Coconut diversity based on chloroplast Single Nucleotide Amplified Polymorphism (SNAP) and Insertion-Deletion (InDel) markers

Abstract

Indonesia is known as a country rich in biodiversity, and a species with high diversity existing in Indonesia is coconut (Cocos nucifera L.). Although the high diversity of Indonesian coconut is recognized, information about its genetics is limited. The genetic relationship between Indonesian coconut and their maternal inheritance is important and has not been widely studied. This study aimed to analyze the genetic diversity of the Indonesian coconut using chloroplast SNAP and InDel markers, and evaluate their haplotype diversity. Sixty-four coconut accessions were evaluated using ten SNAP primers and five InDel primers based on cpDNA. All of the primers successfully amplified the cpDNA of most evaluated coconut accessions. Based on five InDel markers, six haplotypes were observed in Cocos nucifera. Phylogenetic analysis based on the combined SNAP and InDel markers divided the 64 coconut accessions into three clusters. The SNAP marker analysis results showed that they are less informative for evaluating coconut genetic diversity. On the other hand, the InDel markers are more informative and useful for coconut genetic diversity evaluation. Therefore, InDel markers based on chloroplast genomes has the potential for future coconut genetic variation analysis, evolutionary study, and DNA fingerprinting. The results should contribute to understanding the Indonesian coconut origins and evolution.