Sintho Wahyuning Ardie
Department Of Agronomy And Horticulture, Faculty Of Agriculture, IPB University, Dramaga Campus, Bogor 16680, Indonesia

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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.
Evaluating the Efficiency of Metsulfuron-Methyl: The Role of Rice Cultivation Practices in Controlling Monochoria vaginalis Kansa Dianti Putri; Guntoro, Dwi; Sintho Wahyuning Ardie; Hariyadi
Journal of Tropical Crop Science Vol. 11 No. 02 (2024): 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.11.02.175-183

Abstract

Monochoria vaginalis is an invasive weed that thrives in rice paddies across Indonesia. Herbicide control is challenging since Monochoria vaginalis is known to be sulfonylurea-resistant in Indonesian rice fields. This weed is highly competitive, with a rapid growth pattern that may diminish rice production. Metsulfuron-methyl, a widely used herbicide, can potentially eliminate sensitive weeds at low dosage levels. This study aimed to identify the optimal dosage of metsulfuron-methyl for controlling Monochoria vaginalis and assess the impact of monoculture rice growing patterns and herbicide application in controlling weeds. The experimental design was a split-plot design with four replications, conducted from June to July 2023 in the Cikabayan Greenhouse at IPB University. The major plot was the Monochoria vaginalis accession: exposed or not exposed to herbicide, consisting of seven sites. The subplot represented the dosage of the active ingredient (a.i.) metsulfuron-methyl: 0, 1, 2, 4, 8, 16, and 32 g.ha-1. In addition to the field experiments, interviews were performed with five farmers from each of the seven Monochoria vaginalis sample accessions to assess rice planting patterns and herbicide usage history. The results showed that metsulfuron-methyl at 1 g.ha-1 reduced weed populations by over 50% in rice accessions Bugel, Palumbonsari, and Ciasem Hilir. Variability in Monochoria vaginalis indicated resistance to metsulfuron-methyl, necessitating greater dosages up to 8 g a.i. per ha-1 for Pasirkaliki and Rancajaya accessions. Our study also indicated that some areas could use lower dosages of herbicides to effectively control Monochoria vaginalis. In contrast to other places that required larger, three-yearly dosages of 100 to 125 g.ha-1, Bugel, Palumbonsari, and Ciasem Hilir used a twice-yearly dosage of 20 g.ha-1. These findings highlight the importance of tailored herbicide application strategies based on local resistance patterns and historical herbicide use to manage Monochoria vaginalis effectively.
Penurunan Risiko Perkembangan Cendawan Terbawa Benih Hotong asal Pulau Buru melalui Perlakuan Air Panas PARLINDO, FITRA; Khairani, Hagia Sophia; Ardie, Sintho Wahyuning
Jurnal Fitopatologi Indonesia Vol. 18 No. 6 (2022): November 2022
Publisher : The Indonesian Phytopathological Society (Perhimpunan Fitopatologi Indonesia)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14692/jfi.18.6.264-268

Abstract

Penurunan Risiko Perkembangan Cendawan Terbawa Benih Hotong (Setaria italica) Asal Pulau Buru Melalui Perlakuan Air Panas Penggunaan benih sehat yang bebas cendawan terbawa benih merupakan faktor penting untuk meningkatkan produksi hotong (Setaria italica). Penelitian ini bertujuan untuk memperkaya teknik eliminasi cendawan terbawa benih melalui perlakuan air panas terhadap benih hotong asal Pulau Buru. Identifikasi cendawan terbawa benih menunjukkan bahwa Boeremia merupakan cendawan dominan pada benih hotong asal Pulau Buru. Perlakuan air panas dengan kombinasi suhu (50 ℃, 52 ℃, 54 ℃) dan lama perlakuan (15, 20, 25 menit) diujikan untuk mencari perlakuan yang paling efektif menekan pertumbuhan cendawan tetapi tidak mengganggu perkecambahan benih. Penelitian ini menunjukkan bahwa perlakuan air panas pada suhu 50 ℃ selama 25 menit mampu menurunkan infestasi cendawan pada perlakuan in vitro dan ad planta berturut-turut sebesar 57% dan 55%. Hal ini mengindikasikan bahwa metode ini dapat diandalkan untuk menyelamatkan kerugian produksi benih hotong akibat perkembangan cendawan patogen.
SiDREB2-based SNAP Marker-Assisted and Multi-Trait Selection in The Early Generation of Foxtail Millet (Setaria italica L. Beauv.) Butarbutar, Lidya Kristina Sari; Syawaluddin, Dwi Dana; Suwarno, Willy Bayuardi; Ardie, Sintho Wahyuning
Journal of Tropical Biodiversity and Biotechnology Vol 9, No 3 (2024): September
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.90407

