Abstract Pinus kesiya (Khasi pine) is the principal pine species in northeast India having high commercial value. Chloroplast microsatellites (cpSSR) were used to study the genetic diversity and population genetic structure of 10 populations of P. kesiya covering entire natural range of distribution in India. A total of 33 primer pairs (cpSSRs) of P. thunberghii and P. sylvestris were tested in P. kesiya for their transferability, out of which 18 chloroplast primers showed positive amplification and 10 were found polymorphic. A total of 250 individuals from 10 different populations were genotyped using the selected 10 cpSSRs. When alleles at each of the 10 loci were jointly analysed a total of 36 size variants were discovered, which combined to designate 90 haplotypes among 250 individuals. None of the haplotype was found common among the populations as they were population specific. The cpSSR indicated that P. kesiya populations have maintained a moderately high genetic diversity (HT=0.638) which is typical in most coniferous species. However, the inter-population genetic diversity was higher than the intra population diversity and the genetic differentiation between populations was also found to be very high (FST=0.47). A Bayesian cluster analysis separated the populations into six clusters where most of the individuals were found in single population clusters with minor admixtures. The distribution of genetic diversity and sub structuring of P. kesiya reflect week pollen mediated gene flow due to geographic isolation and genetic drift. The study has revealed useful cpSSR markers for P. kesiya, which were lacking earlier and also added an insight into the state of Khasi pine forest in the region, which can be useful for the better management and future conservation programs.

中文翻译：

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使用叶绿体 SSR 标记研究卡西松（Pinus Kesiya Royle Ex. Gordon）遗传多样性的微卫星分析

摘要 卡西松（Khasi pine）是印度东北部的主要松树品种，具有很高的商业价值。叶绿体微卫星 (cpSSR) 被用于研究覆盖印度整个自然分布范围的 10 个 P. kesiya 种群的遗传多样性和种群遗传结构。在 P. kesiya 中测试了总共 33 对 P. thunberghii 和 P. sylvestris 的引物对 (cpSSR) 的可转移性，其中 18 条叶绿体引物显示阳性扩增，10 条发现多态性。使用选定的 10 个 cpSSR 对来自 10 个不同群体的总共 250 个个体进行了基因分型。当对 10 个基因座中的每一个的等位基因进行联合分析时，总共发现了 36 个大小变异，这些变异结合起来指定了 250 个个体中的 90 个单倍型。没有发现任何一种单倍型在人群中是常见的，因为它们是人群特异性的。cpSSR 表明 P. kesiya 种群保持了中等高度的遗传多样性（HT = 0.638），这在大多数针叶树种中是典型的。然而，种群间遗传多样性高于种群内多样性，并且种群之间的遗传差异也非常高（FST=0.47）。贝叶斯聚类分析将种群分成六个集群，其中大多数个体都在具有少量混合物的单个种群集群中被发现。P. kesiya 的遗传多样性分布和亚结构反映了由于地理隔离和遗传漂变导致的周花粉介导的基因流动。该研究揭示了 P. kesiya 的有用 cpSSR 标记，