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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 Biodiversitas Journal of Biological Diversity
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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Morphological traits and Zn content of several cassava genotypes in nutrient solution culture Pratama, Syilvia Nosya; Sudarsono; Ardie, Sintho Wahyuning; Sukma, Dewi
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 51 No. 2 (2023): Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy)
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24831/ija.v51i2.44535

Abstract

Leaf morphological characters and nutrient content in leaf tissue can vary depending on plant genotype. The nutrient solution culture can produce leaves with good nutritional content. Therefore, this research aimed to evaluate and validate cassava putative mutants' morphological traits and Zn content using a nutrient solution culture system. This research was carried out from January to May 2022 at the greenhouse of Cikabayan Experimental Garden, IPB University, Bogor. This study used two cassava cultivars and ten mutant genotypes from the cassava research team of IPB University, resulting from mutation breeding by gamma irradiation. The plant characters observed in this study included the number of leaves, length and width of the leaflet, leaf colour, plant height, fresh and dry weight leaf, and analysis of Zn content. The data were analyzed using ANOVA at a significant level of α = 5%, followed by Tukey's further test. The results showed that the G2D1-422 genotype had a higher Zn content than the wild type (Ratim/G2) and the other genotypes. The high Zn genotypes (G2D1-422) and low Zn genotypes (Ratim (G2) had not significantly different in fresh and dry leaf weight. Meanwhile, the plant genotype did not affect other growth characteristics such as plant height, the number of leaves, and the length and width of the leaflets, and overall, the characters were similar between the observed genotypes.
Mutation site identification confers glyphosate resistance in goosegrass (Eleusine indica L. Gaertn) from Jonggol, Bogor, Indonesia Ferdinans, Ferdinans; Guntoro, Dwi; Ardie, Sintho Wahyuning
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 51 No. 1 (2023): Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy)
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (403.132 KB) | DOI: 10.24831/ija.v51i1.45944

Abstract

Glyphosate resistance is a serious problem in weed control, especially in oil palm plantations. However, evaluation of suspected resistant weeds such as Eleusine indica L. Gaertn at the gene level is still scarce in Indonesia. Here, target-site resistance to glyphosate of the EPSPS gene was evaluated. The objective of this study was to identify glyphosate resistance caused by mutation points in goosegrass biotypes from oil palm plantation in Jonggol, West Java, Indonesia. Bio-assay analysis was carried out by planting goosegrass in pots. Glyphosate was applicated using eight-level, namely 0, 0.125x, 0.25x, 0.5x, x, 2x, 4x, and 8x, where x was the recommended dose (972 g ha-1) for three replications. Weed damage was evaluated from plant biomass and then regression analysis was performed to obtain the LD50 and resistance index. The E. indica from block V had a reduced sensitivity status with 2.343 value of resistance index, and those from Block II biotype had a sensitive status with 1.588 resistance index. Alignment of the EPSPS gene showed no mutation was observed at two target-points, indicating that increasing resistance of E. indica in the study site could be controlled by other factors. Nevertheless, E. indica of block V biotype had a resistance potential due to the highest LD50. It is necessary to evaluate further the possibility of mutation in other target-points of the EPSPS gene. Keywords: bio-assay; EPSPS; LD50; resistance index; sequencing; target-site resistance
Confirmations on gene introgression events and hybridity for BLB resistance and yield in rice Ashan, Muh Aswad; Reflinur; Ardie, Sintho Wahyuning
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 51 No. 3 (2023): Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy)
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24831/jai.v51i3.51194

