ArticlePlant biotechnology journal2021
Genome-wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness.
Article in Plant biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 41 citations in OpenAlex.
- Multi-parent mapping reveals epistatic architecture and elite haplotypes for multi-trait improvement in cotton.Genome biology · 2026Article
- A Natural Major Module Confers the Trade-Off between Phenotypic Mean and Plasticity of Grain Chalkiness in Rice.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Natural variation of an E3 ubiquitin ligase encoding gene Chalk9 regulates grain chalkiness in rice.Nature communications · 2025Article
- TheInternational journal of molecular sciences · 2025Article
- The LCG1-OsBP5/OsEBP89-Wx module regulates the grain chalkiness and taste quality in rice.Plant biotechnology journal · 2025Article
- Extreme-Phenotype Genome-Wide Association Analysis for Growth Traits in Spotted Sea Bass (Animals : an open access journal from MDPI · 2024Article
- Modern Plant Breeding Techniques in Crop Improvement and Genetic Diversity: From Molecular Markers and Gene Editing to Artificial Intelligence-A Critical Review.Plants (Basel, Switzerland) · 2024Review
- Improving Rice Quality by Regulating the Heading Dates of Rice Varieties without Yield Penalties.Plants (Basel, Switzerland) · 2024Article
- Pyramiding of Low Chalkiness QTLs Is an Effective Way to Reduce Rice Chalkiness.Rice (New York, N.Y.) · 2024Article
- Genome-wide association mapping of quantitative trait loci for chalkiness-related traits in rice (Frontiers in genetics · 2024Article
- Unravelling marker trait associations linking nutritional value with pigmentation in rice seed.The plant genome · 2023Article
- High Daytime Temperature Responsive MicroRNA Profiles in Developing Grains of Rice Varieties with Contrasting Chalkiness.International journal of molecular sciences · 2023Article
- Mapping of qChalk1 controlling grain chalkiness in japonica rice.Molecular biology reports · 2023Article
- Molecular mapping and characterization of QTLs for grain quality traits in a RIL population of US rice under high nighttime temperature stress.Scientific reports · 2023Article
- Unraveling the genetics underlying micronutrient signatures of diversity panel present in brown rice through genome-ionome linkages.The Plant journal : for cell and molecular biology · 2023Article
- Genome-wide association mapping and gene expression analysis reveal candidate genes for grain chalkiness in rice.Frontiers in plant science · 2023Article
- Genetic architecture of head rice and rice chalky grain percentages using genome-wide association studies.Frontiers in plant science · 2023Article
- Low Light Stress Increases Chalkiness by Disturbing Starch Synthesis and Grain Filling of Rice.International journal of molecular sciences · 2022Article
- Verifying the Breeding Value of A Rare Haplotype ofPlants (Basel, Switzerland) · 2022Article
- Reconstruction of the High Stigma Exsertion Rate Trait in Rice by Pyramiding Multiple QTLs.Frontiers in plant science · 2022Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
Abstract
Rice varieties whose quality is graded as excellent have a lower percent grain chalkiness (PGC) of two per cent and below with higher whole grain yields upon milling, leading to higher economic returns for farmers. We have conducted a genome-wide association study (GWAS) using a combined population panel of indica and japonica rice varieties, and identified a total of 746 single nucleotide polymorphisms (SNPs) that were strongly associated with the chalk phenotype, covered 78 Quantitative Trait Loci (QTL) regions. Among them, 21 were high-value QTLs, as they explained at least 10 % of the phenotypic variance for PGC. A combined epistasis and GWAS was applied to dissect the genetics of the complex chalkiness trait, and its regulatory cascades were validated using gene regulatory networks. Promising novel epistatic interactions were found between the loci of chromosomes 6 (PGC6.1) and 7 (PGC7.8) that contributed to lower PGC. Based on haplotype mining only a few modern rice varieties confounded with a lower chalkiness, and they possess several PGC QTLs. The importance of PGC6.1 was validated through multi-parent advanced generation intercrosses and several low-chalk lines possessing superior haplotypes were identified. The results of this investigation have deciphered the underlying genetic networks that can reduce PGC to 2%, and will thus support future breeding programs to improve the grain quality of elite genetic material with high-yielding potentials.
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