Genetic diversity and structure of Pyrus accessions of Indian Himalayan region based on morphological and SSR markers

Genetic diversity and phylogenetic relationships among 48 pear accessions belonging to six species were determined using 23 morphological traits and 20 simple sequence repeat (SSR) primers. To assess the genetic diversity, data on morphological (both quantitative and qualitative) traits were recorded during 2010–2012 using standard pear descriptors. It was observed that the traits ratio of fruit length to diameter, persistency of calyx on mature fruits and fruit surface and pulp texture were important in detecting variation across pear species. At molecular level, 20 SSR primers amplified 190 polymorphic alleles with an average of 9.5 alleles per primer. Size of amplified alleles ranged from 85 to 450 bp. Mean polymorphic information content (PIC) was 0.80 showing high level of SSR polymorphism. Bayesian model-based STRUCTURE analysis assigned genotypes into five clusters and also showed the extent of admixture within individuals. Genotypes belonging to Pyrus pyrifolia were clustered into two different clusters indicating broad genetic base for this species while Pyrus communis genotypes appeared to have conserved genetic makeup. Dendrogram-based on Jaccard’s similarity coefficient and neighbor-joining tree showed two major groups of Asiatic (P. pyrifolia, Pyrus pashia, Pyrus serotina and Pyrus jacquemontiana) and European (P. communis) pears. However, accessions belonging to P. pyrifolia were further divided into subgroups. Cluster analysis based on morphological traits was in agreement with the dendrogram and structure clusters obtained with SSR data. The Mantel matrix correspondence test was used to further compare the molecular and morphological similarity matrices and positive correlation coefficient (r = 0.164; P = 0.001) was observed. Results of this study present important information about genetic structure of Indian pear accessions which can contribute significantly to future breeding and improvement programmes in this species.