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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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RAPD ANALYSIS TO DETECT SOMACLONAL VARIATION OF PINEAPPLE IN VITRO CULTURES DURING MICROPROPAGATION Ika Roostika; Nurul Khumaida; Sintho Wahyuning Ardie
BIOTROPIA Vol. 22 No. 2 (2015): BIOTROPIA Vol. 22 No. 2 December 2015
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (21.504 KB) | DOI: 10.11598/btb.2015.22.2.422

Abstract

Plant off-type formation has become a concern in pineapple micropropagation, and reliable methods are required to detect and minimize this problem. This study was conducted to confirm the occurrence of somaclonal variation during the micropropagation of pineapple clone Simadu. The effects of culture period (long vs. short duration) and regeneration methods (direct organogenesis, indirect organogenesis, and somatic embryogenesis) were evaluated to determine their contribution to somaclonal variation. RAPD analysis using ten primers was performed to confirm genetic variation. The results showed that RAPD assays could be applied for early detection of somaclonal variation in pineapple, with OPA primers performing better than OPJ primers. Phenotypic variation observed in four-year-old field-grown pineapple plants and plantlets was associated with genetic variation. The findings demonstrated that the long culture period was the main factor contributing to somaclonal variation, while regeneration method and plant growth regulators also played a role in inducing genetic changes. Newly initiated cultures showed a higher level of genetic similarity. Therefore, applying an appropriate micropropagation strategy is necessary to minimize plant off-types. It is recommended to avoid using long-term cultures as mother stock and to apply direct organogenesis rather than indirect organogenesis or somatic embryogenesis for pineapple micropropagation.
Markers-traits association for iron toxicity tolerance in selected Indonesian rice varieties YUDHISTIRA NUGRAHA; DWINITA W UTAMI; IDA ROSDIANTI; SINTHO WAHYUNING ARDIE; MUNIF GHULAMMAHDI; SUWARNO SUWARNO; HAJRIAL ASWIDINNOOR
Biodiversitas Journal of Biological Diversity Vol. 17 No. 2 (2016)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d170251

Abstract

Nugraha Y, Utami DW, Rosdianti I, Ardie SW, Ghulammahdi M, Suwarno, Aswidinnoor H. 2016. Markers-traits association for iron toxicity tolerance in selected Indonesian rice varieties. Biodiversitas 17: 753-763. Ferrous iron toxicity is a mineral disorder frequently occurring under flooded soils condition where rice is cultivated. Here we study identification the Single Nucleotide Polymorphism (SNPs) markers associated with iron toxicity tolerance characters. The phenotypical data was collected from exploiting of twenty-four rice genotypes that were grown under Yoshida + 0.2% agar solution with treatment of 400 mg. L-1 Fe2+ and control conditions. The same genotypes were grown in iron toxicity acute and control sites at Taman Bogo, Lampung Province, Indonesia. The Principle Component Analysis (PCA) of the phenotypic data showed that 18 rice genotypes were selected representing grouping of related characters to iron toxicity condition. The genotyping of selected genotypes was carried out using multiplexes of 384 SNPs Golden Gate Illumina© assay. We identified, TBGI380435 which located on 14.45 Mbp of chromosome 9 was associated to leaf bronzing and relative shoot weight characters in the greenhouse experiment. The marker was associated with heavy metal transport detoxification (HTDT). The results are expected to assist in locating the potential candidate genes or Fe toxicity tolerance and to allow for precise marker-assisted selection. This research will serve for rice improvement through marker-assisted breeding and genomic selection in Indonesia. Keywords: Golden gate assay, grain yield, leaf bronzing scores, principle component analysis, single nucleotide polymorphism Abbreviations: SNPs = Single Nucleotide Polymorphisms, AM = Association Mapping, LD= Linkage Disequilibrium, GG= Golden Gate Assay, NGS= Next Generation sequencing ,QTL = Quantitative Trait Loci, LBS = Leaf Bronzing Score, PCA = Principle Component Analysis, SES = Standard Evaluation System For Rice, GLM = General Linear Model, PC = Principle Component, HTDT = Heavy Metal Transport Detoxification
Male-sterile induction method in foxtail millet (Setaria italica) Rizki Bagus Nugroho; WILLY BAYUARDI SUWARNO; NURUL KHUMAIDA; SINTHO WAHYUNING ARDIE
Biodiversitas Journal of Biological Diversity Vol. 21 No. 9 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210951

