Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies
Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies
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DOI：
10.1093/pcp/pcaa019
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发表时间：
2020-05-01
影响因子：
4.9
通讯作者：
Ebana, K.
中科院分区：
文献类型：
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作者：
Tanaka, N.;Shenton, M.;Ebana, K.
基因库为作物改良提供了获取各种材料的途径。为了有效地利用和评价这些资源，已经建立了核心收藏，如国家农业和粮食研究组织基因库中的世界稻米核心收藏。由于WRC由69个具有高度遗传多样性的品种组成，它已被用于超过300个项目。为了更深入地调查现有的WRC数据，并进一步促进使用Genebank水稻种质资源的研究，我们对这69个种质资源进行了全基因组重测序，通过对水稻ssp.日本晴基因组。我们总共获得了2，805，329个单核苷酸多态性（SNP）和357，639个插入-缺失。根据主成分分析和种群结构分析，这些数据的WRC可以分为三个主要群体。我们应用TASUKE，一个多基因组浏览器来可视化不同的WRC基因组序列，并对影响种子特性和抽穗期的基因的单倍型组进行分类。因此，TASUKE提供了WRC基因型作为反向遗传学的工具。我们研究了紧凑的WRC人口全基因组关联研究（GWAS）的适用性。抽穗期受大量数量性状位点（QTL）的影响，与已知基因无关，但与种子相关的几种表型与已知基因相关。因此，对于强效应的QTL，紧凑型WRC在GWAS中表现良好。这些信息使我们能够了解Genebank中保存的37，000份水稻种质的遗传多样性，并找到与不同表型相关的基因。序列数据已保存在DNA数据库Japan Sequence Read Archive（日本序列读取档案馆）（补充表S1）。
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).