Abstract

Melon (C. melo L.) is an economically important vegetable crop cultivated worldwide. The melon collection in the U.S. National Plant Germplasm System (NPGS) is a valuable resource to conserve natural genetic diversity and provide novel traits for melon breeding. Here we use the genotyping-by-sequencing (GBS) technology to characterize 2083 melon accessions in the NPGS collected from major melon production areas as well as regions where primitive melons exist. Population structure and genetic diversity analyses suggested that C. melo ssp. melo was firstly introduced from the centers of origin, Indian and Pakistan, to Central and West Asia, and then brought to Europe and Americas. C. melo ssp. melo from East Asia was likely derived from C. melo ssp. agrestis in India and Pakistan and displayed a distinct genetic background compared to the rest of ssp. melo accessions from other geographic regions. We developed a core collection of 383 accessions capturing more than 98% of genetic variation in the germplasm, providing a publicly accessible collection for future research and genomics-assisted breeding of melon. Thirty-five morphological characters investigated in the core collection indicated high variability of these characters across accessions in the collection. Genome-wide association studies using the core collection panel identified potentially associated genome regions related to fruit quality and other horticultural traits. This study provides insights into melon origin and domestication, and the constructed core collection and identified genome loci potentially associated with important traits provide valuable resources for future melon research and breeding.

Highlights

  • Melon (C. melo L.; 2n = 2 × =24) is a highly polymorphic member of the Cucurbitaceae family

  • To obtain a more accurate classification of the National Plant Germplasm System (NPGS) melon accessions, we manually reviewed the data provided in the NPGS for all melon accessions, including their places of origin and photos, combined with literature (e.g., Pitrat et al 2000) and our knowledge of the materials

  • The genetic composition of 2083 available melon accessions maintained in the NPGS, collected from ssp. agrestis and ssp. melo, were characterized using the GBS technology, providing 89,204 raw single nucleotide polymorphisms (SNPs) and 78,152 biallelic SNPs

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Summary

Introduction

Melon (C. melo L.; 2n = 2 × =24) is a highly polymorphic member of the Cucurbitaceae family. It is an economically important fruit crop grown primarily in temperate and semi-tropical regions with a worldwide production of 27.5 million metric tonnes in 2019 (FAOSTAT; http://www.fao.org/faostat/en). Later it was concluded that Asia is the center of origin, and the abundant diversity of melon across India and East Asia further supports this conclusion (Akashi et al 2002; Dhillon et al 2007; Tanaka et al 2007; Dwivedi et al 2010). A recent analysis of a diverse collection of C. melo accessions from Asia, Australia and African, suggested two independent melon domestication events, one in Africa and the other in Asia (Endl et al 2018). Recent studies based on the large-scale genome resequencing data demonstrated three independent domestication events in melon, two in India and one in Africa (Zhao et al 2019), consistent with the abundant diversity of melon found across India and Africa (Akashi et al 2002)

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