Genome-wide SNP-discovery and analysis of genetic diversity in oil palm using double digest restriction site associated DNA sequencing

Abstract

The oil palm conventional breeding is faced with many challenges, including the long breeding cycle and limited genetic variations available from the existing breeding populations. Recent genomic research revealed the genetic properties of various oil palm populations and could be exploited by recombining favorable alleles through molecular breeding and selection. In aimed to discover high quality single nucleotide polymorphisms (SNPs) sampled from 236 diverse genetic backgrounds palms, a paired-end ddRAD-sequencing was employed to discover allelic variations. Whole 195.62 Gb clean data were generated using ddRAD-seq. After stringent filtering, 8 189 SNPs in the annotated genes were discovered based on the oil palm EG05 reference genome. The high polymorphism rate was observed across the assayed populations, whereby 29 % of loci showed moderate to high putative impact on amino acid changes in silico as predicted by SnpEff software. The Angola and Deli origins seemed to have undergone inbreeding as reflected by the fixation index and the lower observed heterozygosity compared to expected heterozygosity. Assessment of genetic stratification and structure was not strong enough to differentiate the core breeding materials according to their prior genetic backgrounds. The results demonstrated the robustness and high-throuputness of ddRAD sequencing method for SNP discovery.