Genomic Strategies for Oil Palm Improvement

The oil palm with its long breeding cycle and large land requirement for field trials is an ideal candidate for genomics guided breeding. However, oil palm improvement even until recently was mostly due to conventional breeding. This is because the linking of markers and gene(s) to traits of interest has been slow for this perennial crop, partly due to the lack of in-depth sequence information in the past.  A modest effort to start sequencing the genome was thus initiated in 2004, which led to sequencing of the hypomethylated regions of the genome. This initiative provided the impetus to sequence the whole genome, which was successfully executed in 2013. The early focus after sequencing the genome was to identify genes influencing important monogenically inherited traits. The availability of a large germplasm collection and a well-executed breeding programme allowed the team to identify the genes influencing fruit form and colour of oil palm. The early discoveries has formed the basis for marker assisted selection in oil palm as well as provided the community tools for quality control in commercial seed production. The focus has now shifted to more complex traits, where stable quantitative trait loci (QTLs) linked to fatty acid composition have  been identified. MPOB and its consortium partners have also unraveled the epigenome of oil palm to help understand DNA methylation alterations in clonal palms. Deciphering of the epigenome and understanding the causes of clonal abnormality has also made large scale tissue culture of oil palm feasible.