Analysis of genetic diversity and population structure in worldwide coconut germplasm (Cocos nucifera L.) using microsatellite markers

• Vegetative, reproductive and fruit component characteristics revealed wide variations among the 16 coconut genotypes. • Genetic diversity analysis revealed an average expected heterozygosity (He) value of 0.36. • Cluster analysis grouped coconut genotypes in two major groups based on their stature. A collection of 96 palms, representing 16 diverse coconut accessions from the International Coconut Genebank for South Asia and the Middle East (ICG-SAME), Kidu, India, was analyzed for genetic diversity and population structure based on 35 simple sequence repeat (SSR) loci. The accessions exhibited high genetic diversity. The number of alleles ranged from 2 to 22, with an average of 6.2 per locus. The effective number of alleles per locus ranged from 1.04 to 3.58, with a mean of 1.86. Gene diversity estimates ranged from 0.224 to 0.457, with a mean of 0.355. Polymorphism information content (PIC) value varied from 0.04 to 0.66 with an average of 0.36. Hierarchical clustering analysis grouped the genotypes into two major clusters with two sub-groups, which corresponded with the geographic origins. The first cluster comprised the dwarf accessions, and the second cluster comprised all the tall accessions. STRUCTURE analysis was consistent with the result of the cluster analysis with the presence of two major populations (K = 2). The results indicated the potential of SSR markers for assessing genetic diversity and marker-assisted selection in coconut.