Morphological characterization and analysis of genetic diversity and population structure in Citrus × jambhiri Lush. using SSR markers

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.