Population Structure and Genetic Diversity of Cucurbita moschata Based on Genome-Wide High-Quality SNPs

Abstract

Pumpkins (Cucurbita moschata) are one of the most important economic crops in genus Cucurbita worldwide. They are a popular food resource and an important rootstock resource for various Cucurbitaceae. Especially, C. moschata is widely used as a rootstock for the commercial production of bloomless cucumbers in East Asia. Since the genetic diversity of the commercial rootstock varieties is narrow, there has been an increasing demand for the trait development of abiotic and biotic stress tolerance breeding. In this study, 2071 high-quality SNPs that were distributed evenly across 20 chromosomes of pumpkins were discovered through the genotyping-by-sequencing (GBS) analysis of 610 accessions of C. moschata germplasm with a global origin. Using these SNPs, various analyses of the genetic diversity and the population structure were performed. Three subgroups were clustered from the germplasm collection, which included East Asia, Africa, and America, and these areas were included the most in each subgroup. Among those groups, accessions from Africa and South Asia showed the highest genetic diversity, which was followed by the Mexico accessions. This result reflected that large gene pools that consist of various native landraces have been conserved in those of countries. Based on the genetic diversity, we finally constructed the C. moschata core collection, which included 67 representative accessions from the 610 germplasms. Five morphological traits that are important in commercial grafting and rootstock seed production, which include the cotyledon length, the cotyledon width, the hypocotyl length, the internode length, and the number of female flowers, were investigated for three years and used to confirm the validity of the core collection selection. The results are expected to provide valuable information about the genetic structure of the worldwide C. moschata germplasm and help to create new gene pools to develop genetically diverse rootstock breeding materials.

Keywords: bloomless cucumber; core collection; genetic diversity; population structure; pumpkins; rootstock.

Figure 1

The genome-wide SNP distribution (2071 SNPs) in the C. moschata chromosomes.

Figure 2

The population structure and the genetic relationship among the three clusters in the C. moschata germplasm collection. (a) The upper dendrogram was produced using the UPGMA method based on the genetic dissimilarity among the 610 germplasm accessions. Seven groups from the entire collection were distinguished in the gray color bar under the tree. The bar plots from the STRUCTURE analysis were listed in the order that is the same as the dendrogram under the tree. The Q-values of each clusters per accession were distinguished with different colors. Cluster 1 is in red, cluster 2 is in green, and cluster 3 is in blue. (b) The PCA of the entire collection colored by the clusters. (c) The F_ST values among the three clusters.