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<p><i>Lithocarpus litseifolius</i> (Hance) Chun, known as “sweet tea”, is a Fagaceae family plant with significant commercial and medicinal value. This study evaluated the genetic diversity and created DNA fingerprints of 38 <i>L. litseifolius</i> germplasm resources collected from 12 provinces across China. Double-digest restriction-site associated DNA sequencing (dd-RAD-seq) was used to develop single nucleotide polymorphism (SNP) markers. A total of 4864 SNPs were selected for characterizing the population genetic analysis. Phylogenetic analysis grouped the 38 <i>L. litseifolius</i> accessions into four main clusters, which was supported by principal component analysis (PCA) results. Structure analysis also divided the accessions into four subpopulations, consistent with the phylogenetic tree and PCA results. KASP primers were designed for 151 SNP loci, of which 108 (71.5%) were successfully converted into Kompetitive allele specific PCR (KASP) markers. The average polymorphism information content (PIC) and observed heterozygosity for these 108 SNPs were 0.366 and 0.321, respectively. A total of 9 KASP marks were successfully developed, demonstrating strong polymorphism and sufficient differentiation capability to distinguish among 38 cultivars of <i>L. litseifolius</i>. The SNP fingerprinting and genetic analysis conducted in this study offer a scientific foundation for screening and identifying <i>L. litseifolius</i> genetic resources, and expanding the genetic knowledge of <i>L. litseifolius</i>.</p>

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Analysis of genetic diversity and development of Kompetitive allele specific PCR (KASP) markers for Lithocarpus litseifolius (Hance) Chun resources based on dd-RAD-Seq

  • 期刊论文

  • 发表日期：

    2025年6月6日

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  • Yuqiao Tian,
  • Shengen Xiao,
  • Yangfeng Chen,
  • Ziqiang Li,
  • Minglei Wang,
  • Xianjin Wu,
  • Yiqing Wang,
  • Zhuwen Xiang,
  • Jin Li,
  • Xiaoyan Qiu

摘要

Lithocarpus litseifolius (Hance) Chun, known as “sweet tea”, is a Fagaceae family plant with significant commercial and medicinal value. This study evaluated the genetic diversity and created DNA fingerprints of 38 L. litseifolius germplasm resources collected from 12 provinces across China. Double-digest restriction-site associated DNA sequencing (dd-RAD-seq) was used to develop single nucleotide polymorphism (SNP) markers. A total of 4864 SNPs were selected for characterizing the population genetic analysis. Phylogenetic analysis grouped the 38 L. litseifolius accessions into four main clusters, which was supported by principal component analysis (PCA) results. Structure analysis also divided the accessions into four subpopulations, consistent with the phylogenetic tree and PCA results. KASP primers were designed for 151 SNP loci, of which 108 (71.5%) were successfully converted into Kompetitive allele specific PCR (KASP) markers. The average polymorphism information content (PIC) and observed heterozygosity for these 108 SNPs were 0.366 and 0.321, respectively. A total of 9 KASP marks were successfully developed, demonstrating strong polymorphism and sufficient differentiation capability to distinguish among 38 cultivars of L. litseifolius. The SNP fingerprinting and genetic analysis conducted in this study offer a scientific foundation for screening and identifying L. litseifolius genetic resources, and expanding the genetic knowledge of L. litseifolius.