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All Journal HAYATI Journal of Biosciences Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) JEJAK BERITA BIOLOGI JURNAL BIOLOGI INDONESIA JURNAL HAMA DAN PENYAKIT TUMBUHAN TROPIKA ANNALES BOGORIENSES Medicinus : Jurnal Kedokteran Annales Bogorienses Jurnal Bioteknologi & Biosains Indonesia Berita Biologi
Satya Nugroho
Pusat Penelitian Bioteknologi LIPI Jl. Raya Bogor Km 46 Cibinong, Bogor 16
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Earth & Planetary Sciences Economics, Econometrics & Finance Immunology & microbiology Medicine & Pharmacology Public Health

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Identification of Drought Tolerant Related Insertional Mutant Lines Using PEG 6000 Nugroho, Satya; Windiastri, Vincentia Esti; Widyajayanti, Dwi; Pantouw, Carla Frieda
Annales Bogorienses Vol. 13 No. 1 (2009): Annales Bogorienses
Publisher : BRIN

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Abstract

Drought is one of the most important abiotic stresses in rice (Oryza sativa) productivity. The development of drought tolerant cultivars are therefore highly desireable. We have developed insertional mutant based on the Japonica rice cv Nipponbare rice by transposons Ac/Ds insertions containing activation-tag and gene trap. Screening of the mutant population for drought tolerant related phenotypes is of our priority. The screening protocol based on PEG 6000 has been developed and was being used to screen 70 mutant lines tocharacterize their responds to the treatment based on different parameters (number of leaf, total weight, plant height, root length and number of germinating seeds). These characters were used to score the Degradation Index and Vigour Index. Results showed varyingresponds of the lines to the osmotic pressure. Some lines showing a good performance indicated by lower Degradation Index and higher Vigour Index have been identified. Some inconsistencies in the performances scored by both indices were thought to be due to seed quality.
Gene Flow from Genetically Modified Rice to Their Weedy and Wild Relatives and Its Environmental Consequences Estiati, Amy; Nugroho, Satya
Annales Bogorienses Vol. 13 No. 1 (2009): Annales Bogorienses
Publisher : BRIN

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Rice is one of the most important food crops in the world. Nearly half of the world population consume rice as their staple food (FAO, 2004). With the increasing of world population, the need to provide more food supplies including rice is obvious. Biotechnology is expected to play major roles in the improvement of crop productivity and quality. Unlike transgenic maize, eventhough many research have been done to improve rice performance by genetic engineering, transgenic rice has not been released or commercialized. Among those research to improve rice performance are the attempt to introduce biotic and abiotic stress tolerant traits, herbicide tolerant trait and beta-carotin biosynthetic pathway. Currently, several genetically modified rice cultivars have been and being tested on limited field trials. Undoubtedly, biotechnology will benefit agriculture and thus providing enough food source to keep up with the ever-increasing needs in the future. However, the release and utilization of such technology in agriculture is still arising concerns about the impact to the environment. Therefore the possibility of the transgene escape to the environment needs to be analyzed. For example, whether the application of such technology can create superweed that resulted in the environment problems. On the other hand, cultivated rice may acquire genes for weediness from pollen-mediated gene flow of weedy or wild rice occurring inside or near cultivated rice fields, which leads to persistence and invasiveness of the cultivated rice, although the chance is low. This article discuss the possibility of the occurrence gene flow from the application of genetically modified rice to surrounding rice plants including its wild relatives and weed, and the requirements or precautions needed to be done to prevent gene flow. 
Phenotypic Screening of Ds Transposon and Activation-tag Insertional Mutant Rice Population for Drought and Salinity Tolerant Related Traits Nugroho, Satya; Zannati, Anky; Situmorang, Apriadi; Windiastri, Vincentia Esti; Widyajayanti, Dwi; Pantouw, Carla Frieda; Astuti, Dwi; Indrayani, Sri; Rachmawati, Syamsidah; Mulyaningsih, Enung Sri; Santoso, Tri Joko; Trijatmiko, Kurniawan Rudi
Annales Bogorienses Vol. 15 No. 1 (2011): Annales Bogorienses
Publisher : BRIN

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The studies of rice genes through functional genomics are greatly facilitated by the availability of the complete genome sequences, including the complete physical map of the japonica rice cv. nipponbare. Using the Ac and Ds transposon, that are capable of transposition in various heterologous plants including the monocotyledon rice, combined with the enhancer element for generating activation taged lines, it is possible to discover and isolate functional genes involved in various important agronomical traits; such as those involved in abiotic stress tolerance (drought, high salt) and biotic stresses diseases and pests. We have developed 1,785 first (T0) generation of mutant nipponbare rice by transposons Ac/Ds insertions containing activation-tag, generated by transformation using Agrobacterium-mediated method. Currently, we have generated approximately 1,000 stable lines with transposon Ds and activation-tag insertion ready for screening. Efficient screening methods for mutant Nipponbare rice lines have been established for agronomically important mutant traits. Among the new phenotypes related to important agronomical traits observed were drought and salt tolerant or sensitive, stunted and robust growth, variable root penetration and other interesting traits such as reduced tillering, rolled leaf and thin tiller. 
Genetic Transformation of Rice cv. Ciherang Using Double T-DNA Vector Harboring cry1Ab Gene Sulistyowati, Yuli; Rachmat, Agus; Zahra, Fatimah; Rachmawati, Syamsidah; Nugroho, Satya
Annales Bogorienses Vol. 15 No. 1 (2011): Annales Bogorienses
Publisher : BRIN

