Development of Single Nucleotide Polymorphisms (SNPs) Marker based on SAD Gene in Oil Palm (Elaeis guineensis Jacq.)

Abstract

Oil palm (Elaeis guineensis Jacq.) is an important economic crop species due to the versatile applications of its crude and kernel oils. The necessity to improve oil palm, which is the world’s most productive oil producing plant under cultivation currently for high yield and oil quality to meet the growing global demand especially in term of its healthy component, oleochemical industrial needs and biodiesel utilization has become a major area of focus for oil palm breeders. Marker assisted selection have played a crucial role in oil palm breeding programs and single nucleotide polymorphism (SNP) maker is one of those technology that has recently attracted breeders. High content of oleic acid (18:1) has proven to be that needed component of oil palm and other vegetable oils that can greatly contribute to oil quality improvement. Stearoyl Acyl-carrier-protein Desaturase (SAD) is a key enzyme for oleic acid biosynthesis which plays an important role in determining the composition of unsaturated fatty acids in oil palm. In oil palm, SAD gene is located in chromosome 7, 8, and 9. This research focused on chromosome 7 and 9. There are 3 exon region in each of these two chromosomes. Specific primers were designed base on the 6 exon and neighboring intron region. Genomic DNA from three oil palm sources were amplified using these specific primers. We identified 9 SNP loci (4 in the exon and 5 in the intron) in SAD gene fragment and developed 9 allele-specific single nucleotide amplified polymorphism (SNAP) marker for oleic acid prediction. Four out of the nine SNAP marker developed and tested on 25 oil palm accessions were polymorphic and reasonably informative. The average expected and observed heterozygosities were 0.391 and 0.404, respectively. The mean polymorphism information content (PIC) was 0.312. Our results showed that these SNAP markers will be useful if validated in larger oil palm population in predicting oleic acid composition and genetic variation in oil palm breeding programs based on SAD gene fragment. This research account for the first specific study of SNAP marker development based on SNPs loci in both intron and exon region of SAD gene sequence in chromosomes 7 and 9 of oil palm. The result of our research will allow direct MAS specifically for oleic acid content and generally for unsaturated fatty acid prediction in oil palm at an early growth stage with less resources and time and also carried on genetic diversity analysis based on SAD gene. In addition, this research result will have set the pitch for further genetic diversity studies on the progeny of cross between the species of oil palm (E.guineensis and E.oleifera). Initial evaluation of the SNAP markers developed in this study is significantly beneficiary for oil palm breeders.