Genome-Wide SNP Identification of The Elaeis guineensis x Elaeis oleifera Population

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Efforts in finding DNA markers for favorable characters of Elaeis oleifera introgressed into Elaeis guineensis genome requires polymorphic DNA markers. To generate high number of polymorphic DNA markers, a genome-wide SNP identification was done by resequencing 12 individual samples using next generation sequencing (NGS) from an E. guineensis x E. oleifera (OxG hybrid) population comprising wild E. oleifera species, interspesific F1 hybrids, pseudo-backcrosses, and advanced E. guineensis samples. The reads generated from the 12 samples have good qualities and 96% of total filtered reads could be demultiplexed and assigned to the corresponding samples. After filtering and trimming, 84% of reads were retained for genome mapping and produced 5.7X to 10.42X genome coverage. Among the 34,410,224 identified SNPs, 98.7% of them were non-coding variants, and based on their location 69.1% of the total SNPs were intergenic SNPs. There were 5,618 SNPs out of the total generated SNPs that were validated using targeted genotyping by sequencing on 500 individuals, and 74% of the SNPs produced high quality calls in at least 95% of the samples. Principal component analysis using the SNPs correctly identified each sample's genetic background. Thus, the SNPs had high quality and could be used to develop marker-assisted selection of the E. guineensis x E. oleifera breeding population.