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<p>Advanced genotyping technologies for understanding the genetic intricacies of fungal pathogens have broad applications in crop protection. Here, we introduce a novel genotyping-by-target sequencing (GBTS) chip, a versatile tool designed for comprehensive genetic analysis of fungal populations. This technology overcomes key limitations of traditional molecular marker-based approaches by providing a more efficient, economic, and streamlined solution while bypassing the need for labor-intensive pathogen culturing. We demonstrate its utility by applying it to profile <i>Puccinia</i> <i>striiformis</i> f. sp. <i>tritici</i> (<i>Pst</i>), the causal agent of wheat stripe rust. Our analysis involved 225 infected leaves collected from wheat fields in the northwest oversummering region for <i>Pst</i> in China. We delineated three genetic groups and revealed frequent gene flow, with closer connectivity between Qinghai and Gansu than either province with Ningxia, a pattern consistent with wind trajectory models. These findings illustrate a highly connected regional epidemic system and highlight the value of the GBTS chip for genomic epidemiology. The methodology established here provides a scalable framework for population genetic studies in other fungal pathogens, promising to enhance disease monitoring and management across agricultural systems.</p>

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The development and validation of a genotyping-by-target sequencing chip for fungal population genetic analysis

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年1月19日

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  • Haohao Yan,
  • Zhe Ma,
  • Qiang Yao,
  • Shiqin Cao,
  • Qiuzhen Jia,
  • Jiaqi Li,
  • Jie Zhao,
  • Weiyi Yan,
  • Juhong Ma,
  • Wen Chen,
  • Bo Zhang,
  • Xuezhen Ma,
  • Xiaojie Wang,
  • Dejun Han,
  • Zhensheng Kang,
  • Lili Huang,
  • Qingdong Zeng

摘要

Advanced genotyping technologies for understanding the genetic intricacies of fungal pathogens have broad applications in crop protection. Here, we introduce a novel genotyping-by-target sequencing (GBTS) chip, a versatile tool designed for comprehensive genetic analysis of fungal populations. This technology overcomes key limitations of traditional molecular marker-based approaches by providing a more efficient, economic, and streamlined solution while bypassing the need for labor-intensive pathogen culturing. We demonstrate its utility by applying it to profile Puccinia striiformis f. sp. tritici (Pst), the causal agent of wheat stripe rust. Our analysis involved 225 infected leaves collected from wheat fields in the northwest oversummering region for Pst in China. We delineated three genetic groups and revealed frequent gene flow, with closer connectivity between Qinghai and Gansu than either province with Ningxia, a pattern consistent with wind trajectory models. These findings illustrate a highly connected regional epidemic system and highlight the value of the GBTS chip for genomic epidemiology. The methodology established here provides a scalable framework for population genetic studies in other fungal pathogens, promising to enhance disease monitoring and management across agricultural systems.