Abstract

Abstract. Nugroho RB, Suwarno WB, Khumaida N, Ardie SW. 2020. Male-sterile induction method in foxtail millet (Setaria italica). Biodiversitas 21: 4325-4330. Male-sterile induction is one technique that can be used to prevent selfing in self-pollination plants, especially for plants with small floret. This study aimed to identify an effective male-sterile induction method that can kill pollen while keeping the stigma receptive in foxtail millet (Setaria italica L. Beauv). The experiment was conducted in a greenhouse at the Cikabayan Experimental Station and the Biology and Biophysics Seed laboratory, Dept. of Agronomy and Horticulture, IPB University, Indonesia from October 2018 to February 2019. The experiment consisted of two sub-experiments that were carried out with a split-plot design with four replications. The male-sterile induction method was the main plot, and the genotype was the subplot. The results from the first experiment showed that alcohol, warm water, and maleic hydrazide treatments were effective for killing pollen in the upper panicle and pollination zones. These treatments were also effective in developing unproductive rachis with different effect patterns on panicles. The results from the second experiment showed that warm water treatment and maleic hydrazide could keep the stigma receptive. From both experiments, warm water treatment was recommended for male-sterile induction in foxtail millet because it was effective in killing pollen, inflicting unproductive rachis in the upper panicle and pollination zones, and kept the stigma receptive.
Development of phenotypic markers and contrast genotype candidates of target minerals related to cassava Sylvia Nosya Pratama; Sudarsono SUDARSONO; Sintho Wahyuning Ardie; NURUL KHUMAIDA; Dewi Sukma
Biodiversitas Journal of Biological Diversity Vol. 22 No. 6 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220606

Abstract

Abstract. Pratama SN, Sudarsono, Ardie W, Khumaida N, Sukma D. 2021. Development of phenotypic markers and contrast genotype candidates of target minerals related to cassava. Biodiversitas 22: 3049- 3056. Cassava leaves have various macro and micro-nutrients with varying levels, such as magnesium, iron, and zinc. The differences in genotypes of cassava may result in different mineral content in cassava leaves. This study aims to determine the estimator phenotypic markers and contrast genotype candidate selection related to target minerals. This study used a one-factor treatment composed of 12 cassava genotypes and arranged in a randomized block design (RBD) which each treatment was repeated 3 times. The observation was conducted on the leaves' qualitative and quantitative characters such as plant growth, leaf morphology, and leaf mineral content characters. The observation was performed at 3 and 6 months after planting. The results showed that the quantitative and qualitative characters that could be used as estimator for mineral content in cassava leaves are the Soil Plant Analysis Development (SPAD)- Chlorophyll value and leaf color. Genotypes G6-1-15-4-3, G6-2-15-1-1, G6-2-15-3-3 (lowest) and Malang (G4D0), G4D1-222, G3D2-413 (highest) could be categorized as contrast genotypes based on SPAD-value and mineral content. The strong positive correlation between Mg and Fe content with SPAD suggested that SPAD is a possible marker for high Mg and Fe content in leaves. Adversely, a weak relationship between SPAD and Zn content in leaves showed that SPAD is a weak marker for Zn content in leaves. Further research related to molecular markers development can be carried out based on these results.
CRISPR/Cas9-mediated genome editing in rice cv. IPB3S results in a semi-dwarf phenotypic mutant NURHAYATI NURHAYATI; Sintho Wahyuning Ardie; Tri Joko Santoso; Sudarsono Sudarsono
Biodiversitas Journal of Biological Diversity Vol. 22 No. 9 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220924

Abstract

Abstract. Nurhayati, Ardie SW, Santoso TJ, Sudarsono. 2021. CRISPR/Cas9-mediated genome editing in rice cv. IPB3S results in a semi-dwarf phenotypic mutant. Biodiversitas 22: 3792-3800. IPB3S is Indonesian lowland rice and high-yielding cultivar. However, plant height posture makes it prone to lodging which could reduce the yield. This study aimed to edit the GA20Ox2 gene by introducing CRISPR/Cas9 GA20Ox2 construct into IPB3S and developing the semidwarf rice mutants. Immature embryo explants of IPB3S were used for the transformation process mediated by EHA105 strain of Agrobacterium tumefaciens carrying pC1300-Cas9/GA20Ox2 and by changing the regeneration medium composition. PCR analysis showed that rice cv. IPB3S genetic transformation gained putative mutant T0 lines carrying the hpt gene (growth efficiency was 47.9%, while transformation efficiency was 19.3%). Using the developed regeneration medium, we have obtained 24 putative rice cv. IPB3S T0 mutant lines carrying hpt. The best medium for regenerating IPB3S was the A medium (regeneration efficiency 73.3%). IPB 8 and IPB 14 were potential to evaluate in the next generation. The shortest plant height for the T1 generation was observed in the IPB 8-3 mutant.
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 Dhika Prita Hapsari Diaguna, Ridwan Didy Sopandie Dwi Guntoro DWINITA W UTAMI Enny Sudarmonowati Enung Sri Mulyaningsih fatimah Fatimah Ferdinans, Ferdinans Firdausya, Andina Fabrini Ghulammahdi, Munif Hagia Sophia Khairani HAJRIAL ASWIDINNOOR Hariyadi Hartana, Alex Heni Safitri Heni Safitri Hermanasari, Rini IDA ROSDIANTI 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 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