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Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies

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...

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Autores principales: Tanaka, N, Shenton, M, Kawahara, Y, Kumagai, M, Sakai, H, Kanamori, H, Yonemaru, J, Fukuoka, S, Sugimoto, K, Ishimoto, M, Wu, J, Ebana, K
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426033/
https://www.ncbi.nlm.nih.gov/pubmed/32101292
http://dx.doi.org/10.1093/pcp/pcaa019
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author Tanaka, N
Shenton, M
Kawahara, Y
Kumagai, M
Sakai, H
Kanamori, H
Yonemaru, J
Fukuoka, S
Sugimoto, K
Ishimoto, M
Wu, J
Ebana, K
author_facet Tanaka, N
Shenton, M
Kawahara, Y
Kumagai, M
Sakai, H
Kanamori, H
Yonemaru, J
Fukuoka, S
Sugimoto, K
Ishimoto, M
Wu, J
Ebana, K
author_sort Tanaka, N
collection PubMed
description 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).
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spelling pubmed-74260332020-08-17 Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies Tanaka, N Shenton, M Kawahara, Y Kumagai, M Sakai, H Kanamori, H Yonemaru, J Fukuoka, S Sugimoto, K Ishimoto, M Wu, J Ebana, K Plant Cell Physiol Regular Papers 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). Oxford University Press 2020-02-26 /pmc/articles/PMC7426033/ /pubmed/32101292 http://dx.doi.org/10.1093/pcp/pcaa019 Text en � The Author(s) 2020. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Regular Papers
Tanaka, N
Shenton, M
Kawahara, Y
Kumagai, M
Sakai, H
Kanamori, H
Yonemaru, J
Fukuoka, S
Sugimoto, K
Ishimoto, M
Wu, J
Ebana, K
Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies
title Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies
title_full Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies
title_fullStr Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies
title_full_unstemmed Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies
title_short Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies
title_sort whole-genome sequencing of the naro world rice core collection (wrc) as the basis for diversity and association studies
topic Regular Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426033/
https://www.ncbi.nlm.nih.gov/pubmed/32101292
http://dx.doi.org/10.1093/pcp/pcaa019
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