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<p>Ginkgo (<i>Ginkgo biloba</i> L.), a living relict of gymnosperms, possesses remarkable ecological, medicinal, and economic importance. Sustaining its conservation and advancing genetic improvement require a comprehensive understanding of genomic variation. However, progress in breeding has been constrained by the scarcity of informative molecular markers and limited knowledge of its genetic diversity. In this study, a genome-wide survey of simple sequence repeats (SSRs) was conducted with evaluation of the genetic diversity of 205 accessions collected from diverse geographic regions of China. A total of 2,374,726 SSR loci were identified across the 12 chromosomes, predominantly di- and tri-nucleotide repeats. Functional enrichment analysis showed that SSR-containing coding regions were associated with biological processes such as gibberellin signaling, RNA metabolism, and plant morphogenesis, suggesting potential regulatory roles in key developmental and metabolic pathways. To validate the in silico predictions, 20 polymorphic SSR markers were experimentally confirmed, providing deeper insights into the genetic variation of ginkgo germplasm. Across all SSR markers, the mean observed heterozygosity and polymorphism information content were 0.525 and 0.534, respectively. Population structure, phylogenetic, and principal component analyses revealed two well-defined genetic clusters largely corresponding to geographic origin. Furthermore, a core set of 32 accessions (15.61% of the total accessions) captured nearly the full allelic diversity of the collection, offering a strategic resource for conservation, association genetic research, and breeding efforts. Collectively, these findings provide genome-wide insights into SSR architecture and genetic diversity, facilitating marker-assisted selection and sustainable utilization of ginkgo.</p>

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Genome-wide characterization of simple sequence repeat markers and assessment of genetic diversity in ginkgo (Ginkgo biloba L.)

  • 期刊论文

  • 发表日期：

    2026年3月18日

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  • Yuehan Wang,
  • Hao Huang,
  • Xin Yang,
  • Weijie Gao,
  • Yuhua Liu,
  • Fangfang Fu,
  • Guibin Wang,
  • Gaiping Wang,
  • Fuliang Cao,
  • Xiaoming Yang

摘要

Ginkgo (Ginkgo biloba L.), a living relict of gymnosperms, possesses remarkable ecological, medicinal, and economic importance. Sustaining its conservation and advancing genetic improvement require a comprehensive understanding of genomic variation. However, progress in breeding has been constrained by the scarcity of informative molecular markers and limited knowledge of its genetic diversity. In this study, a genome-wide survey of simple sequence repeats (SSRs) was conducted with evaluation of the genetic diversity of 205 accessions collected from diverse geographic regions of China. A total of 2,374,726 SSR loci were identified across the 12 chromosomes, predominantly di- and tri-nucleotide repeats. Functional enrichment analysis showed that SSR-containing coding regions were associated with biological processes such as gibberellin signaling, RNA metabolism, and plant morphogenesis, suggesting potential regulatory roles in key developmental and metabolic pathways. To validate the in silico predictions, 20 polymorphic SSR markers were experimentally confirmed, providing deeper insights into the genetic variation of ginkgo germplasm. Across all SSR markers, the mean observed heterozygosity and polymorphism information content were 0.525 and 0.534, respectively. Population structure, phylogenetic, and principal component analyses revealed two well-defined genetic clusters largely corresponding to geographic origin. Furthermore, a core set of 32 accessions (15.61% of the total accessions) captured nearly the full allelic diversity of the collection, offering a strategic resource for conservation, association genetic research, and breeding efforts. Collectively, these findings provide genome-wide insights into SSR architecture and genetic diversity, facilitating marker-assisted selection and sustainable utilization of ginkgo.