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<p>Grain chalkiness is a key determinant of rice quality and market value, yet the genetic mechanisms underlying this complex trait remain to be fully elucidated. In this study, we integrated bulked segregant analysis coupled with whole-genome resequencing (BSA-seq) and Kompetitive Allele-Specific PCR (KASP) assays to identify quantitative trait loci (QTLs) and preliminary candidate genes controlling rice grain chalkiness. An F<sub>2</sub> mapping population derived from a cross between the <i>indica</i> rice lines YD86 and YH2103 was phenotyped for chalkiness-related traits and subjected to genomic analysis. Through systematic mapping, we identified a novel QTL on chromosome 7, designated as qDEC7.01, which is significantly associated with grain chalkiness. Preliminary candidate genes within this interval were predicted based on functional annotation and polymorphic single-nucleotide polymorphisms (SNPs) between the parental lines. These findings provide valuable genetic resources for fine mapping, gene cloning, and the development of rice varieties with reduced chalkiness.</p>

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Conjunctive analysis of BSA-Seq and KASP markers unveils the preliminary candidate genes controlling chalkiness of rice grain

  • 期刊论文

  • 发表日期：

    2026年5月22日

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  • Mingfeng Tang,
  • Zhongwei Wang,
  • Tingting Zeng,
  • Tingting Fu,
  • Wei Zhang,
  • Yongchuan Huang,
  • Yanjie Yao,
  • Yongyang Fan,
  • Xianwei Zhang

摘要

Grain chalkiness is a key determinant of rice quality and market value, yet the genetic mechanisms underlying this complex trait remain to be fully elucidated. In this study, we integrated bulked segregant analysis coupled with whole-genome resequencing (BSA-seq) and Kompetitive Allele-Specific PCR (KASP) assays to identify quantitative trait loci (QTLs) and preliminary candidate genes controlling rice grain chalkiness. An F2 mapping population derived from a cross between the indica rice lines YD86 and YH2103 was phenotyped for chalkiness-related traits and subjected to genomic analysis. Through systematic mapping, we identified a novel QTL on chromosome 7, designated as qDEC7.01, which is significantly associated with grain chalkiness. Preliminary candidate genes within this interval were predicted based on functional annotation and polymorphic single-nucleotide polymorphisms (SNPs) between the parental lines. These findings provide valuable genetic resources for fine mapping, gene cloning, and the development of rice varieties with reduced chalkiness.