Insights on Genetic Diversity, Population Structure, and Linkage Disequilibrium in Globally Diverse Coconut Accessions Using Genotyping-by-Sequencing

OMICS. 2021 Dec;25(12):796-809. doi: 10.1089/omi.2021.0159. Epub 2021 Nov 10.


Genotyping-by-sequencing (GBS) has emerged as a cost-effective approach for genome-wide discovery of single-nucleotide polymorphism (SNP) markers and high-throughput genotyping. In this study, 96 coconut palms, representing 16 accessions from globally diverse origins, were genotyped using the GBS strategy. A total of 10,835 high-quality SNPs, which were identified after stringent filtering, were utilized to assess genetic diversity, population structure, and linkage disequilibrium (LD) analyses. The polymorphism information content (PIC) values of SNPs ranged from 0.1 to 0.4, with a large proportion of SNPs (8633 nos.; 79.7%) having a higher PIC in the range of 0.3-0.4. The genetic diversity analysis revealed the existence of a high level of variation in coconut accessions, with an average expected heterozygosity (He) value of 0.43. Unweighted neighbor-joining phylogenetic tree and Bayesian-based model population structure grouped coconut genotypes into four main clusters. The accessions are generally clustered based on their height (tall or dwarf), with a few accession clusterings based on geographical origins. Investigation of LD pattern in coconut indicated a relatively rapid LD decay with a short range (9 kb). The results obtained in this study will contribute to enhancing the capacity of coconut researchers to utilize genetic diversity for further genetic improvement. In addition, it would open up possibilities for performing genomic studies such as genome-wide association studies and genomic selection to accelerate the efficiency and speed of coconut genetic improvement.

Keywords: coconut; diversity analysis; genebank; genotyping-by-sequencing; linkage disequilibrium; population structure; single-nucleotide polymorphisms.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bayes Theorem
  • Cocos* / genetics
  • Genetic Variation / genetics
  • Genome-Wide Association Study*
  • Genotype
  • Linkage Disequilibrium / genetics
  • Phylogeny
  • Polymorphism, Single Nucleotide / genetics