Development of gene based markers for mapping analysis in oil palm

Gene based SNP markers for oil palm were developed from cloned candidate genes that are involved in fatty acid (FA), triacylglycerol and pyruvate-acetyl CoA synthesis pathways of oil palm. Based on exon/introns splice junctions, a total of 28 specific primer pairs corresponding to 22 gene loci were designed and tested for polymorphism between 23 parents (13 dura and 10 pisifera ) used in an oil palm breeding programme. Single strand conformation polymorphism polyacrylamide gel electrophoresis (SSCP) was used to detect the polymorphism. More than 80% of the gene loci showed clear polymorphic patterns in target parents which progenies of at least 3, up to all 14 crosses would display segregation for the markers. The gene based SNP markers developed in this study do not only provide potential marker tools for further QTL mapping analysis in multiple crosses but can also be used as anchor points for further comparing and integrating oil palm linkage maps developed from individual progenies.