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

Abstract

Background: The 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.

Results: A 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.

Conclusions: Our 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.

Keywords: Elaeis guineensis; Expression microarray; Gene expression; Oil palm; Oil yield.

Fig. 1

GO classification comparison across six different time points for differentially expressed genes. The ten highest representative GO categories from each time point are shown in the bar chart. The total of these ten GO categories represents over 55% of GO counts in each time point

Fig. 2

Differentially expressed genes involved in fatty acid biosynthesis pathway. a KAR (ketoacyl-ACP reductase), b KAS III (β- ketoacyl-ACP synthases III), c KAS I (β- ketoacyl-ACP synthases I) (Isotig17406), d KAS I (Isotig26074). Eight biological replicates of HY and LY were used for each time point (12-20 WAP) except for 22 WAP (six HY and seven LY)

Fig. 3

Differentially expressed genes in the glycolysis pathway (a) GAPDH (Glyceraldehyde-3-phosphate dehydrogenase) and (b) Pyruvate Dehydrogenase (E1 component). Eight biological replicates of HY and LY were used for each time point (12-20 WAP) except for 22 WAP (six HY and seven LY)

Fig. 4

Differentially expressed genes in the TCA Cycle. (a) Succinate Dehydrogenase and (b) ATP-Citrate Lyase. Eight biological replicates of HY and LY were used for each time point (12-20 WAP) except for 22 WAP (six HY and seven LY)

Fig. 5

Summary of the differentially expressed genes in pathways that are involved directly or indirectly in lipid biosynthesis in high-yielding oil palm. Green represents up-regulated, red represents down-regulated genes and blue represents non-differentially expressed genes. The curved arrow represents the carbon flux that is channeled through the Sucrose Synthase 2 pathway