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All Journal HAYATI Journal of Biosciences Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Buletin Agrohorti Jurnal Fitopatologi Indonesia Jurnal Hortikultura Indonesia (JHI) BIOTROPIA - The Southeast Asian Journal of Tropical Biology Jurnal Agro Teknologi Tropika Indonesian Journal of Agricultural Science AGRIVITA, Journal of Agricultural Science Journal of Tropical Biodiversity and Biotechnology JURNAL BIOLOGI INDONESIA Jurnal Penelitian Pertanian Tanaman Pangan Journal of Tropical Crop Science Agritrop : Jurnal Ilmu-Ilmu Pertanian (Journal of Agricultural Science) Buletin Palma Berita Biologi
Sintho Wahyuning Ardie
Department Of Agronomy And Horticulture, Faculty Of Agriculture, IPB University, Dramaga Campus, Bogor 16680, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Economics, Econometrics & Finance Environmental Science Immunology & microbiology Medicine & Pharmacology Veterinary

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Journal : HAYATI Journal of Biosciences

 1 
Endophytic Fungi Isolated from the Mangrove Species Rhizophora apiculata and Their Efficacy as Herbicides Za’aziza Ridha Julia; Nampiah Sukarno; Sintho Wahyuning Ardie; Irmanida Batubara; Soekisman Tjitrosoedirdjo; Mashuri Waite
HAYATI Journal of Biosciences Vol. 29 No. 5 (2022): September 2022
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.29.5.605-620

Abstract

Endophytic fungi play an important role on mangrove growth and development, however research on the endophytic fungi of the mangrove Rhizophora apiculata is limited. The endophytic fungi produce diverse bioactive compounds involved in the mangrove’s adaptation to varied biotic and abiotic stresses and could have applied uses in agriculture or medicine. The purpose of this research was to isolate endophytic fungi of Rhizophora apiculata mangrove and to study their activity as herbicides on the weed Gomphrena globosa. The fungi were isolated using the surface sterilization method and identified based on morphological characteristics and molecular characteristics using ITS regions of rDNA. Herbicidal activity of the fungal filtrates extracted by ethyl acetate were tested on seed germination and seedling growth of G. globosa. Five fungal isolates were obtained, namely Penicillium citrinum, Diaporthe eucalyptorum, Diaporthe musigena, Colletotrichum queenslandicum, and Diaporthe tectonae. All isolates were able to grow on PDA medium containing 0, 25, 50, 75, and 100 (% v/v) seawater concentrations, but the growth rate varied by species and seawater concentration. In general, all five isolates showed herbicidal activity by delaying seed germination and reducing shoot and root growth. P. citrinum showed the highest herbicidal activity compared to the other isolates. Analysis using Gas Chromatography-Mass Spectrometry of the crude extract of P. citrinum filtrate identified 7 main compounds: 3-Methoxy-2-methyl-cyclohex-2-enone, Cyclohexane-carbohexaldehyde, 6-methyl-3-(1-methylethyl)-2-oxo, Cyclopropane carboxylic acid, 1-(2-propenyl)-1,1-dimethylethyl ester, 2-Hydroxy-4-isopropyl-7-methoxytropone, Beta-Asarone, Oxane, 4-(2-amino-1-hydroxyethyl)-4-(3,4-dimethoxyphenyl)-, and Diisooctyl-phthalate. These compounds should be studied further to determine which ones are responsible for the herbicidal activity.
The Genetic Variability of Indonesian Local Foxtail Millet Accession Based on Agro-morphological Traits and Early Salinity Tolerance Evaluation Utilizing SiDREB2-based SNAP Marker Sri Ratnawati; Rika Miftakhul Jannah; Yuli Irvana Dewi; Ramadaniarto Rizqullah; Willy Bayuardi Suwarno; Sintho Wahyuning Ardie
HAYATI Journal of Biosciences Vol. 31 No. 1 (2024): January 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.1.82-93

