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<p>Structural variants (SVs) are key drivers of genome plasticity and adaptation in plants, yet their roles in woody perennials remain understudied. Here, we build a comprehensive SV landscape based on a haplotype-resolved chromosomal genome assembly and population resequencing of 302 <i>Populus tomentosa</i> accessions. We reconstruct the evolutionary trajectories of SVs, revealing that they shape subpopulation differentiation through both independent and joint genomic variations. Integrating transcriptomics, we demonstrate that SVs exert broad dosage and <i>cis</i>-acting regulatory effects. Furthermore, segmental duplications drive SV hotspot formation, and these regions are significantly enriched for adaptive signals. SV-based GWAS reveals 61 candidate genes influencing wood-related traits under adaptive selection. Functionally, a causal 54-bp insertion in the <i>PtoERD3</i> promoter balances lignin-mediated growth and drought adaptation. Additionally, we implement an optimized genomic prediction method with an accuracy of 0.94 for wood-related traits. Finally, we propose an SV-based breeding navigation map to improve the accuracy of multi-trait selection.</p>

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Mapping structural variants in Populus tomentosa reveals adaptive signatures and improves prediction of wood properties

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年6月16日

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  • Leishi Zhong,
  • Donghai Zhang,
  • Rui Huang,
  • Jiaxuan Zhou,
  • Wenke Zhang,
  • Lianzheng Li,
  • Zhuoying Jin,
  • Mengjiao Zhang,
  • Chongde Tian,
  • Mingjia Yuan,
  • Yixuan Zhang,
  • Peng Li,
  • Liang Xiao,
  • Mingyang Quan,
  • Deqiang Zhang,
  • Jinlong Li,
  • Qingzhang Du

摘要

Structural variants (SVs) are key drivers of genome plasticity and adaptation in plants, yet their roles in woody perennials remain understudied. Here, we build a comprehensive SV landscape based on a haplotype-resolved chromosomal genome assembly and population resequencing of 302 Populus tomentosa accessions. We reconstruct the evolutionary trajectories of SVs, revealing that they shape subpopulation differentiation through both independent and joint genomic variations. Integrating transcriptomics, we demonstrate that SVs exert broad dosage and cis-acting regulatory effects. Furthermore, segmental duplications drive SV hotspot formation, and these regions are significantly enriched for adaptive signals. SV-based GWAS reveals 61 candidate genes influencing wood-related traits under adaptive selection. Functionally, a causal 54-bp insertion in the PtoERD3 promoter balances lignin-mediated growth and drought adaptation. Additionally, we implement an optimized genomic prediction method with an accuracy of 0.94 for wood-related traits. Finally, we propose an SV-based breeding navigation map to improve the accuracy of multi-trait selection.