Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array

Abstract

Gene expression changes that occur during mesocarp development are a major research focus in oil palm research due to the economic importance of this tissue and the relatively rapid increase in lipid content to very high levels at fruit ripeness. Here, we report the development of a transcriptome-based 105,000-probe oil palm mesocarp microarray. The expression of genes involved in fatty acid (FA) and triacylglycerol (TAG) assembly, along with the tricarboxylic acid cycle (TCA) and glycolysis pathway at 16 Weeks After Anthesis (WAA) exhibited significantly higher signals compared to those obtained from a cross-species hybridization to the Arabidopsis (p-value < 0.01), and rice (p-value < 0.01) arrays. The oil palm microarray data also showed comparable correlation of expression (r2 = 0.569, p < 0.01) throughout mesocarp development to transcriptome (RNA sequencing) data, and improved correlation over quantitative real-time PCR (qPCR) (r2 = 0.721, p < 0.01) of the same RNA samples. The results confirm the advantage of the custom microarray over commercially available arrays derived from model species. We demonstrate the utility of this custom microarray to gain a better understanding of gene expression patterns in the oil palm mesocarp that may lead to increasing future oil yield.

Deciphering key proteins of oil palm (Elaeis guineensis Jacq.) fruit mesocarp development by proteomics and chemometrics

“…The KARs and ENRs which were involved in the FA biosynthesis pathway were up‐regulated corroborates previous study . The HAD was abundance at 18 WAA then decreased towards ripening (20 WAA) displaying a different trend compared to the upregulation of transcriptome towards oil palm fruit ripening . Previous studies also reported that FA biosynthetic enzymes were upregulated throughout oil palm fruit ripening at transcriptome and proteome levels .…”

“…Moreover, almost all the key FA biosynthetic machinery indicated the utmost transcription level at 17 WAA where the onset of oil accumulation starts . The highly expressed proteins associated with lipid biosynthesis correspond to an increase in transcriptome and proteome levels throughout mesocarp development . This finding is in parallel with the FAS enzyme activities in lipid biosynthesis which regulates the oil yield and quality in developing fruits .…”

“…A comparison of transcripts in mesocarp, endosperm and embryo of oil palm during development was carried out to provide an understanding of the mechanisms that direct the variations of oil content and fatty acid composition, lipid composition and tissues . In addition, the oil palm mesocarp microarray was reported as an alternative to the gene expression profile in oil palm mesocarp by sequencing the temporal variations of oil assembly at the proteome level . Furthermore, chromoplast proteins which are necessary for most of the physiological processes such as fatty acid biosynthesis in oil palm mesocarp have been studied using proteomics approaches .…”

Key glycolytic branch influences mesocarp oil content in oil palm

“…Our Group previously found differential in gene expression as well as protein and metabolite levels in glycolysis pathway were associated with mesocarp oil content 3 , 4 , 16 . In this study, we validated the oil palm glycolytic gene function through loss-of-function mutants in Saccharomyces cerevisiae as a model system.…”

Review: Omics and Strategic Yield Improvement in Oil Crops

“…All mesocarp samples were characterized using parallel profiling techniques for the transcript (cDNA microarrays), protein/peptide (UPLC-MS, MALDI-TOF/TOF-MS) and metabolite (GC-MS, CE-MS, LC-MS) levels. A custom oil palm transcriptome microarray was developed using the Agilent platform [111] as a tool to study gene expression profiles of mesocarp tissue. Biochemical changes before, during, and after oil biosynthesis in the fruit mesocarp were compared to gain a deeper understanding of the control of oil biosynthesis in the oil palm [104].…”