Development and characterization of single‐nucleotide polymorphism markers from 454 transcriptome sequences in oil palm (Elaeis guineensis)

Abstract

AbstractOil palm (Elaeis guineensis) has recently emerged as the world's most important economic crop, with the world production of palm oil surpassing that of soybean. The utilization of palm oil as a feedstock in biodiesel production has triggered a dramatic rise in its global demand. In recent years, marker‐assisted selections have played a pivotal role in oil palm breeding programmes as they have several advantages over traditional breeding approaches. We have explored the possibility of developing single‐nucleotide polymorphism (SNP) markers in Elaeis guineensis using the 454‐derived transcriptomic sequence data. We have identified 823 putative SNP positions in silico using a set of highly stringent criteria. Forty‐six bi‐allelic SNP positions were validated by the traditional Sanger sequencing method. The polymorphism information contents (PICs) and the observed heterozygosity (HO) ranged from 0.066 to 0.375 and 0 to 0.928, respectively. These SNP markers will be useful for the construction of high‐density genetic maps (allowing the identification of commercially desirable quantitative trait loci), genetic variation studies and the population structure analyses in E. guineensis.