Genetic diversity analysis of selected coconut (Cocos nucifera l.) varieties using EST-SSR markers

Abstract

Coconut (Cocos nucifera L.) is a major crop among coastal regions in Asia including the Philippines. However, due to the decline in the economic production of coconut, the Philippine Coconut Authority (PCA) created a research program to increase nut production from 46 nuts per tree per year to 150 nuts per tree per year by producing hybrids. In this study, the genetic diversity and population structure of 18 coconut populations being grown ex situ in the field germplasm of Philippine Coconut Authority – Zamboanga Research Center (PCA – ZRC) were analyzed using novel EST-SSR markers. Seven out of 27 EST-SSRs revealed adequate polymorphism for the subsequent analyses with an average of 2.14 alleles per marker, which is relatively low. A high degree of genetic diversity (He) was observed with values ranging from 0.200 (MYD) to 0.514 (PYT) with an average of 0.313. Furthermore, the heterozygosity values for BAND and TACD was found to be relatively high for dwarf populations (0.343), which aligns with the findings of Perera et al. (2016) that BAND is highly heterozygous and closely related to the Philippine tall varieties. The mean FST value (0.367) is higher than the FIS (0.016), indicating that genetic variation is observed within subpopulations. The UPGMA dendrogram revealed PYT and WAT as genetically divergent. These can be found in the Pacific and Indo-Atlantic islands, respectively, the two origins of talls proposed by Gunn et al (2011). The results of this study are useful in selecting superior coconut varieties and developing hybrids with better agronomical quality.