Abstract

A superior variety of rice with high yield and resistance to diseases is expected to meet the increasing demand for this one of the most important carbohydrate sources worldwide. Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the major biotic stresses limiting rice production. Combining BLB resistance and high-yield traits is possible through gene pyramiding. Introgression of targeted traits in the parental genotypes and hybridity confirmation in the F1 generation are important initial steps in gene pyramiding. This study aimed to confirm the presence of targeted genes in parent genotypes using specific molecular markers and to confirm the hybridity of F1 plants generated from three crosses combinations of Inpari 32 (as the female parent) and three Code-qTSN4 lines (as the male parents) using SSR markers. This study successfully confirmed the introgression of BLB-resistance genes in Inpari 32 (Xa4, Xa7, and Xa21) and in Code-qTSN4 (Xa4, Xa7). The introgression of yield-related QTL, qTSN4, was confirmed in the three Code-qTSN4 lines (A10-1, B12-2, and A16-5) by RM17483 marker. Five SSR markers (RM5, RM55, RM105, RM223, and RM561) successfully confirmed the hybridity of F1 derived from Inpari 32xA10-1 (five individuals), Inpari 32xB12-2 (one individual), Inpari 32xA16-5 (two individuals). These confirmed hybrids can be further evaluated in the F2 generation. Keywords: Gene pyramiding; molecular marker; SSR; qTSN4; Xoo.
ANALISIS IN SILICO PROTEIN BIOSINTESIS LIGNIN PADA TANAMAN SORGUM (Sorghum bicolor L. Moench) Windiastri, Vincentia Esti; Ardie, Sintho Wahyuning; Nugroho, Satya
Berita Biologi Vol 22 No 2 (2023): Berita Biologi
Publisher : BRIN Publishing (Penerbit BRIN)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55981/beritabiologi.2023.690

Abstract

Lignin adalah bahan alam yang dapat dimanfaatkan sebagai bahan mentah dalam industri biofuel dan bioenergi. Peningkatan produksi lignin mendorong tersedianya sumber lignin terbaharukan dan ramah lingkungan. Sorgum berpotensi digunakan sebagai sumber biomassa untuk produksi lignin. Produksi lignoselulosa dari sorgum per tahunnya mencapai 19–47 ton/ha. Meskipun demikian, untuk memanfaatan sorgum sebagai sumber lignin secara optimal diperlukan peningkatan kandungan total lignin pada tanaman sorgum. Rekayasa genetika dalam modifikasi kandungan lignin dapat menjadi jawaban. Namun, informasi mengenai gen biosintesis lignin masih terbatas. Untuk memperoleh informasi protein biosintesis lignin pada sorgum (Sorghum bicolor L.Moench) dan protein homolognya dari tanaman monokotil yang lain, analisis bioinformatika mengenai protein biosintesis lignin telah dilakukan. Analisis dilakukan menggunakan program Blast-p, Mega-X, Conserved Domain Database, InterPro dan MEME. Hasil dari analisis yang dilakukan menggambarkan bahwa protein biosintesis lignin membentuk klaster searah dengan arah divergensi taksonomi tanaman monokotil. Protein lignin dari sorgum mengelompok bersama Mischanthus, tebu dan jagung. Pohon kekerabatan protein COMT menghasilkan bootstrap tertinggi untuk protein lignin sorgum di antara pohon filogeni protein-protein yang lain. Hasil penyejajaran keluarga protein COMT sorgum (XP_002445083.1) dengan protein COMT dari Mischanthus, tebu, jagung dan Arabidopsis menunjukkan bahwa protein XP_002445083.1 mempunyai karakter fungsional yang saling mirip. Sehingga dapat disimpulkan bahwa XP_002445083.1 diduga adalah protein COMT dari sorgum.
ANALISIS EKSPRESI RELATIF DAN PENYEJAJARAN GEN Bmr12 PADA AKSESI SORGUM (Sorghum bicolor L. Moench) Windiastri, Vincentia Esti; Sintho Wahyuning Ardie; Miyamoto, Takuji; Umezawa, Toshiaki; Satya Nugroho
Berita Biologi Vol 23 No 3 (2024): Berita Biologi
Publisher : BRIN Publishing (Penerbit BRIN)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55981/berita_biologi.2024.952

