ArticlePlant biotechnology journal2023
Time-ordering japonica/geng genomes analysis indicates the importance of large structural variants in rice breeding.
Article in Plant biotechnology journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 25 citations in OpenAlex.
- Different genomic footprint of small insertion-deletion and structural variants determines the genetic divergence of indica and japonica rice.BMC genomics · 2026Article
- Pangenome analysis reveals the genetic mechanism underlying high-altitude adaptation in Qinghai-Xizang (Tibet) Plateau Rhododendron.Journal of integrative plant biology · 2026Article
- Dissecting Agronomically favorable genotypes in temperate japonica rice via haplotype analysis of a Japan-MAGIC population.The Plant journal : for cell and molecular biology · 2026Article
- Feeding the future: Genetic gatekeepers provide more rice grains per plant.Plant physiology · 2025Article
- Comprehensive Analysis ofGenes · 2025Article
- CRISPR/Cas9- and Cas3-mediated modification of copy number variation in rice.Frontiers in genome editing · 2025Article
- Introgression among subgroups is an important driving force for genetic improvement and evolution of the Asian cultivated riceFrontiers in plant science · 2025Review
- Article
- Genome evolution and diversity of wild and cultivated rice species.Nature communications · 2024Article
- Pan-genome analysis of 13 Spinacia accessions reveals structural variations associated with sex chromosome evolution and domestication traits in spinach.Plant biotechnology journal · 2024Article
- Enhancing grain shape, thermotolerance, and alkaline tolerance via Gγ protein manipulation in rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Article
- A comprehensive lettuce variation map reveals the impact of structural variations in agronomic traits.BMC genomics · 2023Article
- Photoperiod Genes Contribute to Daylength-Sensing and Breeding in Rice.Plants (Basel, Switzerland) · 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
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Authors and funding
25 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Temperate japonica/geng (GJ) rice yield has significantly improved due to intensive breeding efforts, dramatically enhancing global food security. However, little is known about the underlying genomic structural variations (SVs) responsible for this improvement. We compared 58 long-read assemblies comprising cultivated and wild rice species in the present study, revealing 156 319 SVs. The phylogenomic analysis based on the SV dataset detected the putatively selected region of GJ sub-populations. A significant portion of the detected SVs overlapped with genic regions were found to influence the expression of involved genes inside GJ assemblies. Integrating the SVs and causal genetic variants underlying agronomic traits into the analysis enables the precise identification of breeding signatures resulting from complex breeding histories aimed at stress tolerance, yield potential and quality improvement. Further, the results demonstrated genomic and genetic evidence that the SV in the promoter of LTG1 is accounting for chilling sensitivity, and the increased copy numbers of GNP1 were associated with positive effects on grain number. In summary, the current study provides genomic resources for retracing the properties of SVs-shaped agronomic traits during previous breeding procedures, which will assist future genetic, genomic and breeding research on rice.
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