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<p>Gene expression diversity is crucial for crop breeding, yet population genomics has focused primarily on sequence polymorphisms. A single reference genome for RNA-seq cannot handle introgression bias. Here, we conduct RNA-seq for 328 wheat lines, including landraces and elite cultivars from China and the United States, to investigate the expression variation underlying agronomic traits. Leveraging pan-genome resources, we identify 23,296 more transcripts than using the Chinese Spring reference. We construct a pan-gene regulatory atlas through eQTL analysis, revealing the tight regulation of introgressed genes. We identify 299 high-confidence candidate genes for 34 agronomic traits and resistance to 8 <i>Blumeria graminis</i> f. sp. <i>tritici</i> isolates, more than one-fifth of which were absent from the Chinese Spring. Utilizing the Kenong 9204 mutant library, 73.7% of the candidates show significant phenotypic effects. Our work mitigates the reference bias and highlights the impact of breeding-driven directional expression changes on wheat adaptation and improvement.</p>

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Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年12月15日

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  • Zhimeng Zhang,
  • Shengwei Ma,
  • Mou Yin,
  • Caihong Zhao,
  • Xinyu Zhao,
  • Yang Yu,
  • Haojie Wang,
  • Xuanzhao Li,
  • Yaoqi Si,
  • Jianqing Niu,
  • Jingzhong Xie,
  • Limin Wang,
  • Jiajie Wu,
  • Yanming Zhang,
  • Qi Zheng,
  • Shusong Zheng,
  • Ni Jiang,
  • Xigang Liu,
  • Hong-Qing Ling,
  • Fei He

摘要

Gene expression diversity is crucial for crop breeding, yet population genomics has focused primarily on sequence polymorphisms. A single reference genome for RNA-seq cannot handle introgression bias. Here, we conduct RNA-seq for 328 wheat lines, including landraces and elite cultivars from China and the United States, to investigate the expression variation underlying agronomic traits. Leveraging pan-genome resources, we identify 23,296 more transcripts than using the Chinese Spring reference. We construct a pan-gene regulatory atlas through eQTL analysis, revealing the tight regulation of introgressed genes. We identify 299 high-confidence candidate genes for 34 agronomic traits and resistance to 8 Blumeria graminis f. sp. tritici isolates, more than one-fifth of which were absent from the Chinese Spring. Utilizing the Kenong 9204 mutant library, 73.7% of the candidates show significant phenotypic effects. Our work mitigates the reference bias and highlights the impact of breeding-driven directional expression changes on wheat adaptation and improvement.