Scholarlink

<p><i>Sophora moorcroftiana</i> (Benth.) Baker is an ecologically important shrub dominating the dry valleys of the Yarlung Tsangpo River on the central Qinghai–Tibet Plateau. However, its population-level genomic variation and adaptive signatures remain poorly characterized. Here we used whole-genome resequencing (WGRS) to investigate genetic diversity and population structure in 180 individuals from nine natural populations in Xizang, China. Sequencing at ~ 15× depth yielded 28.27&#xa0;million high-quality SNPs. Within-population genetic diversity was moderate overall, with observed heterozygosity (Ho) ranging from 0.2178 to 0.3002, nucleotide diversity (π) from 0.2435 × 10⁻³ to 0.2789 × 10⁻³, and uniformly positive Tajima’s D values (1.0782–1.2805). Pairwise genetic differentiation was also moderate (mean FST = 0.066; range 0.0375–0.0896). ADMIXTURE, PCA, and a SNP-based phylogenetic tree consistently resolved four genetic clusters that corresponded primarily to major river-basin groupings rather than elevation. TreeMix analysis inferred a directional gene-flow event from the Cheshire population into Rinpung, while linkage disequilibrium decay varied markedly among populations, from rapid decay in Taktse to slow decay in Gonggar, indicating heterogeneous demographic histories. A selective-sweep comparison between two climatically contrasting but elevationally similar sites (Sangzhuzi vs. Sangri) identified 180 candidate genes, with 99 and 81 genes under putative selection in each population, respectively. These genes were significantly enriched in pathways related to flavonoid biosynthesis, terpene metabolism, oxidoreductase activity, and other secondary-metabolism and one-carbon processes associated with UV protection, drought tolerance, and oxidative-stress regulation. Together, our results provide the first genome-wide portrait of genetic diversity and fine-scale population structure in <i>S. moorcroftiana</i>, and highlight how microclimatic heterogeneity and valley-bounded dispersal shape local adaptation in a key dry-valley shrub of the Qinghai–Tibet Plateau.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Genetic diversity analysis of Xizang Sophora Moorcroftiana (Benth.) Baker based on whole-genome resequencing

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年1月10日

查看全文
  • Duozhuoga Mei,
  • Bingzhang Li,
  • Fangfang Fu,
  • Guibin Wang,
  • Shuangyuan Yu,
  • Fuliang Cao,
  • Yuhua Liu,
  • Tingting Dai

摘要

Sophora moorcroftiana (Benth.) Baker is an ecologically important shrub dominating the dry valleys of the Yarlung Tsangpo River on the central Qinghai–Tibet Plateau. However, its population-level genomic variation and adaptive signatures remain poorly characterized. Here we used whole-genome resequencing (WGRS) to investigate genetic diversity and population structure in 180 individuals from nine natural populations in Xizang, China. Sequencing at ~ 15× depth yielded 28.27 million high-quality SNPs. Within-population genetic diversity was moderate overall, with observed heterozygosity (Ho) ranging from 0.2178 to 0.3002, nucleotide diversity (π) from 0.2435 × 10⁻³ to 0.2789 × 10⁻³, and uniformly positive Tajima’s D values (1.0782–1.2805). Pairwise genetic differentiation was also moderate (mean FST = 0.066; range 0.0375–0.0896). ADMIXTURE, PCA, and a SNP-based phylogenetic tree consistently resolved four genetic clusters that corresponded primarily to major river-basin groupings rather than elevation. TreeMix analysis inferred a directional gene-flow event from the Cheshire population into Rinpung, while linkage disequilibrium decay varied markedly among populations, from rapid decay in Taktse to slow decay in Gonggar, indicating heterogeneous demographic histories. A selective-sweep comparison between two climatically contrasting but elevationally similar sites (Sangzhuzi vs. Sangri) identified 180 candidate genes, with 99 and 81 genes under putative selection in each population, respectively. These genes were significantly enriched in pathways related to flavonoid biosynthesis, terpene metabolism, oxidoreductase activity, and other secondary-metabolism and one-carbon processes associated with UV protection, drought tolerance, and oxidative-stress regulation. Together, our results provide the first genome-wide portrait of genetic diversity and fine-scale population structure in S. moorcroftiana, and highlight how microclimatic heterogeneity and valley-bounded dispersal shape local adaptation in a key dry-valley shrub of the Qinghai–Tibet Plateau.