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

Abstract

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).

Investigation of the Genetic Diversity of a Rice Core Collection of Japanese Landraces using Whole-Genome Sequencing

“…2013 ), and JRC21, 43 and 44 carry a 1-bp deletion in DTH8 ( Table�1 ). JRC21, 42, 43 and 44 were categorized as indica in the phylogenetic tree based on WGS data ( Fig.�1 ), and these two mutations were also detected only from indica accessions in the WRC ( Tanaka et�al. 2020 ).…”

“…S1–S3). Previously, GWAS with WRC only detected high impact QTLs, such as Rc , waxy and GS3 ( Tanaka et�al. 2020 ).…”

“…An 8-bp deletion on exon 7 in Hd2 was commonly observed both in the JRC and WRC; however, it was only distributed in accessions categorized into indica group both in JRC and WRC ( Table�1 ) ( Tanaka et�al. 2020 ).…”

“…Phenotyping of such large populations is time-consuming. Previously, Tanaka et�al. (2020) reported that several peaks related to seed traits were detected by using the WRC core collection in GWAS and these peaks were close to well-known genes, such as Rc , waxy and GS3 .…”

“…(2020) reported that several peaks related to seed traits were detected by using the WRC core collection in GWAS and these peaks were close to well-known genes, such as Rc , waxy and GS3 . Although the WRC represents a highly structured population, for some traits, this core collection that consists of only 69 rice cultivars could match the performance of a larger GWAS population ( Tanaka et�al. 2020 ).…”