Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies.
Core collection
Genetic diversity
Genome-wide association study
Journal
Plant & cell physiology
ISSN: 1471-9053
Titre abrégé: Plant Cell Physiol
Pays: Japan
ID NLM: 9430925
Informations de publication
Date de publication:
01 May 2020
01 May 2020
Historique:
received:
31
10
2019
accepted:
16
02
2020
pubmed:
27
2
2020
medline:
31
12
2020
entrez:
27
2
2020
Statut:
ppublish
Résumé
Genebanks provide access to diverse materials for crop improvement. To utilize and evaluate them effectively, core collections, such as the World Rice Core Collection (WRC) in the Genebank at the National Agriculture and Food Research Organization, have been developed. Because the WRC consists of 69 accessions with a high degree of genetic diversity, it has been used for >300 projects. To allow deeper investigation of existing WRC data and to further promote research using Genebank rice accessions, we performed whole-genome resequencing of these 69 accessions, examining their sequence variation by mapping against the Oryza sativa ssp. japonica Nipponbare genome. We obtained a total of 2,805,329 single nucleotide polymorphisms (SNPs) and 357,639 insertion-deletions. Based on the principal component analysis and population structure analysis of these data, the WRC can be classified into three major groups. We applied TASUKE, a multiple genome browser to visualize the different WRC genome sequences, and classified haplotype groups of genes affecting seed characteristics and heading date. TASUKE thus provides access to WRC genotypes as a tool for reverse genetics. We examined the suitability of the compact WRC population for genome-wide association studies (GWASs). Heading date, affected by a large number of quantitative trait loci (QTLs), was not associated with known genes, but several seed-related phenotypes were associated with known genes. Thus, for QTLs of strong effect, the compact WRC performed well in GWAS. This information enables us to understand genetic diversity in 37,000 rice accessions maintained in the Genebank and to find genes associated with different phenotypes. The sequence data have been deposited in DNA Data Bank of Japan Sequence Read Archive (DRA) (Supplementary Table S1).
Identifiants
pubmed: 32101292
pii: 5758272
doi: 10.1093/pcp/pcaa019
pmc: PMC7426033
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
922-932Informations de copyright
� The Author(s) 2020. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.
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