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MPOB and Collaborators Solve Mystery of Clonal Abnormality and Discover the Importance of Good Karma in Oil Palm Tissue Culture

Published: Wednesday September 9, 2015.

MPOB scientists scored a major breakthrough by unlocking a puzzle that has mystified the oil palm industry for three decades. The successful development of oil palm tissue culture in the 70s heralded a new era for oil palm crop improvement as it allowed for the mass propagation of thousands of uniform elite clones with the potential to increase oil yield by 30%. However, the emergence of clonal abnormality in the mid 80s put the brakes on large-scale cultivation of oil palm clones. The occurrence and severity of MANTLED is highly unpredictable thus greatly reducing confidence in tissue culture. In 2013, MPOB shared the oil palm genome sequence with scientists across the world, generating an explosion of research in oil palm genomics. Leveraging the oil palm genome, MPOB and its long standing partner Orion Genomics together with Cold Spring
Harbor Laboratory and oil palm industry members Felda Global Venture, United Plantations Berhad, Applied Agricultural Resources Sdn Bhd and AAR discovered the trigger for clonal abnormality. The discovery again put MPOB and its collaborators on the international map when it was published in the epub version of Nature on 9 September 2015. The scientists discovered that clonal abnormality is an epigenetic phenomenon. A retrotransposon (jumping gene) known as Karma embedded in Elaeis guineensis DEFICIENS (EgDEF), a regulatory gene involved in defining the floral architecture of oil palm determines if an oil palm clone is normal or abnormal. Dense methylation near the Karma splice site (termed the Good Karma epiallele) predicts normal clones, whereas hypomethylation (the Bad Karma epiallele) predicts MANTLED abnormality. A diagnostic assay that predicts the clonal fidelity with 100% accuracy is now finally available.
The finding comes on the heels of the discovery of the shell gene (in 2013) and the fruit colour gene (2014) by MPOB and collaborators and shows the power of the genome sequence in unlocking the vast potential of the genetics of the oil palm. The discoveries pave the way for improved sustainability by optimizing land use and reducing demand on additional land, water, and resources.