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<p>Chromosomal segment substitution lines (CSSLs) serve as ideal materials for creating natural variation, mapping quantitative trait loci (QTL), and enabling breeding by design. In this study, Z668, a CSSL developed in the Nipponbare background with eight substituted segments from the <i>indica</i> restorer line R225 (average length 3.63&#xa0;Mb), exhibited significant dwarfism compared to Nipponbare.&#xa0;Additionally,&#xa0;it showed a 39.9% increase in grain length, a 31.9% increase in the length-to-width ratio, and a 25.9% increase in 1000-grain weight, while grain width decreased by 3.3%. Then, seven QTL associated with grain size were identified in a F<sub>2</sub> population from Nipponbare/Z668. Subsequently, 5 single-segment substitution lines (S1–S5) were developed, and within them were 13 QTL associated with grain size. Genetic analysis and fine-mapping confined <i>qGL3.4</i>, a locus controlling grain length with incomplete dominant inheritance, to a 300&#xa0;kb interval between RM6266 and SSR3 on chromosome 3.&#xa0;Further substitution mapping with six additional single-segment substitution lines (SSSLs) (S6–S12) narrowed <i>qGL3.4</i> down to a 700&#xa0;kb region within the largest substitution interval.&#xa0;Within this region, gene prediction and DNA sequencing revealed five genes with sequence differences between Nipponbare and Z668. Based on qRT-PCR expression analysis, candidate gene 1 (<i>LOC_Os03g42710</i>) and candidate gene 3 (<i>LOC_Os03g42790</i>) were prioritized as candidate genes for <i>qGL3.4</i>.</p>

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QTL analysis of single-segment substitution lines dissected from a rice CSSL-Z668 and fine-mapping of qGL3.4 for grain length

  • 期刊论文

  • 发表日期：

    2025年12月16日

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  • Si-Qian Xiang,
  • Yu-Zhu Tao,
  • Zhao-Peng Yu,
  • Zhuo-Wen Zhao,
  • Han Zhang,
  • Qiao-Long Li,
  • Lu Li,
  • Ao-Ni Xiang,
  • Jing-Hong Xu,
  • Fan Zhang,
  • Xu Yan,
  • Zheng-Lin Yang,
  • Ying-Hua Ling,
  • Chang-Wei Zhang,
  • Guang-Hua He,
  • Fang-Ming Zhao

摘要

Chromosomal segment substitution lines (CSSLs) serve as ideal materials for creating natural variation, mapping quantitative trait loci (QTL), and enabling breeding by design. In this study, Z668, a CSSL developed in the Nipponbare background with eight substituted segments from the indica restorer line R225 (average length 3.63 Mb), exhibited significant dwarfism compared to Nipponbare. Additionally, it showed a 39.9% increase in grain length, a 31.9% increase in the length-to-width ratio, and a 25.9% increase in 1000-grain weight, while grain width decreased by 3.3%. Then, seven QTL associated with grain size were identified in a F2 population from Nipponbare/Z668. Subsequently, 5 single-segment substitution lines (S1–S5) were developed, and within them were 13 QTL associated with grain size. Genetic analysis and fine-mapping confined qGL3.4, a locus controlling grain length with incomplete dominant inheritance, to a 300 kb interval between RM6266 and SSR3 on chromosome 3. Further substitution mapping with six additional single-segment substitution lines (SSSLs) (S6–S12) narrowed qGL3.4 down to a 700 kb region within the largest substitution interval. Within this region, gene prediction and DNA sequencing revealed five genes with sequence differences between Nipponbare and Z668. Based on qRT-PCR expression analysis, candidate gene 1 (LOC_Os03g42710) and candidate gene 3 (LOC_Os03g42790) were prioritized as candidate genes for qGL3.4.