ArticlePlant communications2022
Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars.
Article in Plant communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 21 citations in OpenAlex.
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- Genome-Wide Association Study Identifies Candidate Genes for Salt Tolerance in Traditional Rice Landraces.Rice (New York, N.Y.) · 2026Article
- Geographic Divergence and Putative Candidate Gene Discovery of Rice Grain Quality in China.Rice (New York, N.Y.) · 2025Article
- Natural variation of GNP2 enhances grain number to benefit rice yield.Nature communications · 2025Article
- BR signalling haplotypes contribute to indica-japonica differentiation for grain yield and quality in rice.Plant biotechnology journal · 2025Article
- Molecular mapping of a novel locus S68 for intrasubspecific hybrid sterility in indica-indica hybrid.Scientific reports · 2025Article
- Genome-wide association study to identify candidate genes for submergence tolerance during rice seed germination.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Refining polyploid breeding in sweet potato through allele dosage enhancement.Nature plants · 2025Article
- Introgression among subgroups is an important driving force for genetic improvement and evolution of the Asian cultivated riceFrontiers in plant science · 2025Review
- Identification of key genes associated with mesocotyl length through a genome-wide association study in rice.Frontiers in plant science · 2025Article
- Time-ordering japonica/geng genomes analysis indicates the importance of large structural variants in rice breeding.Plant biotechnology journal · 2023Article
- A chromosome-level genome assembly of an early matured aromaticFrontiers in plant science · 2023Article
- Introgression of a Complex Genomic Structural Variation Causes Hybrid Male Sterility inInternational journal of molecular sciences · 2022Article
- Natural variation ofFrontiers in plant science · 2022Article
- Candidate gene discovery for salt tolerance in rice (Frontiers in plant science · 2022Article
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Authors and funding
15 authors at 8 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hybridization between Xian/indica (XI) and Geng/japonica (GJ) rice combined with utilization of plant ideotypes has greatly contributed to yield improvements in modern GJ rice in China over the past 50 years. To explore the genomic basis of improved yield and disease resistance in GJ rice, we conducted a large-scale genomic landscape analysis of 816 elite GJ cultivars representing multiple eras of germplasm from China. We detected consistently increasing introgressions from three XI subpopulations into GJ cultivars since the 1980s and found that the XI genome introgressions significantly increased the grain number per panicle (GN) and decreased the panicle number per plant. This contributed to the improvement of plant type during modern breeding, changing multi-tiller plants to moderate tiller plants with a large panicle size and increasing the blast resistance. Notably, we found that key gene haplotypes controlling plant architecture, yield components, and pest and disease resistance, including IPA1, SMG1, DEP3, Pib, Pi-d2, and Bph3, were introduced from XI rice by introgression. By GWAS analysis, we detected a GN-related gene Gnd5, which had been consistently introgressed from XI into GJ cultivars since the 1980s. Gnd5 is a GRAS transcription factor gene, and Gnd5 knockout mutants showed a significant reduction in GN. The estimated genetic effects of genes varied among different breeding locations, which explained the distinct introgression levels of XI gene haplotypes, including Gnd5, DEP3, etc., to these GJ breeding pedigrees. These findings reveal the genomic contributions of introgressions from XI to the trait improvements of GJ rice cultivars and provide new insights for future rice genomic breeding.
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