Genetic Diversity and Population Structure in the Landrace Accessions of Gossypium hirsutum

In this study, genetic diversity and population structure was assessed in a set of 185 Gossypium hirsutum L. landrace accessions, collected mainly from Central America during the mid-1900s using genomewide simple sequence repeat (SSR) markers. Genotyping the diversity panel using 122 SSRs detected 143 marker loci. A total of 819 alleles were identified across 143 markers loci, and out of these, 23.3% were unique alleles, observed only in one accession. Average genetic distance between accessions was 0.36, suggesting higher levels of genetic variation present in the cotton tropical landrace germplasm. Using Bayesian model-based structure analysis, five major subgroups were identified that roughly corresponded to the geographical origins of accessions. Substantial admixture was observed as accessions from different geographical locations were grouped together. Results from phylogenetic analysis, principal component analysis, and analysis of molecular variance supported clustering based on STRUCTURE analysis. Pair-wise kinship estimates suggested that most of the accessions were unrelated. Finally, core sets representing various levels of allelic richness were identified using POWERMARKER. Assessing genetic diversity, population structure, and identifying the core sets in the land-races will facilitate the utilization of unexploited tropical genetic diversity towards developing improved cotton cultivars.