Abstract

Foxtail millet (Setaria italica L. Beauv.) is a grain-producing crop with high nutritional benefits and adaptability to broad environmental conditions. Indonesian local foxtail millet accessions are valuable genetic resources for crop improvement of the species. This study aims to assess the biodiversity of Indonesian local foxtail millet accessions and estimate their salinity tolerance level utilizing the SiDREB2-based SNAP marker and early evaluation at the seedling stage. Our results showed that eight Indonesian local foxtail millet accessions, namely Toraja, Mauliru-2, Hambapraing, NTB-1, ICERI-5, ICERI-6, Botok-4, and Botok-10, had high variability based on agro-morphological traits. The Hambapraing and Mauliru-2 were the potential accessions with high yield estimates (2.33 ton.ha-1 and 1.93 ton.ha-1) and early harvest time (<110 DAT). ICERI-6 was indicated as a salinity-tolerant genotype based on the SiDREB2-based marker and early salinity evaluation at the seedling stage, while Toraja, Mauliru-2, NTB-1, and Botok-4 were categorized as sensitive genotypes. Germplasm variability and the estimated salinity tolerance level of Indonesian local foxtail millet accessions presented in this study serve as essential information in the foxtail millet breeding for high productivity, early harvest time, and salinity tolerant variety.
Flowering Phenology and SiDREB2-based SNAP Marker-assisted Hybridity Confirmation for Artificial Hybridization of Indonesian Foxtail Millet (Setaria italica L. Beauv) Genotypes Nugroho, Rizki Bagus; Chusnah, Uswatun; Suwarno, Willy Bayuardi; Ardie, Sintho Wahyuning
HAYATI Journal of Biosciences Vol. 31 No. 6 (2024): November 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.6.1082-1094

Abstract

Foxtail millet hybrid development encounters challenges due to its self-pollinating nature, small florets, and tool availability for confirming true hybrid. Our research aimed to assess flowering phenology and explore artificial hybridization employing SiDREB2 based-SNAP marker. The research consisted of three experiments. The first experiment focused on the panicle phenology of foxtail millet, while the second experiment focused on floret phenology and reproductive organs. The artificial hybridization successfulness was validated with SNAP markers based on the SiDREB2 gene in the third experiment. Observations on two genotypes (ICERI-5 and ICERI-6) revealed panicle initiation at 49–69 days after planting (DAP), with anthesis occurring 6 days after panicle emergence (DAPE). Florets exhibited the formation of reproductive organs at 3 DAPE, delineating distinct stages of pollen development leading up to anthesis. Our findings emphasized the significance of implementing male-sterile induction treatment at 4 DAPE to regulate pollen development for successful hybridization by 6 DAPE. The hybrid evaluation revealed varied germination rates and confirmed hybrid percentages across different crossing series, validated by SiDREB2-based SNAP marker. ICERI-5×Botok-4 exhibited high germination but a low confirmed hybrid percentage, while Botok-4×ICERI-5 and Botok-10×ICERI-6 showed the opposite trend. Reciprocal crossings showed unilateral incompatibility in confirmed hybrid percentage.
Evaluation of Agronomic Performance and Genetic Diversity in Indonesian Pigmented Rice Using SCoT (Start Codon Targeted) Markers Safitri, Vika Ayu; Fatimah, Fatimah; Wahyu, Yudiwanti; Ardie, Sintho Wahyuning; Mahrup, Mahrup
HAYATI Journal of Biosciences Vol. 33 No. 1 (2026): January 2026
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.33.1.103-113

Abstract

Indonesia is rich in biodiversity, including rice (Oryza sativa L.), one of the most important and widely cultivated crops. However, the utilization of local Indonesian rice germplasm in breeding programs remains limited due to the lack of reliable characterization data. Therefore, it’s essential to establish a reliable method to ensure variety protection by breeders. In addition, understanding the relationship between morphological traits and genetic diversity is crucial for a targeted breeding study aimed at evaluating genetic diversity among 12 local rice genotypes from Indonesia through agronomic traits and molecular analysis using start codon targeted (SCoT) markers. Statistical analyses, including cluster and diversity indices, were applied to interpret the data. Characterization was conducted based on the descriptors from The International Rice Research Institute (IRRI) and Bioversity International, while molecular analysis employed 23 selected SCoT primers. The effectiveness of the markers was assessed through polymorphism percentage, PIC values, and cluster analysis. A polymorphism level of 69% was observed, with PIC values ranging from 0.3610 to 0.4646, suggesting that the SCoT markers used provided adequate informativeness for diversity analysis. The study revealed high genetic variability, with heritable traits and informative SCoT markers, demonstrating their potential for pre-breeding and diversity analysis.  
Panicle Trait Diversity and Its Impact on the Productivity of Indonesian Foxtail Millet (Setaria italica L. Beauv.) Genotypes Luthfiani, Marisa Vidya; Pahlevi, M Reza; Purwoko, Bambang Sapta; 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.33.3.566-574

