ArticleJournal of advanced research2022
Selective and comparative genome architecture of Asian cultivated rice (Oryza sativa L.) attributed to domestication and modern breeding.
Article in Journal of advanced research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Whole-Genome Variants Resource of 144 Oryza rufipogon Accessions.Scientific data · 2026Article
- Different genomic footprint of small insertion-deletion and structural variants determines the genetic divergence of indica and japonica rice.BMC genomics · 2026Article
- Identification of QTLs and genes regulating panicle number through genome-wide association studies inFrontiers in plant science · 2026Article
- Natural variation in OsTPS8 confers differential regulation of chalkiness and seed vigor in indica and japonica rice.Nature genetics · 2026Article
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- Identification of submergence tolerance QTLs/genes during seed germination in 432 rice varieties by GWAS.BMC plant biology · 2025Article
- A pangenome reference of wild and cultivated rice.Nature · 2025Article
- The selection and application of tiller number QTLs in modern wheat breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Comprehensive Analysis ofGenes · 2025Article
- Introgression among subgroups is an important driving force for genetic improvement and evolution of the Asian cultivated riceFrontiers in plant science · 2025Review
- Integrating QTL mapping, BSA-seq and RNA-seq to identify candidate genes regulating seed storability from Dongxiang wild rice.Frontiers in plant science · 2025Article
- Article
- Article
- A rice variation map derived from 10 548 rice accessions reveals the importance of rare variants.Nucleic acids research · 2023Article
- Intra-Varietal Diversity and Its Contribution to Wheat Evolution, Domestication, and Improvement in Wheat.International journal of molecular sciences · 2023Article
- Evolution of different rice ecotypes and genetic basis of flooding adaptability in Deepwater rice by GWAS.BMC plant biology · 2022Article
- Genome-Wide Association Study Reveals Candidate Genes for Root-Related Traits in Rice.Current issues in molecular biology · 2022Article
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35 authors.
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Abstract
introductionRice, Oryza sativa L. (Os), is one of the oldest domesticated cereals that has also gone through extensive improvement in modern breeding.
objectivesHow rice was domesticated and impacted by modern breeding.
methodsWe performed comprehensive analyses of genomic sequences of 504 accessions of Os and 456 accessions of O. rufipogon/O. nivara (Or).
resultsThe natural selection on Or before domestication and the natural and artificial selection during domestication together shaped the well-differentiated genomes of two subspecies, geng(j) (japonica) and xian(i) (indica), while breeding has made apparent genomic imprints between landrace and modern varieties of each subspecies, and also between primary modern and advanced modern varieties of xian(i). Selection during domestication and breeding left genome-wide selective signals covering ∼ 22.8 % and ∼ 8.6 % of the Os genome, significantly reduced within-population genomic diversity by ∼ 22 % in xian(i) and ∼ 53 % in geng(j) plus more pronounced subspecific differentiation. Only ∼ 10 % reduction in the total genomic diversity was observed between the Os and Or populations, indicating domestication did not suffer severe genetic bottleneck.
conclusionOur results revealed clear differentiation of the Or accessions into three large populations, two of which correspond to the well-differentiated Os subspecies, geng(j) and xian(i). Improved productivity and common changes in the same suit of adaptive traits in xian(i) and geng(j) during domestication and breeding resulted apparently from compensatory and convergent selections for different genes/alleles acting in the common KEGG terms and/or same gene families, and thus maintaining or even increasing the within population diversity and subspecific differentiation of Os, while more genes/alleles of novel function were selected during domestication than modern breeding. Our results supported the multiple independent domestication of Os in Asia and suggest the more efficient utilization of the rich diversity within Os by exploiting inter-subspecific and among population diversity in future rice improvement.
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