ArticleBMC biology2018
Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci.
Article in BMC biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed.
- Functional conservation and diversity of phytochrome B and its potential applications in crop improvement.Plant communications · 2026Review
- Integrating Multi-omics Analysis to Decipher the Genetic Basis of Heterosis in Xieyou9308.Rice (New York, N.Y.) · 2025Article
- Effects ofPlants (Basel, Switzerland) · 2025Article
- Feeding the future: Genetic gatekeepers provide more rice grains per plant.Plant physiology · 2025Article
- Enhancing grain shape, thermotolerance, and alkaline tolerance via Gγ protein manipulation in rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud.G3 (Bethesda, Md.) · 2023Article
- Identification of QTL for kernel weight and size and analysis of the pentatricopeptide repeat (PPR) gene family in cultivated peanut (Arachis hypogaea L.).BMC genomics · 2023Article
- QTL mapping and identification of candidate genes for cold tolerance at the germination stage in wild rice.Genes & genomics · 2023Article
- Double Mutation ofInternational journal of molecular sciences · 2023Article
- The Pyramiding of Elite Allelic Genes Related to Grain Number Increases Grain Number per Panicle Using the Recombinant Lines Derived fromInternational journal of molecular sciences · 2023Article
- A chromosome-level genome assembly of an early matured aromaticFrontiers in plant science · 2023Article
- Time-ordering japonica/geng genomes analysis indicates the importance of large structural variants in rice breeding.Plant biotechnology journal · 2023Article
- The ties of brotherhood between japonica and indica rice for regional adaptation.Science China. Life sciences · 2022Article
- Bin mapping-based QTL analyses using three genetic populations derived from indica-japonica crosses uncover multiple grain shape heterosis-related loci in rice.The plant genome · 2022Article
- Article
- Raman Fingerprints of Rice Nutritional Quality: A Comparison between Japanese Koshihikari and Internationally Renowned Cultivars.Foods (Basel, Switzerland) · 2021Article
- Systems biology for crop improvement.The plant genome · 2021Review
- Proteomics and Post-Translational Modifications of Starch Biosynthesis-Related Proteins in Developing Seeds of Rice.International journal of molecular sciences · 2021Review
- Elucidation of the relationship between yield and heading date using CRISPR/Cas9 system-induced mutation in the flowering pathway across a large latitudinal gradient.Molecular breeding : new strategies in plant improvement · 2021Article
- High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice.Frontiers in plant science · 2021Article
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9 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundTwo of the most widely cultivated rice strains are Oryza sativa indica and O. sativa japonica, and understanding the genetic basis of their agronomic traits is of importance for crop production. These two species are highly distinct in terms of geographical distribution and morphological traits. However, the relationship among genetic background, ecological conditions, and agronomic traits is unclear.
resultsIn this study, we performed the de novo assembly of a high-quality genome of SN265, a cultivar that is extensively cultivated as a backbone japonica parent in northern China, using single-molecule sequencing. Recombinant inbred lines (RILs) derived from a cross between SN265 and R99 (indica) were re-sequenced and cultivated in three distinct ecological conditions. We identify 79 QTLs related to 15 agronomic traits. We found that several genes underwent functional alterations when the ecological conditions were changed, and some alleles exhibited contracted responses to different genetic backgrounds. We validated the involvement of one candidate gene, DEP1, in determining panicle length, using CRISPR/Cas9 gene editing.
conclusionsThis study provides information on the suitable environmental conditions, and genetic background, for functional genes in rice breeding. Moreover, the public availability of the reference genome of northern japonica SN265 provides a valuable resource for plant biologists and the genetic improvement of crops.
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