Differential gene expression at different stages of mesocarp development in high- and low-yielding oil palm

Abstract

BackgroundThe oil yield trait of oil palm is expected to involve multiple genes, environmental influences and interactions. Many of the underlying mechanisms that contribute to oil yield are still poorly understood. In this study, we used a microarray approach to study the gene expression profiles of mesocarp tissue at different developmental stages, comparing genetically related high- and low- oil yielding palms to identify genes that contributed to the higher oil-yielding palm and might contribute to the wider genetic improvement of oil palm breeding populations.ResultsA total of 3412 (2001 annotated) gene candidates were found to be significantly differentially expressed between high- and low-yielding palms at at least one of the different stages of mesocarp development evaluated. Gene Ontologies (GO) enrichment analysis identified 28 significantly enriched GO terms, including regulation of transcription, fatty acid biosynthesis and metabolic processes. These differentially expressed genes comprise several transcription factors, such as, bHLH, Dof zinc finger proteins and MADS box proteins. Several genes involved in glycolysis, TCA, and fatty acid biosynthesis pathways were also found up-regulated in high-yielding oil palm, among them; pyruvate dehydrogenase E1 component Subunit Beta (PDH), ATP-citrate lyase, β- ketoacyl-ACP synthases I (KAS I), β- ketoacyl-ACP synthases III (KAS III) and ketoacyl-ACP reductase (KAR). Sucrose metabolism-related genes such as Invertase, Sucrose Synthase 2 and Sucrose Phosphatase 2 were found to be down-regulated in high-yielding oil palms, compared to the lower yield palms.ConclusionsOur findings indicate that a higher carbon flux (channeled through down-regulation of the Sucrose Synthase 2 pathway) was being utilized by up-regulated genes involved in glycolysis, TCA and fatty acid biosynthesis leading to enhanced oil production in the high-yielding oil palm. These findings are an important stepping stone to understand the processes that lead to production of high-yielding oil palms and have implications for breeding to maximize oil production.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3855-7) contains supplementary material, which is available to authorized users.

Comparative RNA-Seq Analysis of High- and Low-Oil Yellow Horn During Embryonic Development

“…It is proposed that two up-regulated accC genes may promote FA biosynthesis at the early stage of embryonic development, which further promote oil accumulation in developing yellow horn embryos, resulting in higher oil content in the high-oil line ( Figure 5 ). In contrast to two above accC genes, one KAR gene was shown to be down-regulated in HO compared to LO at 54 daa, which was different from what was observed in high oil-yielding palm previously [ 7 ]. In the plastid, the extension of FA from malonyl-ACP is iteratively catalyzed by a type II FA synthase (FAS) system consisting of 3-ketoacyl-ACP synthase (KAS), KAR, hydroxyacyl-ACP dehydrogenase (HAD), and enoyl-ACP reductase (EAR) [ 28 ].…”

“…Previous studies in several oil-producing crops have confirmed a link between increased PK or PDHC expression and higher oil accumulation [ 41 ]. It has also been shown that in high-oil palms, PDHC was up-regulated compared to the low-oil group [ 7 ]. Similarly, in this study, PKc and PDHC/E2 (downstream genes involved in glycolysis) were found to be significantly up-regulated in HO compared to LO yellow horn at 40 and 54 daa.…”

“…To date, a large number of studies have investigated mechanistic differences in oil biosynthetic pathways between high- and low-oil lines in various oil-producing crops such as oil palm [ 7 ], rape seed [ 8 , 9 , 10 ], soybean [ 11 ], sunflower [ 12 ], and maize [ 13 , 14 ]. These studies used a variety of approaches, including microarray/gene expression [ 8 , 11 ], proteomics studies [ 14 , 15 ], metabolomic studies [ 16 ], enzyme activities [ 12 , 17 ], and microscopic analysis of oil bodies [ 9 ] to try to elucidate genes associated with oil content.…”

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

“…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 .…”