Characterization of Lignin Biosynthesis Encoding Gene, SiCOMT, from Nine Indonesian Foxtail Millet (Setaria italica (L.) P. Beauv.) Genotypes

Ramadaniarto Rizqullah; Nirwanti Saenal; M Reza Pahlevi; Willy Bayuardi Suwarno; Daisuke Tsugama; Sintho Wahyuning Ardie

doi:10.4308/hjb.33.3.575-583

Authors

Ramadaniarto Rizqullah Plant Breeding and Biotechnology Study Program, IPB University, Bogor 16680, Indonesia
Nirwanti Saenal Agronomy and Horticulture Study Program, IPB University, Bogor 16680, Indonesia
M Reza Pahlevi Plant Breeding and Biotechnology Study Program, IPB University, Bogor 16680, Indonesia https://orcid.org/0009-0008-6807-8302
Willy Bayuardi Suwarno Department of Agronomy and Horticulture, IPB University, Bogor 16680, Indonesia https://orcid.org/0000-0002-7189-7906
Daisuke Tsugama Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan https://orcid.org/0000-0002-4946-678X
Sintho Wahyuning Ardie Department of Agronomy and Horticulture, IPB University, Bogor 16680, Indonesia https://orcid.org/0000-0003-0563-1373

DOI:

https://doi.org/10.4308/hjb.33.3.575-583

Abstract

Caffeic acid O-methyltransferase (COMT) is an essential enzyme that catalyzes the biosynthesis of lignin monomer units. Foxtail millet (Setaria italica) possesses three COMT-encoding genes. However, only SiCOMT1 and SiCOMT2 are considered expressed. This study investigates the characteristics of the two COMT-encoding genes across nine Indonesian foxtail millet genotypes. Phylogenetic analysis revealed that SiCOMT1 is closely related to N-methyltransferase genes, which are not involved in the lignin biosynthesis pathway. Meanwhile, SiCOMT2 is closely related to O-methyltransferase genes involved in lignin biosynthesis. SiCOMT2 from nine Indonesian foxtail millet genotypes exhibits 15 synonymous and three non-synonymous SNPs. SiCOMT2 amino acid showed Ala67Thr and Pro72Ala variations within the methyltransferase dimerization domain, and Glu146Asp within the O-methyltransferase domain. Among these, the Pro72Ala substitution is predicted to reduce the structural stability of the encoded protein. These findings suggest that SiCOMT2 may serve as a promising target for future genetic research and crop improvement strategies aimed at enhancing biomass quality by modifying lignin content and composition.

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Author Biographies

Ramadaniarto Rizqullah, Plant Breeding and Biotechnology Study Program, IPB University, Bogor 16680, Indonesia

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Nirwanti Saenal, Agronomy and Horticulture Study Program, IPB University, Bogor 16680, Indonesia

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M Reza Pahlevi, Plant Breeding and Biotechnology Study Program, IPB University, Bogor 16680, Indonesia

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Willy Bayuardi Suwarno, Department of Agronomy and Horticulture, IPB University, Bogor 16680, Indonesia

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Daisuke Tsugama, Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan

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Sintho Wahyuning Ardie, Department of Agronomy and Horticulture, IPB University, Bogor 16680, Indonesia

Associate Professor in Plant Biotechnology at the Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University