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<p>Yunnan Province has been widely recognized as an important center of origin, domestication, and diversification of tea plants, and its large-leaf tea (<i>Camellia sinensis</i> var. <i>assamica</i>) germplasm represents a valuable resource for tea conservation and breeding. In this study, 216 large-leaf tea accessions collected from four major tea-producing regions of Yunnan Province, including Baoshan (BS), Lincang (LC), Menghai County in Xishuangbanna (MH), and Pu’er (PE), were analyzed using 20 polymorphic simple sequence repeat (SSR) markers. The SSR loci showed relatively high polymorphism, with mean values of 6.53 for the number of alleles (<i>Na</i>), 3.11 for the effective number of alleles (<i>Ne</i>), 1.17 for Shannon’s information index (<i>I</i>), and 0.546 for expected heterozygosity (<i>He</i>). Among the four populations, MH had a relatively high mean number of alleles, whereas PE had the highest Shannon’s information index and expected heterozygosity. Analysis of molecular variance (AMOVA) showed that 98% of the genetic variation occurred within populations and 2% among populations. The overall genetic differentiation coefficient (<i>Fst</i> = 0.027) and pairwise <i>Fst</i> values ranging from 0.013 to 0.034 were consistent with weak genetic differentiation. The <i>Nm</i> estimate derived from <i>Fst</i> was consistent with substantial historical allele sharing, shared ancestry, or human-mediated germplasm movement, but should not be interpreted as a direct measure of contemporary gene flow. The Evanno method supported K = 3 as the primary STRUCTURE solution, whereas the K = 4 pattern and discriminant analysis of principal components suggested subtle genetic distinctiveness of PE and close genetic affinity between BS and LC. These findings suggest that Yunnan large-leaf tea germplasm contains considerable SSR-based genetic diversity but exhibits weak regional differentiation. The observed pattern may reflect the combined effects of seed-based propagation, natural crossing, shared ancestry, and long-term human-mediated movement of planting materials. This study provides useful information for the conservation, management, and breeding utilization of Yunnan large-leaf tea germplasm.</p>

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Simple sequence repeat (SSR) marker-based genetic diversity and population structure of large-leaf tea germplasm across four major tea-producing regions of Yunnan, China

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  • 发表日期：

    2026年7月31日

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  • Qihuan Ding,
  • Wuxiang Fu,
  • Ning Chi,
  • Jianmei Su,
  • Shanshan Wu,
  • Zhanxia Ma

摘要

Yunnan Province has been widely recognized as an important center of origin, domestication, and diversification of tea plants, and its large-leaf tea (Camellia sinensis var. assamica) germplasm represents a valuable resource for tea conservation and breeding. In this study, 216 large-leaf tea accessions collected from four major tea-producing regions of Yunnan Province, including Baoshan (BS), Lincang (LC), Menghai County in Xishuangbanna (MH), and Pu’er (PE), were analyzed using 20 polymorphic simple sequence repeat (SSR) markers. The SSR loci showed relatively high polymorphism, with mean values of 6.53 for the number of alleles (Na), 3.11 for the effective number of alleles (Ne), 1.17 for Shannon’s information index (I), and 0.546 for expected heterozygosity (He). Among the four populations, MH had a relatively high mean number of alleles, whereas PE had the highest Shannon’s information index and expected heterozygosity. Analysis of molecular variance (AMOVA) showed that 98% of the genetic variation occurred within populations and 2% among populations. The overall genetic differentiation coefficient (Fst = 0.027) and pairwise Fst values ranging from 0.013 to 0.034 were consistent with weak genetic differentiation. The Nm estimate derived from Fst was consistent with substantial historical allele sharing, shared ancestry, or human-mediated germplasm movement, but should not be interpreted as a direct measure of contemporary gene flow. The Evanno method supported K = 3 as the primary STRUCTURE solution, whereas the K = 4 pattern and discriminant analysis of principal components suggested subtle genetic distinctiveness of PE and close genetic affinity between BS and LC. These findings suggest that Yunnan large-leaf tea germplasm contains considerable SSR-based genetic diversity but exhibits weak regional differentiation. The observed pattern may reflect the combined effects of seed-based propagation, natural crossing, shared ancestry, and long-term human-mediated movement of planting materials. This study provides useful information for the conservation, management, and breeding utilization of Yunnan large-leaf tea germplasm.