ArticleBMC genomics2026
Genetic diversity analysis of Xizang Sophora Moorcroftiana (Benth.) Baker based on whole-genome resequencing.
Article in BMC genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
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.
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