Molecular Markers for Analysis of Genetics Diversity and Identification of Oil Palm Hybrid Varieties

Abstract

The genetic diversity studies and SHELL type analysis of oil palm are achieved by molecular marker. Thirteen simple sequence repeat (SSR) markers loci were selected to
distinct 10 oil palm populations viz. Deli Dura, AVROS, Yangambi, Nigeria, Calabar, Ghana,
Ekona, DAMI, Tanzania and La Me. The results showed that male parent oil palm, La Me
had the most genetical differentiation from other male and female parent populations,
followed by Calabar, Nigeria, Tanzania and Ghana. Among male parent oil palms, AVROS
had the most genetic similarity to female parent, Deli Dura followed by DAMI. In addition,
the new SSR markers were reselected for investigating the genetic diversity of Deli Dura
populations as well as the progenies derived from inter-specific hybridization between
Elaeis guineensis and E. oleifera. The obtained data are efficient to differentiate all oil palm
populations. Moreover, the primers mEgCIR3428, mEgCIR3519 and mEgCIR0874, were
sufficient to be used as markers in identifying Surat Thani 1-8 oil palm varieties. For
analysis of oil palm SHELL type, the MADS-box gene of 129 samples including 3 shell
types, Dura, Pisifera and Tenera from 10 distinct oil palm populations were sequenced
and performed multiple nucleotides alignment. The SNPs that can differentiate the oil
palm SHELL type in each population were discovered as follow, SNPENGC (T/C) in Ekona
Ghana Calabar and Nigeria, SNPTaYa (A/T) in Tanzania Yangambi, SNPDA (C/G) in DAMI, SNPLaAv(C/A) in La Me and AVROS, SNPTan (C/G) in Tanzania. The obtained data of SNPs loci wereused to generate 4 sets of primers and probes for accurately and rapidly determining oil palm SHELL type with real-time PCR. These markers are very applicable for quality control
of Tenera oil palm seedling production for reducing or eliminating Dura contamination, and distinguishing the female and male parent genotype efficiently.