Genetic diversity, population structure and association analysis in coconut (Cocos nucifera L.) germplasm using SSR markers

Abstract

AbstractA world-wide coconut germplasm collection (79 genotypes) was analyzed for genetic diversity and population structure based on 48 simple sequence repeat (SSR) loci. The genotypes displayed moderately high amount of genetic diversity, which was strongly structured according to geographical origins. Number of SSR alleles ranged from 2 to 7 with an average of 4.1 per locus. Gene diversity (expected heterozygosity) estimates ranged from 0.162 to 0.811 with a mean of 0.573. Polymorphism information content values ranged from 0.149 to 0.785 with an average of 0.522. Hierarchical clustering analysis grouped the genotypes into two major clusters with two sub-groups in each, which corresponded with the geographic origins. The first cluster comprised of ‘Tall’ genotypes originated from Indo-Atlantic and South Asia regions. The second cluster comprised mostly of ‘Dwarf’ genotypes and some Tall genotypes which originated from Indo-Pacific and South-East Asia regions. Model-based clustering by STRUCTURE analysis also supported the presence of clear genetic structuring in the collection with two major populations (K = 2) and four sub-populations (K = 4). The proportion of SSR locus-pairs in linkage disequilibrium was low (2.4%). Association analysis in a subset of 44 genotypes detected a single SSR locus, CnCir73 (chromosome 1) putatively associated with fruit yield component traits, which corresponded with a previously mapped quantitative trait locus in coconut.