melon Germplasm

Abstract

Melon is one of the most important fruit crops in China, and has been the focus of much effort in breeding new cultivars but only limited effort in basic studies (e.g., germplasm collection, assessment, and utilization). In this study, we assessed the genetic diversity and population structure in a large melon collection (570 Chinese accessions and 42 exotic accessions) using 26 microsatellite markers distributed evenly in the genome. A total of 355 alleles, a high level of gene diversity (0.713), and a low observed heterozygosity (0.177) were detected among the whole panel. Using a model-based population structure analysis, all accessions were assigned to one of two main groups (P1 and P2), which were largely in line with their subspecies classification and geographic distribution. P1 comprised 279 accessions, most of which were from Northwest China, while P2 comprised 333 accessions, most of which were from the northeast, central, and east regions in China. Each of the two main groups was further subdivided into two subgroups that had different fruit features. Principal component analysis also gave similar results in positioning the 612 melon accessions. AMOVA, pairwise FST, and Nei’s genetic distance confirmed the differentiation between the groups and subgroups. The accessions from Northwest China revealed a high level of genetic diversity, as did accessions from Northeast, Central, and East China. Subsequently, we constructed a core collection representing 19.4 % of the whole panel and showing 100 % coverage of alleles. Our results provide an effective aid for future germplasm conservation and association genetics as well as development of appropriate breeding strategies in melon.