ArticlePlant & cell physiology2020
Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies.
Article in Plant & cell physiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
- Structural, genetic, and adaptive basis of superhydrophobicity in rice leaves.Plant physiology · 2026Article
- Rice Annotation Project Database (RAP-DB): Literature-Curated Gene Annotation and Integrated Omics Resources for Rice Functional Genomics and Molecular Breeding.Rice (New York, N.Y.) · 2026Article
- Genomic insights into the medieval cultivation history of influential high-yielding Asian rice.Scientific reports · 2026Article
- Article
- Uncrossing the 'X': Characterization of alternative alleles for KSLX in Oryza.Phytochemistry · 2025Article
- Biomarker genes for model-based prediction of drought-stress perception levels in rice.BMC plant biology · 2025Article
- GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data.Database : the journal of biological databases and curation · 2025Article
- Gene Pyramiding Strategies for Sink Size and Source Capacity for High-Yield Japonica Rice Breeding.Rice (New York, N.Y.) · 2025Review
- Genome-wide analysis of Udai21: Unraveling the genetic basis of superior eating quality in rice.PloS one · 2025Article
- Genetic dissection of resistance to Phytophthora sojae using genome-wide association and linkage analysis in soybean [Glycine max (L.) Merr.].TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Transcriptome-based prediction for polygenic traits in rice using different gene subsets.BMC genomics · 2024Article
- Impact of rice GENERAL REGULATORY FACTOR14h (GF14h) on low-temperature seed germination and its application to breeding.PLoS genetics · 2024Article
- Development of SNP genotyping assays for heading date in rice.Breeding science · 2024Article
- Metabolic diversity analysis and genome wide assessment of oxalate accumulation in the leaves of rice (Plant biotechnology (Tokyo, Japan) · 2024Article
- Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice.Rice (New York, N.Y.) · 2023Article
- Genetics of chilling response at early growth stage in rice: a recessive gene for tolerance and importance of acclimation.AoB PLANTS · 2023Article
- Elucidation of genetic variation and population structure of melon genetic resources in the NARO Genebank, and construction of the World Melon Core Collection.Breeding science · 2023Article
- Development of 12 sets of chromosome segment substitution lines that enhance allele mining in Asian cultivated rice.Breeding science · 2023Article
- A developed system to extract specific responses of increment length in rice shoots under gradient changes in nitrogen concentration regimes.Plant biotechnology (Tokyo, Japan) · 2023Article
- Introduction of Genome Editing Reagents and Genotyping of Derived Edited Alleles in Soybean (Glycine max (L.) Merr.).Methods in molecular biology (Clifton, N.J.) · 2023Article
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12 authors.
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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).
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