Elucidation of genetic variation and population structure of melon genetic resources in the NARO Genebank, and construction of the World Melon Core Collection

Numerous genetic resources of major crops have been introduced from around the world and deposited in Japanese National Agriculture and Food Research Organization (NARO) Genebank. Understanding their genetic variation and selecting a representative subset (“core collection”) are essential for optima...

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Bibliographic Details
Published in:Breeding Science 2023, Vol.73(3), pp.269-277
Main Authors: Shigita, Gentaro, Dung, Tran Phuong, Pervin, Mst. Naznin, Duong, Thanh-Thuy, Imoh, Odirich Nnennaya, Monden, Yuki, Nishida, Hidetaka, Tanaka, Katsunori, Sugiyama, Mitsuhiro, Kawazu, Yoichi, Tomooka, Norihiko, Kato, Kenji
Format: Article
Language:English
Subjects:
Agricultural research
Collection
core collection
crop origin
Cucumis melo
Cucurbitaceae
Cytoplasm
Datasets
Domestication
Fruits
Genetic diversity
Genetic relationship
genetic resource
Genetic resources
Genomes
Genotyping
genotyping-by-sequencing
Geographical distribution
Nucleotides
Phylogenetics
Phylogeny
Population genetics
Population structure
Research Paper
Single-nucleotide polymorphism
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Summary:Numerous genetic resources of major crops have been introduced from around the world and deposited in Japanese National Agriculture and Food Research Organization (NARO) Genebank. Understanding their genetic variation and selecting a representative subset (“core collection”) are essential for optimal management and efficient use of genetic resources. In this study, we conducted genotyping-by-sequencing (GBS) to characterize the genetic relationships and population structure in 755 accessions of melon genetic resources. The GBS identified 39,324 single-nucleotide polymorphisms (SNPs) that are distributed throughout the melon genome with high density (one SNP/10.6 kb). The phylogenetic relationships and population structure inferred using this SNP dataset are highly associated with the cytoplasm type and geographical origin. Our results strongly support the recent hypothesis that cultivated melon was established in Africa and India through multiple independent domestication events. Finally, we constructed a World Melon Core Collection that covers at least 82% of the genetic diversity and has a wide range of geographical origins and fruit morphology. The genome-wide SNP dataset, phylogenetic relationships, population structure, and the core collection provided in this study should largely contribute to genetic research, breeding, and genetic resource preservation in melon.
ISSN:1344-7610
1347-3735
DOI:10.1270/jsbbs.22071