Genetic diversity analysis of dwarf accessions from the Philippine Coconut Authority-Zamboanga Research Center using simple sequence repeat markers

Abstract

Dwarf coconuts (Cocos nucifera) provide many economic benefits such as coconut oil, copra, and desiccated coconut, providing a source of income for small farm farmers in the Philippines. There has been a decline in the economic production of coconut, losing to other crops like oil palm (Rivera et al., 1999). To address this problem, research to increase its production by producing hybrids have been going on at the Philippine Coconut Authority (PCA). Twenty local varieties and six foreign varieties from PCA-Zamboanga Research Center (PCAZRC) were studied, with three individuals form each variety. Genomic DNA was extracted from leaves. Previously published simple sequence repeat (SSR) makers were screened for polymorphisms. Eight markers that showed distinct polymorphisms were used to Polymerase Chain Reaction (PCR) amplify the eight SSR regions of twenty-six dwarf varieties from PCA-ZRC. Using polyacrylamide gel electrophoresis (PAGE), banding profiles of each variety was scored. Profiles were assessed for genetic diveristy using NTSYS-pc version 2.1 (Rholf, 2000) to create a phylogenetic dendrogram, and GenAlEx 6.5 (Peakall, Smouse, 2012). The phylogenetic dendrogram indicated local and foreign varieties formed separate clusters. Fourteen varieties (5 foreign, 9 local) showed no heterozygosity, and twelve (1 foreign, 11 local) showed varying levels of heterozygosity. The genetic diversity within the twenty-six varieties is low (Fis values=0.034), between the varieties the genetic diversity is high (Fst values=0.882). These findings suggest that genetically distant dwarfs varieties may be used for breedingxi programs. This information can be used for varietal improvement for the varieties with low heterozygosity.