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All Journal Menara Perkebunan Jurnal Bioteknologi & Biosains Indonesia (JBBI) Jurnal Bioteknologi & Biosains Indonesia
Setiowati, Retno Diah
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Environmental Science Health Professions

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IDENTIFICATION OF KEY NITROGEN USE EFFICIENCY-RELATED GENES IN OIL PALM USING BIOINFORMATICS APPROACHES Permatasari, Galuh Wening; Setiowati, Retno Diah; Wening, Sri
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol. 12 No. 1 (2025)
Publisher : BRIN - Badan Riset dan Inovasi Nasional

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55981/jbbi.2025.10477

Abstract

Efficient nitrogen use is crucial for maximizing oil palm yield while reducing environmental impact. Poor nitrogen utilization causes excessive growth and nutrient loss. This study uses bioinformatics to identify key genes linked to nitrogen use efficiency, providing insights for genetic improvement and sustainable cultivation.Protein-protein interaction (PPI) networks, functional enrichment, and structural modeling were employed to uncover candidate genes regulating nitrogen uptake and metabolism. Sixty-two nitrogen use efficiency associated genes from rice (Oryza sativa) were analyzed via BLASTp against the E. guineensis genome (NCBI), selecting those with >80% similarity. PPI networks were constructed using STRING-db and analyzed in Cytoscape v3.7.1. Functional enrichment (Gene Ontology) and structural analysis (AlphaFold, PyMol v2.5.4) were performed. Twelve nitrogen use efficiency related genes were identified, with CESA4, CESA7, and CESA9 emerging as key regulators based on high degree and betweenness values in PPI analysis. These genes are linked to plant cell wall biosynthesis. Structural analysis showed high similarity to rice homologs, with RMSD values of 0.338 Å (CESA4) and 0.396 Å (CESA9), indicating strong conservation area. Their structural relevance suggests they are promising targets for molecular breeding marker to enhance nitrogen utilization and sustainability in oil palm.
Identification of metabolites for biomarker of nitrogen and potassium use efficiency in oil palm Setiowati, Retno Diah; Sri Wening; Nuringtyas, Tri Rini; Rahayu, Megayani Sri; Sudarsono, Sudarsono
Menara Perkebunan Vol. 93 No. 1 (2025): 93(1), 2025
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v93i1.631

Abstract

Nutrient-use efficiency in oil palm is important for economic and environmental reasons. This research aimed to identify biomarkers to discriminate between tolerant and susceptible oil palms to potassium (K) and nitrogen (N) deficiency. A screening of oil palm materials for N or K use efficiency was conducted using an omission trial experiment, where only targeted nutrient was applied as treatment, while all other nutrients were applied as recommended. The treatment was performed in the main nursery for ten months to identify progenies with contrasting traits. Metabolite analysis was performed to identify specific metabolites as biomarkers for N-efficient and K-efficient palms. Samples taken from the roots of the contrasting progenies were treated with liquid nitrogen prior to grinding into a powder for liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis. The LC-HRMS analysis showed 277 metabolites from K and N treatments after data trimming, which were then analysed in MetaboAnalyst 6.0 for biomarker identification. The results showed that some metabolites were statistically significant. Metabolites identified in more than one analysis have a higher likelihood of being considered as biomarkers. In this experiment, we compared PLS-DA, sPLS-DA, and Random Forest. However, some identified metabolites were not to occur naturally in the treatment palms. Some amino acids and antioxidants were promising biomarkers to differentiate the N-deficiency-tolerant and K-deficiency-tolerant palms. Thus, the biomarkers facilitate the breeding scheme to create a nutrient-efficient palm planting material.
IDENTIFICATION OF KEY NITROGEN USE EFFICIENCY-RELATED GENES IN OIL PALM USING BIOINFORMATICS APPROACHES Permatasari, Galuh Wening; Setiowati, Retno Diah; Wening, Sri
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol. 12 No. 1 (2025)
Publisher : BRIN - Badan Riset dan Inovasi Nasional

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55981/jbbi.2025.10477

Abstract

Efficient nitrogen use is crucial for maximizing oil palm yield while reducing environmental impact. Poor nitrogen utilization causes excessive growth and nutrient loss. This study uses bioinformatics to identify key genes linked to nitrogen use efficiency, providing insights for genetic improvement and sustainable cultivation.Protein-protein interaction (PPI) networks, functional enrichment, and structural modeling were employed to uncover candidate genes regulating nitrogen uptake and metabolism. Sixty-two nitrogen use efficiency associated genes from rice (Oryza sativa) were analyzed via BLASTp against the E. guineensis genome (NCBI), selecting those with >80% similarity. PPI networks were constructed using STRING-db and analyzed in Cytoscape v3.7.1. Functional enrichment (Gene Ontology) and structural analysis (AlphaFold, PyMol v2.5.4) were performed. Twelve nitrogen use efficiency related genes were identified, with CESA4, CESA7, and CESA9 emerging as key regulators based on high degree and betweenness values in PPI analysis. These genes are linked to plant cell wall biosynthesis. Structural analysis showed high similarity to rice homologs, with RMSD values of 0.338 Å (CESA4) and 0.396 Å (CESA9), indicating strong conservation area. Their structural relevance suggests they are promising targets for molecular breeding marker to enhance nitrogen utilization and sustainability in oil palm.
Co-Authors Megayani Sri Rahayu PERMATASARI, Galuh Wening Sri Wening Sudarsono Tri Rini Nuringtyas