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

A novel transcript of oil palm (Elaeis guineensis Jacq.), Eg707, is specifically upregulated in tissues related to totipotency

In this study, we report the molecular characterization of clone Eg707 isolated from cell suspension culture of the oil palm. The deduced polypeptide of clone Eg707 is highly similar to an unknown protein from Arabidopsis thaliana. The presence of an Ald-Xan-dh-C2 superfamily domain in the deduced protein sequence suggested that Eg707 protein might be involved in abscisic acid biosynthesis. Eg707 might be present as a single copy gene in the oil palm genome. This gene is highly expressed in tissue cultured materials compared to vegetative and reproductive tissues, suggesting a role of this gene during oil palm somatic embryogenesis or at the early stages of embryo development. Expression analysis of Eg707 by RNA in situ hybridization showed that Eg707 transcripts were present throughout somatic embryo development starting from proembryo formation at the embryogenic callus stages till the maturing embryo stages. Since proembryo formation within the embryogenic callus is one of the first key factors in oil palm somatic embryo development, it is suggested that Eg707 could be used as a reliable molecular marker for detecting early stage of oil palm somatic embryogenesis

Isolation and Characterization of Potential Markers for Prolific Explant Tissues of Oil Palm (Elaeis Guineensis Jacq.)

Tissue culture is a promising technology for the mass propagation of elite oil palm. Although this approach has been widely used in the local oil palm plantation companies, the callogenesis and embryogenesis rates remain low. Therefore, the application of markers for early diagnosis of embryogenic potential would help in reducing the cost for tissue culture of oil palm. The first part of this study was aimed to identify DNA markers for oil palm prolific explant tissues via representational difference analysis (RDA), a technique whereby the differences between two highly related genomes can be identified. In this part, a total of five forward and reverse RDA were performed using the explant tissues possessing different proliferation ability; measurement was based on the previous tissue culture data of respective oil palm tissue culture agencies. Among the difference products identified, 13:14 C58 which was putatively enriched in non-prolific tissues, possesses a few nucleotide differences when aligned with the equivalent DNA region of the highly prolific tissues. However, further verification is needed to confirm its ability as a marker for distinguishing the non-prolific explant tissues from the highly prolific explant tissues. The second part of this study was aimed to characterize one of the previously identified putative embryogenic markers known as Eg707 (FJ196136) using a technique called in situ hybridization. The gene expression of Eg707 was detected in all the tested tissues committed to embryogenic pathway as early as in embryogenic callus up to the germinating embryo. Since the formation of proembryo in embryogenic callus is regarded as the first key factor in oil palm somatic embryo development, Eg707 could be used as a potential molecular marker for early detection of oil palm somatic embryogenesis. The third part of this study was aimed to validate the efficiency of previously identified promising candidate embryogenic markers. Expression profile of five oil palm embryogenic-related genes were generated in this study using real time PCR with mRNA from oil palm leaf explant tissues that exhibit different proliferation ability in tissue culture. Two of the transcripts possess a higher potential to be used as a marker as early at the leaf explant stage of the oil palm tissue culture process. The two transcripts were grouped into two categories based on their expression profiles of either continuous or time-dependent. However, the expression profile of each gene did not correlate very well across samples possessing similar proliferation ability from various agencies. Thus, more oil palm genotypes should be analyzed to obtain a more robust selection of the markers for screening of oil palm leaf explants within a particular agency

DNA methylation changes in clonally propagated oil palm

One of the main challenges faced by the oil palm industry is fruit abnormalities, such as the “mantled” phenotype that can lead to reduced yields. This clonal abnormality is an epigenetic phenomenon and has been linked to the hypomethylation of a transposable element within the EgDEF1 gene. To understand the epigenome changes in clones, methylomes of clonal oil palms were compared to methylomes of seedling-derived oil palms. Whole-genome bisulfite sequencing data from seedlings, normal, and mantled clones were analyzed to determine and compare the context-specific DNA methylomes. In seedlings, coding and regulatory regions are generally hypomethylated while introns and repeats are extensively methylated. Genes with a low number of guanines and cytosines in the third position of codons (GC3-poor genes) were increasingly methylated towards their 3′ region, while GC3-rich genes remain demethylated, similar to patterns in other eukaryotic species. Predicted promoter regions were generally hypomethylated in seedlings. In clones, CG, CHG, and CHH methylation levels generally decreased in functionally important regions, such as promoters, 5′ UTRs, and coding regions. Although random regions were found to be hypomethylated in clonal genomes, hypomethylation of certain hotspot regions may be associated with the clonal mantling phenotype. Our findings, therefore, suggest other hypomethylated CHG sites within the Karma of EgDEF1 and hypomethylated hotspot regions in chromosomes 1, 2, 3 and 5, are associated with mantling

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