Genome-wide SNP discovery and core marker sets for assessment of genetic variations in cultivated pumpkin (Cucurbita spp.)

Nam Ngoc Nguyen,Sang-Min Chung,Younghoon Park,Jin-Kee Jung,Sung-Chur Sim,Minkyung Kim,Gung Pyo Lee,Eun-Jo Shim

doi:10.1038/s41438-020-00342-9

Abstract

Three pumpkin species Cucurbita maxima, C. moschata, and C. pepo are commonly cultivated worldwide. To identify genome-wide SNPs in these cultivated pumpkin species, we collected 48 F1 cultivars consisting of 40 intraspecific hybrids (15 C. maxima, 18 C. moschata, and 7 C. pepo) and 8 interspecific hybrids (C. maxima x C. moschata). Genotyping by sequencing identified a total of 37,869 confident SNPs in this collection. These SNPs were filtered to generate a subset of 400 SNPs based on polymorphism and genome distribution. Of the 400 SNPs, 288 were used to genotype an additional 188 accessions (94 F1 cultivars, 50 breeding lines, and 44 landraces) with a SNP array-based platform. Reliable polymorphisms were observed in 224 SNPs (78.0%) and were used to assess genetic variations between and within the four predefined populations in 223 cultivated pumpkin accessions. Both principal component analysis and UPGMA clustering found four major clusters representing three pumpkin species and interspecific hybrids. This genetic differentiation was supported by pairwise Fst and Nei’s genetic distance. The interspecific hybrids showed a higher level of genetic diversity relative to the other three populations. Of the 224 SNPs, five subsets of 192, 96, 48, 24, and 12 markers were evaluated for variety identification. The 192, 96, and 48 marker sets identified 204 (91.5%), 190 (85.2%), and 141 (63.2%) of the 223 accessions, respectively, while other subsets showed <25% of variety identification rates. These SNP markers provide a molecular tool with many applications for genetics and breeding in cultivated pumpkin.

Highlights

Pumpkin (Cucurbita spp.; 2n = 2x = 40) is a major crop in the Cucurbitaceae family including cucumber, melon, and watermelon
Next-generation sequencing (NGS) technologies have led to rapid Single nucleotide polymorphisms (SNPs) discovery and high-throughput genotyping
As an Nextgeneration sequencing (NGS)-based method, genotyping by sequencing (GBS) is a cost-effective approach based on genome complexity reduction for identifying genomewide SNPs26

Summary

Introduction

Pumpkin (Cucurbita spp.; 2n = 2x = 40) is a major crop in the Cucurbitaceae family including cucumber, melon, and watermelon. The Cucurbita genus consists of at least 12 diverse species; three major cultivated species are C. maxima Duchesne, C. moschata Duchesne, and C. pepo L.1. The cultivated varieties in these species produce thicker, more highly colored, and less fibrous fruit flesh relative to wild species[2]. The International Union for the Protection of New Varieties of Plant (UPOV) has harmonized PVP systems among 76 member countries and organizations (as of February 2020). Within this PVP system, a new variety must have distinctness, uniformity, and stability (DUS) to be eligible for registration and protection.

Methods

Results

Conclusion