Characterization of genomic variation on three Indonesian oil palm genotypes analyzed using next-generation sequencing HiSeq

Oil palm is an important estate crop and Indonesia is the largest palm oil producer in the world. Since the average yield is relatively low, a more efficient breeding program that utilizes the latest technological developments in DNA analysis is necessary. The objectives of this study were to (1) characterize genomic variations of three Indonesian oil palm genotypes based on whole genome sequencing using next-generation sequencing (NGS) HiSeq; (2) provide genomic data resources for future oil palm breeding program. Whole genome sequencing was performed on three Indonesian oil palm genotypes (Dura, Pisifera, and Elaeis oleifera from Brazil). Sequence data were aligned with that of the Eg5 genome reference sequences. The average sequence coverage depth for all loci was 34 and more than 95% of the genome was sequenced at least ten times. Comparison of the sequences revealed 3,735,311 sequence changes, an average of one sequence change per 197 bases. Among these changes, 3,371,088 were SNPs and 364,233 were insertions and deletions (indels). DNA variations found within exons total 329,087. Of these, 214,068 SNPs variations were capable of causing modification in the amino acid composition of the encoded proteins (nonsynonymous mutations). A genomic database was constructed to manage DNA variations resulted from this study. The SNPs collected from this study should be useful for constructing high density oil palm SNP chip to expedite future national oil palm breeding program.