Abstract

Gen Bmr12 (SbCOMT) diperkirakan mempunyai fungsi dalam penentuan kandungan total lignin pada sorgum karena mutasi gen Bmr12 menyebabkan kandungan total lignin tanaman mutan tereduksi. Pada penelitian sebelumnya telah dikelompokkan aksesi-aksesi sorgum di Indonesia berdasarkan kandungan lignin tinggi dan lignin rendah (Buleleng Empok, JP dan Pahat). Untuk mengetahui pola ekspresi gen Bmr12 pada kedua kelompok sorgum yang berbeda, maka dilakukan analisis level ekspresi relatif dari sorgum berlignin tinggi yang diwakili oleh aksesi KS, 4183, dan SMM; dan sorgum berlignin rendah yang diwakili oleh aksesi Buleleng Empok, JP dan Pahat. Sebagai data pendukung, dilakukan pula perunutan gen Bmr12 yang diisolasi dari aksesi KS, 4183, Buleleng Empok dan Pahat. Hasil analisis tersebut memperlihatkan adanya perbedaan pola ekspresi gen Bmr12. Level tertinggi ada pada aksesi 4183A, dan yang terendah adalah aksesi Pahat. Keempat aksesi lainnya mempunyai pola ekspresi yang hamper sama. Perunutan dan penyejajaran gen Bmr12 memperlihatkan adanya substitusi basa nitrogen yang mengarah ke substitusi asam amino pada aksesi KS. Namun substitusi tersebut tidak mengganggu fungsi gen Bmr12 dalam biosintesis lignin.
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.
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.
Water and Crop Management Technologies: Physiological Response and Yield of Biofortified Rice Guntoro, Dwi; Ardie, Sintho Wahyuning; Diaguna, Ridwan; Hapsari, Dhika Prita; Sholiha, Nabila Fairuz; Putri, Prabawati Hyunita; Wahyudi, Wahyudi; Mursyalatiyus, Isnainy Dinul; Novianti, Shilfa; Purwandani, Junia Anindya; Anggraeni, Ratih Prajnaparamita; Rahardjo, Budi
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.13.01.241-253

Abstract

Biofortified rice has emerged as one of the most promising strategies to enhance the micronutrient content of staple crops, offering a practical pathway to reduce stunting and improve nutritional security. In response to the challenges posed by climate change, water scarcity, and the need for more efficient production systems, this study examined the effects of water- and crop- management technologies on the physiological performance and yield of biofortified rice. A factorial randomized complete block design compared continuous flooding and alternate wetting and drying (AWD) irrigation with two crop management systems: conventional and a new technology. The AWD system enhanced photosynthesis without significantly affecting transpiration or stomatal conductance, indicating improved carbon assimilation and more efficient water use. Both AWD and the new technology individually increased dry grain yield per clump, while their combination produced heavier grains, higher productivity, greater 1000-grain weight, and improved water-use efficiency compared with other treatments. Although yield differences were not statistically significant, the consistent upward trends indicate synergistic potential when nutrient management is optimized. Overall, integrating AWD irrigation with new technology crop management can enhance resource efficiency in biofortified rice cultivation while maintaining yield stability under water- limited conditions.
Optimizing SCoT-PCR Parameters for Reproducible Genetic Diversity Analysis in Cassava, Rice, Maize, and Foxtail Millet Yudiansyah Yudiansyah; Ismiyanti Ismiyanti; Susilawati Susilawati; M Reza Pahlevi; Sintho Wahyuning Ardie
Journal of Tropical Crop Science Vol. 13 No. 02 (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.13.02.494-503

