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Key message <p>Twenty-one novel QTL for grain protein and fat contents, including six major stable QTL, were identified, and five of the most promising candidate genes were predicted for these traits.</p> Abstract <p>Protein and fat constitute two principal nutrient components in foxtail millet, serving as critical sources of essential amino acids and polyunsaturated fatty acids for human dietary requirements. Dissecting the genetic architecture of grain protein content (GPC) and grain fat content (GFC) is critical for enhancing their quantity and quality through molecular breeding, thereby meeting future nutritional needs. Here, using a biparental recombinant inbred line (RIL) population, we reveal that genetic factors constitute the predominant drivers of phenotypic variation in GPC and GFC, with both traits exhibiting broad-sense heritability estimates exceeding 80%. Furthermore, we identified a significant positive correlation between GPC and GFC. Linkage analysis identified 21 quantitative trait loci (QTL) with six major stable QTL, 72 combined QTL, and 54 epistatic QTL pairs for GPC and GFC across six environments. Phenotype–genotype association analysis revealed significant differences in GPC or GFC among RILs carrying different genotypes for any of the six major stable QTL. Orthologous and pathway-driven analyses identified 14 candidate genes for GPC and five candidate genes for GFC within the identified QTL regions, including five most promising candidates (<i>Seita.5G398800</i>, <i>Seita.5G401000</i>, <i>Seita.9G026300</i>, <i>Seita.5G429700</i>, and <i>Seita.3G015600</i>). Haplotype analysis of 577 foxtail millet accessions revealed strong correlations between two genes (<i>Seita.3G015600</i> and <i>Seita.5G429700</i>) and GFC. These findings broaden our understanding of the genetic basis of grain protein and fat contents in foxtail millet and provide valuable targets for future breeding programs.</p>

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Genetic basis of grain protein and fat contents preliminarily decoded in a foxtail millet biparental recombinant inbred line population

  • 期刊论文

  • 发表日期：

    2025年10月14日

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  • Shaohua Chai,
  • Yan Guo,
  • Chuanxing Wang,
  • Tian Tian,
  • Zhixiu Ma,
  • Yongjiang Wu,
  • Yujie Li,
  • Yajun Li,
  • Hongqi Chen,
  • Jinfeng Gao,
  • Baili Feng,
  • Pu Yang

摘要

Key message

Twenty-one novel QTL for grain protein and fat contents, including six major stable QTL, were identified, and five of the most promising candidate genes were predicted for these traits.

Abstract

Protein and fat constitute two principal nutrient components in foxtail millet, serving as critical sources of essential amino acids and polyunsaturated fatty acids for human dietary requirements. Dissecting the genetic architecture of grain protein content (GPC) and grain fat content (GFC) is critical for enhancing their quantity and quality through molecular breeding, thereby meeting future nutritional needs. Here, using a biparental recombinant inbred line (RIL) population, we reveal that genetic factors constitute the predominant drivers of phenotypic variation in GPC and GFC, with both traits exhibiting broad-sense heritability estimates exceeding 80%. Furthermore, we identified a significant positive correlation between GPC and GFC. Linkage analysis identified 21 quantitative trait loci (QTL) with six major stable QTL, 72 combined QTL, and 54 epistatic QTL pairs for GPC and GFC across six environments. Phenotype–genotype association analysis revealed significant differences in GPC or GFC among RILs carrying different genotypes for any of the six major stable QTL. Orthologous and pathway-driven analyses identified 14 candidate genes for GPC and five candidate genes for GFC within the identified QTL regions, including five most promising candidates (Seita.5G398800, Seita.5G401000, Seita.9G026300, Seita.5G429700, and Seita.3G015600). Haplotype analysis of 577 foxtail millet accessions revealed strong correlations between two genes (Seita.3G015600 and Seita.5G429700) and GFC. These findings broaden our understanding of the genetic basis of grain protein and fat contents in foxtail millet and provide valuable targets for future breeding programs.