Rough lemon (Citrus × jambhiri Lush.) is one of the important species largely used as a rootstock for commercial plantations of Citrus across the world. In the present study, thirty-eight accessions of C. jambhiri were characterized using morphological and SSR markers for diversity analysis and population structure studies. Morphological characterization of 27 qualitative and 14 quantitative characters indicated the existence of moderate to sufficiently high amount of variability as revealed from the pair-wise similarity analysis value of 0.36. Molecular diversity analysis using 17 SSR primers detected 85.29% polymorphism indicating existence of moderately high amount of variability between the accessions in terms of studied loci. A total of 60 bands were generated, of which all the 60 were polymorphic (100%). The total number of alleles produced varied from 1 to 5 alleles with an average of 3.52 alleles per locus. Although the correlation between the morphological and molecular data was low in the analysed accessions of C. jambhiri, both methods allowed the clustering of accessions based on the analysed traits. Population genetic analysis by SSR markers revealed that accessions collected from North Eastern India were most diverse in terms of genetic diversity parameters and genetic distance analysis of populations showed that the accessions from North East and Himachal Pradesh were most similar genetically while population collected from Himachal Pradesh and Karnataka were the most distinct genetically. Structure analysis of different populations revealed that there is no genetic differentiation happening between the populations.

粗柠檬（Citrus×jambhiri Lush。）是重要的物种之一，在世界范围内被广泛用作柑橘商业种植的砧木。在目前的研究中，C。jambhiri的38个种质使用形态学和SSR标记进行特征分析，以进行多样性分析和种群结构研究。从成对相似性分析值0.36可以看出，27个定性和14个定量特征的形态学特征表明存在中等到足够高的变异性。使用17个SSR引物进行的分子多样性分析检测到85.29％的多态性，表明就研究的基因座而言，种质之间存在中等程度的变异性。总共产生了60条带，其中所有60条都是多态的（100％）。产生的等位基因总数在1至5个等位基因之间，每个基因座平均3.52个等位基因。虽然在分析的种质中形态学和分子数据之间的相关性很低。C. jambhiri，这两种方法都允许根据分析的特征对种质进行聚类。用SSR标记进行的群体遗传分析显示，从印度东北部收集的种质在遗传多样性参数上最为多样，种群的遗传距离分析表明，从东北和喜马al尔邦收集的种质在遗传上最相似，而从喜马al尔邦和喜马al尔邦收集的种质最为相似。卡纳塔克邦在基因上是最独特的。对不同种群的结构分析表明，这些种群之间没有发生遗传分化。