The conservation and utilization of germplasm is contingent on its proper characterization at morphological or molecular levels. The present study aimed to elucidate the population sub-structure of 470 temperate rice germplasm collections of the Kashmir Valley. Analysis was carried out using KASP (Kompetitive Allele Specific PCR) assay on 213 genomic loci. Of these, a restricted set of 114 KASP loci were selected by the elimination of redundant, i.e. tightly linked markers based on map positions. STRUCTURE grouping was carried out to reveal three distinct sub-populations, K1, K2 and K3 comprising of 209, 156 and 105 germplasm accessions, respectively. Population F_ST values for K1, K2 and K3 were at 0.60, 0.24, 0.69, respectively, with highest pair-wise F_ST obtained between K2 and K3 (0.53). Analysis using the restricted set of 114 markers gave a better inferred membership with a low average admixture of 15.1% compared with 22.6% based on the whole marker set. An improved agreement between STRUCTURE grouping and principal coordinate analysis was reached using the restricted marker set. Φ_ST values calculated based on nucleotide diversity also suggested three sub-populations: K2, mostly indica germplasm; K1 mostly exotic temperate japonica; and K3, local japonica varieties and landraces. Polymorphic SNPs and haplotypes were discovered which discriminated the three sub-populations. Fifteen KASP markers were most important in discriminating K2 from K1 and K3 and included SNPs associated with domestication within the Wx, Ghd7 and Ghd8 genes. KASP markers are cheaper than SSR markers. Some of the KASP markers were highly discriminatory, using both model and distance based approaches, and so can be used as a cost-effective tool for efficient maintenance and use of rice genetic resources.

种质的保存和利用取决于其在形态学或分子水平上的正确表征。本研究旨在阐明克什米尔谷地470个温带水稻种质资源的种群亚结构。使用KASP（竞争性等位基因特异性PCR）分析法对213个基因组位点进行了分析。其中，通过消除冗余（即基于地图位置的紧密链接的标记）选择了一组受限的114个KASP基因座。进行结构分组以揭示三个不同的亚群，K1，K2和K3，分别包含209、156和105个种质种质。K1，K2和K3的总体F _ST值分别为0.60、0.24、0.69，成对F _ST最高在K2和K3（0.53）之间获得。使用114个标记的受限集合进行的分析得出的推断成员更好，平均掺混物的比例为15.1％，而基于整个标记集的平均值为22.6％。使用限制标记集可以达到结构分组和主坐标分析之间的改进协议。Φ _ST值基于核苷酸多样性计算还建议三个子群：K2，大多籼稻种质; K1主要是异国温带粳稻；和K3，当地的粳稻品种和地方品种。发现了区分三个亚群的多态性SNP和单倍型。十五种KASP标记对于区分K2和K1和K3最重要，包括与Wx，Ghd7内驯化相关的SNP。和Ghd8基因。KASP标记比SSR标记便宜。使用基于模型和基于距离的方法，某些KASP标记具有很高的歧视性，因此可以用作有效维护和利用水稻遗传资源的具有成本效益的工具。