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<p>The tea plant (<i>Camellia sinensis</i>) is a key cash crop in the genus <i>Camellia</i>. While extensive genetic research has characterized famous tea regions such as Wuyi Mountain, Yunnan, and Fujian, the Shaoyang region—despite being an important yet underexplored tea-producing area in central China with unique germplasm resources adapted to local climatic conditions—has remained genetically poorly characterized. To address this gap, we employed restriction-site associated DNA sequencing (RAD-seq) on 55 Shaoyang germplasm samples, which identified approximately 15.3 million single nucleotide polymorphisms (SNPs). From these, we selected 1,309 high-quality SNPs and conducted in-depth analysis of 1,001 candidate loci, yielding average expected heterozygosity, minor allele frequency (MAF), observed heterozygosity, and polymorphic information content (PIC) values of 0.3668, 0.4220, 0.4841, and 0.4020, respectively. Leveraging these SNP data, we developed 16 kompetitive allele-specific PCR (KASP) markers and employed them to genotype all 55 samples. The resulting DNA fingerprints, constructed using these KASP markers, effectively differentiated all accessions and revealed three major genetic clusters that were both interconnected and distinct. This research represents the initial comprehensive molecular characterization of Shaoyang tea germplasm, providing foundational resources for germplasm conservation, cultivar authentication, and molecular breeding in this unique tea-producing region.</p>

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Analysis of genetic diversity and population structure in Shaoyang tea plants (Camellia sinensis) utilizing KASP markers and SNP loci

  • 期刊论文

  • 发表日期：

    2026年4月16日

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  • Jin Li,
  • Xiao-Yan Qiu,
  • Chang-Qing Xie,
  • Han Tang,
  • Ai-Ming Tang,
  • Jun Tang

摘要

The tea plant (Camellia sinensis) is a key cash crop in the genus Camellia. While extensive genetic research has characterized famous tea regions such as Wuyi Mountain, Yunnan, and Fujian, the Shaoyang region—despite being an important yet underexplored tea-producing area in central China with unique germplasm resources adapted to local climatic conditions—has remained genetically poorly characterized. To address this gap, we employed restriction-site associated DNA sequencing (RAD-seq) on 55 Shaoyang germplasm samples, which identified approximately 15.3 million single nucleotide polymorphisms (SNPs). From these, we selected 1,309 high-quality SNPs and conducted in-depth analysis of 1,001 candidate loci, yielding average expected heterozygosity, minor allele frequency (MAF), observed heterozygosity, and polymorphic information content (PIC) values of 0.3668, 0.4220, 0.4841, and 0.4020, respectively. Leveraging these SNP data, we developed 16 kompetitive allele-specific PCR (KASP) markers and employed them to genotype all 55 samples. The resulting DNA fingerprints, constructed using these KASP markers, effectively differentiated all accessions and revealed three major genetic clusters that were both interconnected and distinct. This research represents the initial comprehensive molecular characterization of Shaoyang tea germplasm, providing foundational resources for germplasm conservation, cultivar authentication, and molecular breeding in this unique tea-producing region.