Research

Yield improvement is a means of reconciling oil production and forest conservation thus reducing its environmental footprint. Genomic techniques coupled with breeding have proved invaluable for increasing the efficiency and precision of oil palm breeding. This is especially relevant considering the long life cycle of the oil palm where each selection cycle spans about 12 years. Sambanthamurthi led the team at the Malaysian Palm Oil Board (MPOB) that sequenced the oil palm genome together with Orion Genomics, making it the world’s first oil palm reference genome. The oil palm has three fruit forms - dura which has a thick shell, shell-less pisifera, and tenera with a thin shell. Tenera is the hybrid of dura × pisifera (DxP) and contains a high mesocarp to fruit ratio, which translates to higher oil yield. While it was known since 1941 that the SHELL gene exhibited monogenic inheritance, the identity of this gene was not known until the sequencing of the oil palm genome led to the discovery by Sambanthamurthi’s team of the SHELL gene and the genetic mechanism of differentiation between the three fruit forms. The team discovered that SHELL is a homologue of the MADS-box gene SEEDSTICK (STK), also known as AGAMOUS-LIKE 11, which controls ovule identity and seed development in Arabidopsis. The shell phenotype is the most important economic trait in oil palm, with major implications for global edible oil production, biofuels, and rainforest conservation. A diagnostic assay was developed for SHELL which allows for screening for high-yielding tenera as early as the seed stage, thus paving the way for improved productivity and sustainability. It also set the pace for further discoveries of economic importance such as the  VIRESCENS (VIR) gene that controls fruit colour. 

 

Fruit colour is an important trait in terms of fruit harvesting and, therefore, oil yield. Sambanthamurthi and team reported that VIR is an R2R3-MYB transcription factor and identified five independent mutant VIR alleles from over 400 oil palm accessions from sub-Saharan Africa that account for the dominant-negative virescens phenotype. Each mutation causes premature termination of the carboxy-terminal domain of VIR, similar to McClintock’s C1-I allele in maize. 

 

Oil palm tissue culture allows for the mass propagation of uniform elite clones with the potential to increase oil yield by 30%. It can expedite the multiplication of palms with superior characteristics related to disease resistance, growth pattern or oil composition. Tissue culture is also an invaluable tool for the regeneration of plantlets modified by modern genetic techniques such as the CRISPR/Cas 9 system for the creation of novel genetic variants. However, the emergence in the mid-80s of a clonal abnormality known as MANTLED that drastically reduces yield and could ruin entire oil palm fields, halted large-scale cultivation of oil palm clones. MANTLED was the elusive target of molecular genetic investigation for over three decades. Sambanthamurthi and team discovered that the methylation status of the retrotransposon Karma inserted in intron 5 of EgDEF1, the oil palm orthologue of the B-class MADS-box genes APETALA3 of Arabidopsis thaliana and DEFICIENS of Antirrhinum majus of the homeotic gene DEFICIENS determines the MANTLED phenotype. Dense methylation of Karma results in normal fruit set, while hypomethylation arising from stressful tissue culture procedures, results in the alternative splicing of EgDEF1 and the formation of a truncated protein giving rise to mantled palms. The discovery led to the development of an assay for epigenetic testing of nursery material for MANTLED.