Genetic diversity and population structure of sweet orange [Citrus sinensis (L.) Osbeck] germplasm of India revealed by SSR and InDel markers

Sweet orange ( Citrus sinensis (L.) Osbeck) is an important commercial citrus fruit crop, cultivated in India and across the world. In India most of the cultivated sweet orange species were introduced varieties. In this study, we used two molecular markers,SSR and InDels, to understand the genetic diversity and population structure of seventy-two sweet orange genotypes. Genetic parameters consisted of total number of alleles, number of polymorphic alleles (effective alleles); genetic diversity (G.D.), expected heterozygosity (He) and polymorphic information content (PIC) were calculated based on molecular data. Two dendrograms were constructed based on the InDels and SSR. In the both the cases they formed three major clusters showing various degrees of variations with respect to members of the clusters. Population structure analysis revealed presence of two distinct sub populations. Therefore, in order to address various challenges and develop sweet orange varieties with desirable traits, there is a need to broaden the genetic base of sweet orange through intensive collection in the northeastern region. These results of intra-specific genetic variability of the collections will dictate the path for the sweet orange breeding and conservation programs in India.