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<p>Chinese fir (<i>Cunninghamia lanceolata</i>) is a cornerstone timber species in China. It has been cultivated for millennia and introduced globally. Here, we present a high-quality chromosome-scale reference genome, revealing a recent burst of transposable elements during the Pliocene. While no whole-genome duplications are observed, tandem and proximal gene duplications expand families linked to environmental adaptation. Population resequencing of 87 provenance accessions and 15 ancient trees, including specimens planted in 1176 by the esteemed Neo-Confucianist Zhu Xi, reveals three principal phylogenetic groups corresponding to major geographic regions: the Yangtze River basin (group I), the Wuyi-Nanling region (group II; superior provenance), and regions along the Hakka migration route (group III). The Wuyi Mountains likely represent a historical hub of germplasm exchange and genetic connectivity. Analysis of 90 advanced-generation seed orchard progeny&#xa0;individuals and 13 elite clones reveals a marked bias in modern breeding practices toward specific lineages (primarily group II), whereas group I, which includes nearly all ancient trees, remains underutilized. These findings provide a genomic framework for understanding the domestication continuum, anthropogenic reshaping, and lineage-biased selection in <i>C. lanceolata</i>, offering insights for sustainable improvement and conservation.</p>

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Genomic insights into the improvement of Chinese fir from ancient domestication continuum to modern breeding

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年5月29日

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  • Zhaodong Hao,
  • Long Wang,
  • Renhua Zheng,
  • Lu Lu,
  • Yingxuan Ma,
  • Ye Lu,
  • Hua Wu,
  • Ye Peng,
  • Tielong Cheng,
  • Xiaohui Zhang,
  • Sanyuan Liu,
  • Shunde Su,
  • Zezhong Lin,
  • Liming Yang,
  • Pengkai Wang,
  • Fuhui Liu,
  • Jinhua Huang,
  • Daiquan Ye,
  • Yong Li,
  • Fuming Xiao,
  • Thomas Laux,
  • Sihai Yang,
  • Jisen Shi,
  • Jinhui Chen

摘要

Chinese fir (Cunninghamia lanceolata) is a cornerstone timber species in China. It has been cultivated for millennia and introduced globally. Here, we present a high-quality chromosome-scale reference genome, revealing a recent burst of transposable elements during the Pliocene. While no whole-genome duplications are observed, tandem and proximal gene duplications expand families linked to environmental adaptation. Population resequencing of 87 provenance accessions and 15 ancient trees, including specimens planted in 1176 by the esteemed Neo-Confucianist Zhu Xi, reveals three principal phylogenetic groups corresponding to major geographic regions: the Yangtze River basin (group I), the Wuyi-Nanling region (group II; superior provenance), and regions along the Hakka migration route (group III). The Wuyi Mountains likely represent a historical hub of germplasm exchange and genetic connectivity. Analysis of 90 advanced-generation seed orchard progeny individuals and 13 elite clones reveals a marked bias in modern breeding practices toward specific lineages (primarily group II), whereas group I, which includes nearly all ancient trees, remains underutilized. These findings provide a genomic framework for understanding the domestication continuum, anthropogenic reshaping, and lineage-biased selection in C. lanceolata, offering insights for sustainable improvement and conservation.