Abstract

Technical optimization of PCR parameters is essential to ensure efficiency and accuracy in genetic analyses. The performance and reproducibility of Start Codon Targeted (SCoT) markers are strongly influenced by annealing temperature (Ta) and primer concentration. Raising Ta from 50 °C to 55 °C reduced both amplicon yield and reproducibility, whereas higher primer concentrations increased amplicon counts without substantially affecting reproducibility. Optimal amplification was achieved at Ta 50 °C with a primer concentration of 2.5 μM, where most primers produced high amplicon numbers with 100% reproducibility. Evaluation of 36 SCoT primers in foxtail millet identified 20 primers with full reproducibility, of which 10 were further tested across cassava, rice, and maize. Primer reproducibility varied among species, and only SCoT‑35 and SCoT-36 consistently achieved 100% reproducibility across all three crops. These results highlight that primer suitability is species‑dependent and emphasize the need for extensive primer screening in each plant species. Overall, optimizing Ta and primer concentrations, combined with careful primer selection, is essential for the reliable, efficient, and cost-effective application of SCoT markers in plant genetic diversity analysis.
Co-Authors Abdul Qadir ADI SETIADI Agus Zainudin Agustina, Ferra Anggita Ahmad Fathoni Aji, Titistyas Gusti Alex Hartana Anas D Susila Anas Dinurrohman Susila Anggraeni, Ratih Prajnaparamita Anjarsari, Nurul Aeni Anshori, Muhammad Fuad Ashan, Muh Aswad Azis Natawijaya Bambang Sapta Purwoko Budi Rahardjo Butarbutar, Lidya Kristina Sari Cahyono, Andy Agus Chusnah, Uswatun Dewi Sukma Dewi Sukma Dhika Prita Hapsari Diaguna, Ridwan Didy Sopandie Dwi Guntoro DWINITA W UTAMI Enny Sudarmonowati Enung Sri Mulyaningsih fatimah Fatimah Ferdinans, Ferdinans Firdausya, Andina Fabrini Fitri Yelli Ghulammahdi, Munif Hagia Sophia Khairani HAJRIAL ASWIDINNOOR Hariyadi Hartana, Alex Heni Safitri Heni Safitri Hermanasari, Rini IDA ROSDIANTI Ifan Maulana Putra Ika Roostika Indrastuti A. Rumanti Irmanida Batubara Ismail maskromo Ismiyanti Ismiyanti Iswari Saraswati Dewi Iswari Saraswati Dewi Junia Anindya Purwandani, Junia Anindya Kansa Dianti Putri Karjunita, Nike Krisantini Lainufar, Putri Aulia Lefin Kafindra Luthfiani, Marisa Vidya M Reza Pahlevi M. Syukur Mahrup Mahrup, Mahrup Mashuri Waite maskromo, Ismail Miyamoto, Takuji Mohamad Rahmad Suhartanto Muaz Adbdul Karim Muaz Adbdul Karim Muhamad Syukur Munif Ghulamahdi MUNIF GHULAMMAHDI Mursyalatiyus, isnainy dinul N. Sri Hartati, N. Sri N. Sri i Hartati Nampiah Sukarno Natawijaya, Azis Nida Yusrina Novianti, Shilfa Nugraha, Yudhistira Nugroho, Candra Catur Nugroho, Rizki Bagus NURHAYATI NURHAYATI NURUL KHUMAIDA NURUL KHUMAIDA Nurul Khumaida Nurul Khumaida Nurul Khumaida Nurulalia, Lia Pahlevi, M Reza Parlindo, Fitra Pasaribu, Pesta Maria Hotnauli Pratama, Syilvia Nosya Prita Sari Dewi Putri, Prabawati Hyunita Rahmawati, Rika Sri Rahmi Henda Yani Ramadaniarto Rizqullah Reflinur Resti Putri Septyani Resti Putri Septyani Rika Miftakhul Jannah Rizki Bagus Nugroho Rizqullah, Ramadaniarto Romy Agus Saputro Romy Agus Saputro Rubiyo Rubiyo Rumanti, Indrastuti A. Sadewi Maharani, Sadewi Saenal, Nirwanti Saepudin, Adam Safitri, dan Heni Safitri, Vika Ayu Satya Nugroho Satya Nugroho Sholiha, Nabila Fairuz Siswati, Leni Siti Kurniawati Slamet Susanto Soekisman Tjitrosoedirdjo SRI RAHAYU Sri Ratnawati Subekti, Isnani Sudarsono Sudarsono Sudarsono Sudarsono Sudarsono Sudarsono Sudarsono SUDARSONO Sudarsono, Sudarsono Susilawati Susilawati Suwarno ,, Suwarno SUWARNO SUWARNO Suwarno Suwarno Suwarno, Suwarno Suwarno, Suwarno Syawaluddin, Dwi Dana Sylvia Nosya Pratama Syukur, M. Tri Joko Santoso TRI JOKO SANTOSO TRI KOESOEMANINGTYAS Tri Lestari Trias Sitaresmi Trikoesoemaningtyas Tsugama, Daisuke Ulfa, Umi Tahniah Umezawa, Toshiaki Vincentia Esti Windiastri, Vincentia Esti Wahyudi Wahyudi Widowati, Sartika Willy Bayuardi Suwarno Wospakrik, Andrean Heskiel YUDHISTIRA NUGRAHA Yudhistira Nugraha Yudiansyah Yudiansyah Yudiansyah Yudiansyah Yudiwanti Wahyu E. Kusumo Yuli Irvana Dewi Yuli Sulistyowati Yullianida , Za’aziza Ridha Julia