Assessment of genetic diversity and association analysis for agro-morphological traits in pepper (Capsicum spp.) using ISSR markers

Study of genetic diversity using genetic markers is necessary to effective conservation of germplasm and to understand its genetic structure. Genetic variability in a species facilitate its adaptation to various environmental conditions. In the present study, genetic variability among 114 genotypes from 30 Pepper accessions were studied suing 11 ISSR primers and 14 morphological traits. Of 1653 locus pairs of ISSR markers, 7.04% showed significant level (P≤0.01) of linkage disequilibrium (LD). By analyzing genetic structure of population based on molecular data and using Bayesian model, 5 subpopulations (K=5) were identified. Association analysis was conducted using mixed linear model by considering kinship and genetic structure matrices as covariates in the model. Some molecular markers multiplied by 8 ISSR primers were identified to be significantly associate with 13 studied traits (P ≤ 0.05). Some markers were common among some studied traits that can be due to pleiotropy or linkage between loci controlling traits. Among studied ISSR primers, molecular markers produced by UBC834 primer showed the most association with the studied traits. Identified markers after validation can be useful in the development of pepper cultivars.