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<p>Rice (<i>Oryza sativa</i> L.) is a vital cereal crop in the world. With societal development, the demand for superior rice quality has increased annually. Chalkiness refers to the white opaque regions in rice endosperm caused by disorganized starch granule structure, which diminishes rice appearance, cooking quality, and processing properties. The chalky grain rate (CGR), defined as the proportion of chalky grains relative to total grains, quantifies chalkiness severity. As a polygenic quantitative trait, chalkiness has been investigated through genome-wide association study (GWAS)—an established method for identifying quantitative trait loci (QTL) using natural populations and high-density single nucleotide polymorphism (SNP) markers. Recent advances in high-throughput genotyping have significantly enhanced GWAS capabilities for dissecting polygenic traits. In this study, we analyzed CGR in 168 representative rice cultivars and conducted GWAS with 3.83 million SNP markers, identifying three associated loci. Through integrated candidate gene analysis, expression profile assay, haplotype assessment, and linkage disequilibrium analysis of locus <i>qPGWC-4-1</i>, we identified <i>CGR1</i> as a key candidate gene. Mechanistically, <i>CGR1</i> may regulate ribosome biogenesis and assembly to influence chalkiness development. The four major haplotypes of <i>CGR1</i> exhibit significant divergence between <i>indica</i> and <i>japonica</i> subspecies. A natural variation at the terminal coding region of <i>CGR1</i> results in the loss of a stop codon. These findings advance our understanding of the genetic regulation of rice chalkiness and provide genetic resources for future quality improvement.</p>

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Genome-wide association study of rice chalky grain rate

  • 期刊论文

  • 发表日期：

    2025年7月9日

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  • Ziang Li,
  • Lin Zhou,
  • Kangwei Ji,
  • Yijie Li,
  • Linhan Li,
  • Sunlu Chen

摘要

Rice (Oryza sativa L.) is a vital cereal crop in the world. With societal development, the demand for superior rice quality has increased annually. Chalkiness refers to the white opaque regions in rice endosperm caused by disorganized starch granule structure, which diminishes rice appearance, cooking quality, and processing properties. The chalky grain rate (CGR), defined as the proportion of chalky grains relative to total grains, quantifies chalkiness severity. As a polygenic quantitative trait, chalkiness has been investigated through genome-wide association study (GWAS)—an established method for identifying quantitative trait loci (QTL) using natural populations and high-density single nucleotide polymorphism (SNP) markers. Recent advances in high-throughput genotyping have significantly enhanced GWAS capabilities for dissecting polygenic traits. In this study, we analyzed CGR in 168 representative rice cultivars and conducted GWAS with 3.83 million SNP markers, identifying three associated loci. Through integrated candidate gene analysis, expression profile assay, haplotype assessment, and linkage disequilibrium analysis of locus qPGWC-4-1, we identified CGR1 as a key candidate gene. Mechanistically, CGR1 may regulate ribosome biogenesis and assembly to influence chalkiness development. The four major haplotypes of CGR1 exhibit significant divergence between indica and japonica subspecies. A natural variation at the terminal coding region of CGR1 results in the loss of a stop codon. These findings advance our understanding of the genetic regulation of rice chalkiness and provide genetic resources for future quality improvement.