A model for predicting flower development in Elaeis guineensis Jacq

The proper development of oil palm fruit is important as the source of oil is the fruit mesocarp and kernel. Prior to fruit formation, the development of flowers is therefore also important. Determination of the flower development stages in oil palm generally involves tedious histological analyses of each sampled inflorescence, making it a costly and inefficient way of gauging the developmental state. In this study, a statistical model was established from the association of physical or macroscopic measurement data to flower development, which was determined via histological analyses. The final reduced ordinal logistic regression model is a partial proportional odds model that uses inflorescence length and palm age as predictors to predict the flower development stage. The likelihood-ratio χ2 test suggested the model adequately fits the data (p<0.01). The model, with a prediction accuracy of 78.5%, can be used for selecting inflorescences of specific development stages from palms aged three to 10 years of field-planting. These stages can be further verified by histological analyses. This lowers the overall costs and time by reducing the number of samples requiring histological analysis prior to downstream studies

Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm

Somaclonal variation arises in plants and animals when differentiated somatic cells are induced into a pluripotent state, but the resulting clones differ from each other and from their parents. In agriculture, somaclonal variation has hindered the micropropagation of elite hybrids and genetically modified crops, but the mechanism responsible remains unknown. The oil palm fruit 'mantled' abnormality is a somaclonal variant arising from tissue culture that drastically reduces yield, and has largely halted efforts to clone elite hybrids for oil production. Widely regarded as an epigenetic phenomenon, 'mantling' has defied explanation, but here we identify the MANTLED locus using epigenome-wide association studies of the African oil palm Elaeis guineensis. DNA hypomethylation of a LINE retrotransposon related to rice Karma, in the intron of the homeotic gene DEFICIENS, is common to all mantled clones and is associated with alternative splicing and premature termination. Dense methylation near the Karma splice site (termed the Good Karma epiallele) predicts normal fruit set, whereas hypomethylation (the Bad Karma epiallele) predicts homeotic transformation, parthenocarpy and marked loss of yield. Loss of Karma methylation and of small RNA in tissue culture contributes to the origin of mantled, while restoration in spontaneous revertants accounts for non-Mendelian inheritance. The ability to predict and cull mantling at the plantlet stage will facilitate the introduction of higher performing clones and optimize environmentally sensitive land resources