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. 2025 May 14;15(1):16784.
doi: 10.1038/s41598-025-01691-y.

1H NMR metabolomic profiling of resistant and susceptible oil palm root tissues in response to Ganoderma boninense at the nursery stage

Syarul Nugroho  1   2 , Hernawan Yuli Rahmadi  3   4 , Arfan Nazhri Simamora  3   4 , Abdul Razak Purba  3
Affiliations

1H NMR metabolomic profiling of resistant and susceptible oil palm root tissues in response to Ganoderma boninense at the nursery stage

Syarul Nugroho et al. Sci Rep. .

Abstract

Oil palm plantations face serious challenges from Ganoderma boninense, a pathogen that causes basal stem rot (BSR), leading to significant productivity losses, with an estimated economic impact of 68.73%. Ganoderma spreads through direct root contact and airborne spores, affecting plantations across Indonesia, Malaysia, and other countries. Understanding the mechanisms of oil palm resistance to Ganoderma is crucial for developing effective strategies. Metabolomic profiling, ¹H NMR spectroscopy, offers a promising tool for identifying and quantifying metabolic changes associated with Ganoderma resistance. This study, ¹H NMR was employed to analyze root tissues of resistant, susceptible, and control oil palm seedlings exposed to Ganoderma. The results indicated that PCA effectively differentiated resistant palms from susceptible ones, while PLS-DA identified 14 significant metabolites. Further analysis using OPLS-DA and ROC revealed that ascorbic acid, D-gluconic acid, D-fructose, and 2-oxoisovalerate could serve as potential biomarkers for screening resistant palms. The metabolites identified in this study hold considerable promise for supporting breeding programs to develop oil palm varieties with enhanced resistance to BSR.

Keywords: 1H NMR; Metabolic biomarkers; Metabolomic profiling; Oil palm resistance.

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Conflict of interest statement

Declarations. Competing interests: The authors declare no competing interests. Ethics declarations: We confirm that all methods in this study were conducted in accordance with relevant guidelines and legislation for plant research. This research does not involve any studies with human or animal participants conducted by any of the authors.

Figures

Fig. 1
Fig. 1
The relative concentration of metabolites in resistant, susceptible, and control root tissues from oil palm seedlings. Each compound class was expressed as a relative percentage across the various resistance categories.
Fig. 2
Fig. 2
Visualization of (a) 2D PCA and (b) 3D PCA of metabolites in resistant, susceptible, and control root tissues from oil palm seedlings.
Fig. 3
Fig. 3
(a) PLS-DA analysis result of metabolites in resistant, susceptible, and control root tissues from oil palm seedlings. (b) Heatmap visualization of metabolites in resistant, susceptible, and control root tissues from oil palm seedlings. Up-regulated metabolites were represented in red, while down-regulated metabolites were shown in blue.
Fig. 4
Fig. 4
ROC curve and Boxplot of ascorbic acid levels in (a) resistant, (b) susceptible, and (c) control root tissues from oil palm seedlings.
Fig. 5
Fig. 5
Pathway analysis of metabolites in (a) resistant, (b) susceptible, and (c) control root tissues from oil palm seedlings (p-value < 0.05 and pathway impact > 1). The horizontal dotted line represents the threshold for statistical significance (p-value), while the vertical line denotes the cutoff for pathway impact scores.
Fig. 6
Fig. 6
(a) Ganoderma boninense isolate. (b) RWB infected with Ganoderma. (c) Sitting germinated seed technique for Ganoderma inoculation in oil palm seedlings. (d) Comparison of resistant and susceptible oil palms after six months of infection (e) Fruiting body of Ganoderma on susceptible oil palm.
See this image and copyright information in PMC

References

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