Genome-Wide Resequencing Revealed the Genetic Diversity of Fraxinus platypoda Oliv. in Northwestern China

Fraxinus platypoda Oliv. (Oleaceae), an ecologically and economically valuable tree species with key distribution areas in northwestern China, faces conservation challenges due to its fragmented groups and scarce individual numbers. To investigate the genetic consequences of this demographic crisis, we analyzed 65 individuals from 11 natural groups in this region using whole-genome resequencing. We identified a total of 60,503,092 single nucleotide polymorphisms (SNPs), and after further filtering, retained 3,394,299 SNPs for subsequent analysis. Population structure analysis (Neighbor-Joining tree, STRUCTURE, and kinship coefficients) revealed two distinct genetic clusters (K = 2), with principal component analysis (PCA) confirming this subdivision. Cluster I, composed of eight individuals from Groups 3, 5, 8, and 11, is highly differentiated from Cluster II and may be ancestral to it. Among the 11 groups, Groups 3 and 11 show a high genetic diversity and differentiation, with Tajima’s D > 0, indicating a long evolutionary history and balancing selection. The remaining nine groups have a low diversity, low differentiation, and frequent gene flow, with Tajima’s D < 0, suggesting directional selection. A mantel test showed no significant link between genetic variation and geographic isolation (p = 0.460). The high differentiation of Cluster I and gene flow of Cluster II are maintained by factors like evolutionary history and reproductive systems. Groups 3 and 11 are highlighted as important genetic resources deserving priority protection. This study offers key genomic data for conserving fragmented tree species and future adaptability research.

• Publication year

  2025

• Venue

  Forests

• Publication date

  2025-05-21

• Fields of study

  Not labeled

• Identifiers
  DOI 10.3390/f16050860
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

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