Identification of Oil Palm's Consistently Upregulated Genes during Early Infections of Ganoderma boninense via RNA-Seq Technology and Real-Time Quantitative PCR.

Liyana Mohd Zuhar,Abu Seman Idris,Zamri Zainal,Noor Azmi Shaharuddin,Siti Aqlima Ahmad,Ahmad Zairun Madihah

doi: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.

Highlights

Oil palm (Elaeis guineensis Jacq.) is one of Malaysia’s most economically significant plantation crops, with approximately 5.90 million hectares of reported cultivation in 2019 [1,2]
To identify potential genes that are involved in the defense mechanisms of oil palm roots towards G. boninense infection, we harvested oil palm roots of Tenera that were artificially infected with the fungus G. boninense at two different times of infection, labeled as early and late infection categories
The classification of the fungus infection stage was made based on the basal stem rot (BSR) severity score on a scale of 0–4, with 0 indicating a healthy-looking palm without any fungal mycelium appearance and 4 regarded as a dead palm

Summary

Introduction

Oil palm (Elaeis guineensis Jacq.) is one of Malaysia’s most economically significant plantation crops, with approximately 5.90 million hectares of reported cultivation in 2019 [1,2]. The highest oil-yielding crop contributes 33.3% of the world’s palm oil production, with export revenue earnings of more than USD 18 billion [3,4]. Malaysian oil palm cultivation suffers from a devastating disease known as basal stem rot (BSR), caused by the fungus Ganoderma boninense. BSR is a fatal disease in the oil palm industry in Malaysia. It causes the internal trunk tissue to rot, reducing the number of standing palms. The threat of BSR disease towards the oil palm industry warrants extensive effort in finding a solution to eradicate this disease permanently

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