Abstract

Setaria italica L. or foxtail millet is known for its nutritious grains and adaptability to unfavorable environmental conditions. High productivity, early heading, medium stature, and tolerance to drought- or salinity stress are among the breeding objectives for foxtail millet. The objective of this study was to select F3 families of foxtail millet from the cross of Botok-10xICERI-6 by weighted selection index and assisted by SiDREB2-based SNAP marker. Genotyping of 178 F3 families using the SiDREB2-based SNAP marker resulted in 29 A/A genotypes, 121 A/G genotypes, and 28 G/G genotypes. Further evaluation was conducted on 48 F3 families consisting of 27 A/A genotypes and 21 A/G genotypes in an augmented randomized complete block design together with their parental genotypes (Botok-10xICERI-6) and three check genotypes (Mauliru-2, NTB-1, and Toraja). Plant height and heading time had high broad-sense heritability, whereas grain weight per plant had a moderate broad-sense heritability. Ten potential F3 families were selected based on a weighted selection index with 20% intensity, comprised of seven A/G genotypes and three A/A genotypes with a weighted selection index ranging from 0.84 to 3.76. The F3 family with pedigree numbers B10I6-15-136, B10I6-15-161, and B10I6-15-70 with A/A genotypes are considered putative transgressive segregants and could be continued to the next generation for further breeding process. 
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.
Genetic Diversity of Yellow and Red Berries Arabica Coffee Populations Grown in a Mix Populations in Garut, West Java, Indonesia, Based on SSR Markers Cahyono, Andy Agus; Ardie, Sintho Wahyuning; Rubiyo, Rubiyo; Sudarsono, Sudarsono
Journal of Tropical Crop Science Vol. 11 No. 03 (2024): 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.11.03.207-216

Abstract

Farmers in Garut, West Java, grow mixed varieties of Arabica coffee (Coffea arabica L.). Subsequently, they use harvested beans as seeds. Intercrossing among varieties may result in hybrid progenies and harvesting hybrid progenies as seed results in genetic variations. This research aims to evaluate the genetic diversity of Arabica coffee grown in a mixed population. Ninety-one Arabica coffees comprised 37 Arabica cv. “Ahernt GRT KN” (yellow-), 45 “Sigararutang” (red-), and nine “S795” (red berries) were sampled. Twenty SSR primer pairs were validated using 15 samples representing three varieties; six were polymorphic and used to genotype 91 Arabica accessions. Genetic data were analyzed using PowerMaker 3.25 and Darwin version 6 software. The results showed that the six SSR loci generated from 2 – 3 alleles, with an average of 2.17 alleles per locus. Genetic analysis of Arabica coffee from Garut, West Java, generated SSR markers with an average PIC of 0,33 across loci and varieties. The PIC within Arabica coffee cv. “Ahernt GRT KN” and “Sigararutang” were low, and within “S795” was moderate. Those PICs indicate the presence of more genetic diversity within “S795” than the other two cultivars. The Ho across Arabica coffee cv. “Sigararutang” and “S795” were lower than the He values, confirming their self-pollination nature. However, the Ho values of Arabica coffee cv. “Ahernt GRT KN” was larger than the others, indicating the presence of residual heterozygosity and a low percentage of recent outcrossing. The low Ho values of “Sigararutang” suggest that Arabica coffee is homozygous. Arabica coffee cv. “S795” also showed a low Ho value, but its moderate He value indicates the presence of more genetic diversity than the othercultivars.
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
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.  
Grafting-Induced Phenotypic and Genomic Variations in Cassava (Manihot esculenta Crantz) through Interspecific Compatibility with M. Glaziovi Ulfa, Umi Tahniah; Sudarsono, Sudarsono; Ardie, Sintho Wahyuning; Mulyaningsih, Enung Sri; Hartati, N. Sri; Anjarsari, Nurul Aeni; Dewi, Prita Sari
Journal of Tropical Crop Science Vol. 12 No. 03 (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.12.03.559-571

Abstract

Grafting is a promising approach to enhance cassava (Manihot esculenta Crantz) productivity, particularly in improving tuber yield and quality. Despite its technical simplicity, research on the morphological and molecular consequences of grafting in cassava is limited. This study aimed to quantitatively assess phenotypic differences between grafted and shoot cutting plants and characterize genetic modifications in shoot apical meristems near the graft union. Three splice-grafting combinations were evaluated: M. glaziovii (cv. "Karet")/"Revita RV1" (KR), "Karet"/ "Carvita 25" (KC), and "Carvita 25"/ "Revita RV1" (CR), alongside shoot-cutting plants of each cultivar. Grafted seedlings and conventional cuttings were transplanted to the field, and growth was monitored up to five months after grafting (5 MAG). Shoot bud samples were collected for RAPD analysis at three months (3 MAG). Grafted plants showed differences in morphology compared to controls, especially in branching architecture, branch angle, stem diameter, and internode length. However, the overall plant form and primary stem type remained stable. The color of emerging shoots consistently reflected their genotypic origin, like scion or rootstock, as did the shoot buds nearest the graft union. RAPD analysis using multiple primers revealed polymorphic banding patterns, with OPE-12 producing the most diverse profiles. While specific bands were associated with each cultivar, grafted regenerants often exhibited altered or novel band profiles, suggesting somaclonal variation or graft-induced genetic/epigenetic changes. Some regenerants displayed unexpected band types, such as C1 in R-KR1 and R-KR3, which were absent from their known parental genotypes. Cluster analysis grouped 45 samples into five major clusters and eight subgroups, indicating genetic divergence among certain grafted combinations, particularly "Carvita 25"–"Revita RV1" and M. glaziovii–"Revita RV1". These results demonstrate that grafting can significantly impact cassava phenotype and genome stability. This study shows that interspecific grafting between cassava (Manihot esculenta Crantz) and M. glaziovii can induce significant phenotypic and genomic variations.
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 Yudhistira Nugraha Yudiansyah Yudiansyah Yudiwanti Wahyu E. Kusumo Yuli Irvana Dewi Yuli Sulistyowati Yullianida , Za’aziza Ridha Julia