Identification of Oil Palm’s Consistently Upregulated Genes during Early Infections of Ganoderma boninense via RNA-Seq Technology and Real-Time Quantitative PCR
Open Access
- 27 September 2021
- Vol. 10 (10), 2026
- https://doi.org/10.3390/plants10102026
Abstract
Basal stem rot (BSR) disease caused by pathogenic fungus Ganoderma boninense is a significant concern in the oil palm industry. G. boninense infection in oil palm induces defense-related genes. To understand oil palm defense mechanisms in response to fungal invasion, we analyzed differentially expressed genes (DEGs) derived from RNA-sequencing (RNA-seq) transcriptomic libraries of oil palm roots infected with G. boninense. A total of 126 DEGs were detected from the transcriptomic libraries of G. boninense-infected root tissues at different infection stages. Functional annotation via pathway enrichment analyses revealed that the DEGs were involved in the defense response against the pathogen. The expression of the selected DEGs was further confirmed using real-time quantitative PCR (qPCR) on independent oil palm seedlings and mature palm samples. Seven putative defense-related DEGs consistently showed upregulation in seedlings and mature plants during G. boninense infection. These seven genes might potentially be developed as biomarkers for the early detection of BSR in oil palm.Keywords
Funding Information
- Malaysian Palm Oil Board (R009411000 (BD6-2.2.2))
- Universiti Putra Malaysia (Graduate Research Fellowship (GRF))
- Minister of Higher Education, Malaysia (MyBrain15 Scholarship)
This publication has 59 references indexed in Scilit:
- Expression of flavonoid 3’-hydroxylase is controlled by P1, the regulator of 3-deoxyflavonoid biosynthesis in maizeBMC Plant Biology, 2012
- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and CufflinksNature Protocols, 2012
- The Pepper Mannose-Binding Lectin Gene CaMBL1 Is Required to Regulate Cell Death and Defense Responses to Microbial PathogensPlant Physiology, 2011
- Thaumatin-like proteins are differentially expressed and localized in phloem tissues of hybrid poplarBMC Plant Biology, 2010
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiationNature Biotechnology, 2010
- Effects of -1,3-glucan from Septoria tritici on structural defence responses in wheatJournal of Experimental Botany, 2009
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeGenome Biology, 2009
- Ectopic Expression of aBasic Helix-Loop-HelixGene Transactivates Parallel Pathways of Proanthocyanidin Biosynthesis. Structure, Expression Analysis, and Genetic Control ofLeucoanthocyanidin 4-ReductaseandAnthocyanidin ReductaseGenes inLotus corniculatusPlant Physiology, 2006
- Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT MethodMethods, 2001
- A new mathematical model for relative quantification in real-time RT-PCRNucleic Acids Research, 2001