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All Journal HAYATI Journal of Biosciences Journal of Tropical Crop Science
Rizqullah, Ramadaniarto
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Agriculture, Biological Sciences & Forestry Earth & Planetary Sciences

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Genetic Variability of Echinochloa crus-galli Ecotypes from West Java, Indonesia, by RAPD Analysis Pasaribu, Pesta Maria Hotnauli; Rizqullah, Ramadaniarto; Ardie, Sintho Wahyuning; Guntoro, Dwi
Journal of Tropical Crop Science Vol. 12 No. 01 (2025): Journal of Tropical Crop Science
Publisher : Department of Agronomy and Horticulture, IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jtcs.12.01.18-24

Abstract

Echinochloa crus-galli (Barnyardgrass: Poaceae), is one of the most detrimental weeds in rice fields globally. As one of the leading rice producers in Indonesia, controlling barnyard grass in rice fields in West Java province is of great importance. Information on the genetic variability of barnyard grass is necessary to determine proper weed control. A molecular marker is considered the most accurate tool in determining genetic variability as its profile is unaffected by the environment. The objective of this study was to evaluate the genetic variability of barnyard grass collected from seven sub-districts in West Java province, Indonesia, using RAPD markers. Genomic DNA of barnyard grass ecotypes from “Bayusari”, “Majalaya”, “Klari”, “Cugenang”, “Cianjur”, “Ciomas”, and “Ciampea” sub-districts were analyzed using eight RAPD primers and resulted in a total of 87 reproducible amplicons. Of these amplicons, 59 were polymorphic, and 28 were monomorphic, with a polymorphism percentage ranging from 37.5-92.8%. Polymorphism information content (PIC) values ranged from 0.21 to 0.41, indicating the used RAPD markers are highly informative. All seven ecotypes were divided into three distinct groups with a coefficient level of 0.77 in a dendrogram constructed following the UPGMA clustering method. Group 1 consisted only of the “Bayusari” ecotype. Group 2 consisted of “Majalaya”, “Klari”, and “Cugenang” ecotypes, while Group 3 consisted of “Cianjur”, “Ciomas”, and “Ciampea” ecotypes. This research indicated remote dispersal of E. crus-galli, since ecotypes from distant locations were found to be closely related
Characterization of Lignin Biosynthesis Encoding Gene, SiCOMT, from Nine Indonesian Foxtail Millet (Setaria italica (L.) P. Beauv.) Genotypes Rizqullah, Ramadaniarto; Saenal, Nirwanti; Pahlevi, M Reza; Suwarno, Willy Bayuardi; Tsugama, Daisuke; Ardie, Sintho Wahyuning
HAYATI Journal of Biosciences Vol. 33 No. 3 (2026): May 2026
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 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.
Improved Performance of SiDREB2-SNAP Marker in Foxtail Millet by Optimum Primer Concentration, PCR Cycle, and DNA Polymerase Specificity Wospakrik, Andrean Heskiel; Rizqullah, Ramadaniarto; Pahlevi, M Reza; Yudiansyah, Yudiansyah; Purwoko, Bambang Sapta; Suwarno, Willy Bayuardi; ARDIE, Sintho Wahyuning
Journal of Tropical Crop Science Vol. 13 No. 01 (2026): Journal of Tropical Crop Science
Publisher : Department of Agronomy and Horticulture, IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jtcs.13.01.103-113

Abstract

Foxtail millet (Setaria italica L. Beauv.) is an emerging carbohydrate-producing crop. It is considered a climate-resilient crop due to its tolerance to abiotic stresses. Breeding for abiotic-tolerant crops requires powerful tools such as molecular markers. The single-nucleotide amplified polymorphism (SNAP) marker, developed from a single-nucleotide DNA variation at a specific location in the plant genome, is a simple yet powerful PCR-based marker widely used in phenotype-related selection. A SiDREB2-based SNAP marker was previously developed based on a base variation at the 558th base pair (an A/G transition) in the SiDREB2 gene and used to estimate the drought tolerance in foxtail millet. However, the specificity of the marker depends on technical aspects, including the type of DNA polymerase used, primer concentration, and the number of PCR cycles. Here, we reported that non-specific and false positive amplicons can be eliminated by utilizing DNA polymerase with no 3’ to 5’ proofreading activity and reducing the final primer concentration to 1.25 μM. PCR cycle number 25 yielded the optimum specificity, while increasing the cycle to 30 resulted in false positive results. Altogether, our results showed that technical optimization is necessary for improving the specificity of the SNAP marker.
Co-Authors Bambang Sapta Purwoko Dwi Guntoro Pahlevi, M Reza Pasaribu, Pesta Maria Hotnauli Saenal, Nirwanti Sintho Wahyuning Ardie Tsugama, Daisuke Willy Bayuardi Suwarno Wospakrik, Andrean Heskiel Yudiansyah Yudiansyah