Genomic and population characterization of a diversity panel of dwarf and tall coconut accessions from the International Coconut Genebank for Latin America and Caribbean

Abstract

The characterization and construction of genetic diversity panels provide valuable information for developing germplasm conservation strategies and applying advanced breeding techniques. Thus, we performed analysis of diversity and genetic structure in Cocos nucifera L. with a collection of dwarf and giant accessions belonging to the International Coconut Genebank for Latin America in the Caribbean.The collection comprises six dwarf accessions (represented by 36 individuals) and six giants (represented by 48 individuals). The analysis of clustering and DAPC performed from a set of 4,044 SNP markers showed the existence of three clusters, one of which was formed exclusively by all dwarf coconut accessions. The giant accessions were separated into two distinct clusters, one formed by accessions from regions bathed by the Paci c Ocean (Southeast Asia and Oceania) and another formed by accessions from regions bathed by the Atlantic Ocean (Brazilian coastline and West Africa). The analysis allowed us to observe that the cluster formed by the accessions of dwarf coconut is closer genetically to the cluster formed by the accessions of giant coconut from the Paci c than the others from the Atlantic. Both groups presented similar genetic diversity (GD) values, 0.25 and 0.26, respectively. The inbreeding coe cient (F) revealed the presence of greater heterozygosity than expected in the dwarf coconut accessions and the inbreeding in the giant accessions. Consequently, we provide important information for maintaining those accessions in the germplasm bank and for future implementation of genomic-wide association studies (GWAS) and genomic selection (GS) with the evaluated accessions. Core IdeasThe giant coconut accessions are structured in two groups according to the Atlantic and Paci c Oceans. The dwarf coconut accessions have low genetic differentiation and are genetically closer to the giant coconut individuals originating in the Paci c Ocean. The giant coconut accessions showed low genetic diversity values, high values for the inbreeding coe cient, and attenuated decline in linkage disequilibrium.