Abstract

Foxtail millet is a climate-resilient cereal crop that is growing in importance in food security and sustainable agriculture. This study aimed to identify panicle traits associated with yield, determine functional traits suitable for selecting high-productivity genotypes, and classify superior local Indonesian foxtail millet genotypes. Eight genotypes were evaluated using a randomized complete block design with three replications. Correlation analysis of 31 panicle traits revealed that grain filling rate, panicle weight, grain weight per panicle, grain weight per plant, and grain numbers on the middle and lower primary branches were positively associated with yield. Several of these traits also exhibited high broad-sense heritability and moderate GCV and PCV values, indicating their potential for selection. Principal component and two-way heatmap cluster analyses identified Buru, ICERI-7, Hambapraing, and Mauliru-2 as high-yielding genotypes. The findings provide critical insights for foxtail millet breeding programs in Indonesia focused on improving yield.
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.
Co-Authors , Krisantini Abdul Qadir Agus Zainudin Agustina, Ferra Anggita Ahmad Fathoni Aji, Titistyas Gusti Alex Hartana Anas D Susila Anas Dinurrohman Susila Anjarsari, Nurul Aeni Anshori, Muhammad Fuad Ashan, Muh Aswad Azis Natawijaya Bambang Sapta Purwoko Butarbutar, Lidya Kristina Sari Cahyono, Andy Agus Chusnah, Uswatun Dewi Sukma Didy Sopandie Dwi Guntoro Enny Sudarmonowati Enung Sri Mulyaningsih fatimah Fatimah Ferdinans, Ferdinans Ghulammahdi, Munif Hagia Sophia Khairani HAJRIAL ASWIDINNOOR Hariyadi Hartana, Alex Heni Safitri Hermanasari, Rini Ika Roostika Indrastuti A. Rumanti Irmanida Batubara Ismail maskromo Iswari Saraswati Dewi Iswari Saraswati Dewi Kansa Dianti Putri Karjunita, Nike Lainufar, Putri Aulia Lefin Kafindra Luthfiani, Marisa Vidya M. Syukur Mahrup Mahrup, Mahrup Mashuri Waite maskromo, Ismail Miyamoto, Takuji Mohamad Rahmad Suhartanto Muaz Adbdul Karim Muaz Adbdul Karim Muhamad Syukur Munif Ghulamahdi N. Sri Hartati, N. Sri N. Sri i Hartati Nampiah Sukarno Natawijaya, Azis Nugraha, Yudhistira Nugroho, Rizki Bagus Nurul Fauziah Nurul Khumaida Nurul Khumaida Nurulalia, Lia Pahlevi, M Reza Parlindo, Fitra Pasaribu, Pesta Maria Hotnauli Pratama, Syilvia Nosya Prita Sari Dewi Rahmawati, Rika Sri Rahmi Henda Yani Ramadaniarto Rizqullah Reflinur Resti Putri Septyani Resti Putri Septyani Rika Miftakhul Jannah Rizqullah, Ramadaniarto Romy Agus Saputro Romy Agus Saputro Rubiyo Rubiyo Rumanti, Indrastuti A. Sadewi Maharani, Sadewi Saenal, Nirwanti Safitri, dan Heni Safitri, Vika Ayu Satya Nugroho Satya Nugroho Siswati, Leni Siti Kurniawati Slamet Susanto Soekisman Tjitrosoedirdjo SRI RAHAYU Sri Ratnawati Subekti, Isnani Sudarsono Sudarsono Sudarsono Sudarsono Sudarsono, Sudarsono Suwarno ,, Suwarno Suwarno Suwarno Suwarno, Suwarno Suwarno, Suwarno Syawaluddin, Dwi Dana Syukur, M. TRI JOKO SANTOSO TRI KOESOEMANINGTYAS Tri Lestari Trias Sitaresmi Trikoesoemaningtyas Tsugama, Daisuke Ulfa, Umi Tahniah Umezawa, Toshiaki Vincentia Esti Windiastri, Vincentia Esti Widowati, Sartika Willy Bayuardi Suwarno Wospakrik, Andrean Heskiel Yudhistira Nugraha Yudiansyah Yudiansyah Yudiwanti Wahyu E. Kusumo Yuli Irvana Dewi Yuli Sulistyowati Yullianida , Za’aziza Ridha Julia