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Article

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

1
Department of Bioresources Engineering, Sejong University, Seoul 05006, Korea
2
Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea
*
Author to whom correspondence should be addressed.
Plants 2021, 10(1), 56; https://doi.org/10.3390/plants10010056
Received: 30 October 2020 / Revised: 24 December 2020 / Accepted: 25 December 2020 / Published: 29 December 2020
(This article belongs to the Special Issue Advances in Plant Breeding)
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. View Full-Text
Keywords: pumpkins; rootstock; bloomless cucumber; population structure; genetic diversity; core collection pumpkins; rootstock; bloomless cucumber; population structure; genetic diversity; core collection
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    Link: https://doi.org/10.5281/zenodo.4398515
    Description: Figure S1: A summary of the individual heterozygosity across 2071 loci for each accession. The X-axis indicates the heterozygosity, and the Y-axis indicates the number of accessions; Figure S2: ΔK from population structure analysis; Figure S3: The core collection distribution within the entire C. moschata germplasm collection in the PCA plot; Table S1: The number of SNPs, and the SNP density among 20 C. moschata chromosomes; Table S2: Information of 610 C. moschata germplasm collection used in this study; Table S3: The list of 67 core collections.
MDPI and ACS Style

Lee, H.-Y.; Jang, S.; Yu, C.-R.; Kang, B.-C.; Chin, J.-H.; Song, K. Population Structure and Genetic Diversity of Cucurbita moschata Based on Genome-Wide High-Quality SNPs. Plants 2021, 10, 56. https://doi.org/10.3390/plants10010056

AMA Style

Lee H-Y, Jang S, Yu C-R, Kang B-C, Chin J-H, Song K. Population Structure and Genetic Diversity of Cucurbita moschata Based on Genome-Wide High-Quality SNPs. Plants. 2021; 10(1):56. https://doi.org/10.3390/plants10010056

Chicago/Turabian Style

Lee, Hea-Young, Siyoung Jang, Chea-Rin Yu, Byoung-Cheorl Kang, Joong-Hyoun Chin, and Kihwan Song. 2021. "Population Structure and Genetic Diversity of Cucurbita moschata Based on Genome-Wide High-Quality SNPs" Plants 10, no. 1: 56. https://doi.org/10.3390/plants10010056

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