Development of an effective SSR-based fingerprinting system for commercial planting materials and breeding applications in oil palm

DNA fingerprints provide the basis for genetic diversity studies and molecular breeding. However, routine and commercial scale DNA fingerprinting in oil palm (Elaeis guineensis Jacq.) remains challenged by the need for a robust yet low cost method. In addition, there is also a need for a precise and reliable marker set capable of distinguishing oil palm genotypes within narrow and mixed genetic population bases at the individual and population level. With the rapid evolution of genotyping and sequencing technologies, a wide range of genotyping tools have been developed but are not yet commercially feasible for oil palm. Consequently, we tested the feasibility of using simple sequence repeat (SSR) markers to genotype oil palm breeding and commercial planting materials of restricted and mixed parentage from Advanced Agriecological Research Sdn Bhd (AAR). The results obtained from screening 33 palms using a selected set of 17 highly polymorphic and informative SSR markers obtained from an initial set of 23 SSR, showed that clones, crosses and sibs within crosses could be separated by their DNA fingerprints. However, as expected palms within clones could not be separated. In another test exercise at the population scale, the four variable but related populations: DeliDumpy Deli x Yangambi x AVROSDumpy Deli x AVROSDumpy Deli x AVROS x La Mewere distinctly separated using 11 SSR from the same pool of 23 polymorphic SSR. There is good potential for this set of 11 SSR markers to be developed for general applicability across all E. guineensis oil palm genetic materials and for use in the Malaysian Plant Variety Protection Act. The set of SSR markers also serve as the base set for the development of marker-assisted and genome-wide selection at AAR