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Rice stem borer (Scirpophaga sp.) is considered as one of the primary pests causing yield decrease in Indonesia. Genetic engineering is considered as one of the most effective way to improve the resistance of rice plants to yellow stem borer since no resistance gene has been found in rice and its wild relatives. A double T-DNA binary vector p2TDNAcryIAb wich carry two independent T-DNA was used to transform Indonesian elite rice cv Ciherang using Agrobacterium-mediated transformation to generate transgenic rice that free from selectable marker genes. One T-DNA containing a selectable marker hygromycin phosphotransferase (hpt) gene and the other carrying the cry1Ab gene. As many as 37 putative transgenic plants from 14 embryos were generated. PCR analysis demonstrated that 22 out of 37 putative transgenic rice contain cry1Ab gene. All Ciherang rice carrying the cry1Ab gene expressing Cry1Ab protein as shown by the immunostrip assay. Further work will be carried out to determine the transgenes copy number, to select marker free transgenic rice, and to evaluate the resistance of transgenic rice against neonates larvae of yellow stem borer.
Insect Bioassay in Biosafety Containment to Select Transgenic Rice (Oryza sativa L.) Harboring Cry1B Gene Resistant to Yellow Stem Borer (Scrirpophaga incertulas Walk.) Estiati, Amy; Nurhasanah, Ade Nena; Nugroho, Satya
Annales Bogorienses Vol. 17 No. 2 (2013): Annales Bogorienses
Publisher : BRIN

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Development of rice varieties resistant to yellow stem borer (YSB) is very crucial. Agrobacterium-mediated transformation of cry1B gene under wound inducible gene promoter mpi (maize proteinase inhibitor) into a local rice variety Rojolele had been conducted. PCR analysis proved that cry1B gene had been integrated into plant genome of 3R25 and 3R5 rice lines. Segregation analysis using PCR for cry1B gene of the two putative transgenic rice lines at third (T2), fourth (T3), fifth (T4), and sixth (T5) generations of 3R25 and 3R5 lines proved that 3R25.7.27, 3R25.7.13.8.2, 3R25.7.13.8.6, 3R25.7.13.8.8, 3R5.26.2, and 3R5.26.5 are homozygous lines for cry1B gene. Insect bioassay on three randomly picked homozygous transgenic rice lines to study the efficacy of cry1B gene toward YSB was conducted in biosafety containment by infestingYSB larvae at first instar into 3R25.7.27, 3R25.7.13.8.6, and 3R5.26.5 transgenic rice lines, using non--transgenic Rojolele, IR64 and IR74 as susceptible controls. The results showed that the percentages of deadhearts symptoms of 3R25.7.27, 3R5.26.2, and 3R25.7.13.8.6 rice lines were lower than those of the susceptible control lines with scores of 0.1 and 0, respectively. While the scores of all three susceptible control plants were 9. The results proved that lines 3R25.7.27, 3R25.7.13.8.6, and 3R5.26.2 were categorized as resistant lines while the non-transgenic Rojolele, IR64, and IR74 were categorized as susceptible lines. The results also showed that the cry1B gene was expressed and produced insecticidal protein CRY1B which were active against YSB to protect rice plant toward YSB infestation.
Isolation and Characterization of OsNAC6 cDNA from Rice (Oryza sativa L.) cv. Nipponbare, Batutegi, and Rojolele Rachmat, Agus; Nugroho, Satya; Nurdiani, Dini; Swastika, Maria; Sukma, Dewi; Aswidinnoor, Hajrial; Sudarsono, Sudarsono
Annales Bogorienses Vol. 18 No. 2 (2014): Annales Bogorienses
Publisher : BRIN

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Transcription factors have an important function in regulating gene expression and plant responses to stresses. The ERF, bZIP, WRKY, MYB, and NAC are stress inducible transcription factors. The OsNAC6 is a member of the NAC transcription factor family in rice and its expression is induced by abiotic stresses, wounding and blast disease. Characterization of OsNAC6 gene sequences would give a better understanding on how OsNAC gene functions biologically. The objectives of this research are to isolate the OsNAC6 cDNA from Nipponbare, Batutegi, and Rojolele cultivars, to characterize their DNA sequences, and to compare their sequences to other NAC genes from other plants available in GenBank DNA databases. Isolated cDNA and sequencing of the fragments resulted in a 912 bp DNA sequences. Translation of the sequences yielded a protein consisted of 303 amino acid residue. Blast analysis of amino acid sequences indicated identity of isolated cDNA from three Indonesian rice cultivars are the OsNAC6 gene. Deduced amino acid residues from amplified cDNAs of Nipponbare, Batutegi, and Rojolele cultivars shared 100% sequence identities to rice OsNAC6 (Acc. # BAA89800), 71-100% sequence identity to a number of OsNAC protein from Oryza sativa and 63-83% sequence identity to NAC protein from other plants.
TOTAL LIGNIN CONTENT AND AGROMORPHOLOGICAL CHARACTER DIVERSITIES OF 30 INDONESIAN RICE (Oryza sativa L.) ACCESSIONS Nugroho, Satya
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol. 9 No. 2 (2022)
Publisher : BRIN - Badan Riset dan Inovasi Nasional

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55981/jbbi.2022.1754

Abstract

Lignin is one of lignocellulosic components in vascular plants, essential in plant mechanical properties, water transport, and defense against pathogens. Furthemore, lignin has been applied in various industry. This study aimed to explore variation of lignin content and its-related morphological traits of Indonesian rice accessions, providing beneficial information for breeding approaches to improve utilization characteristics of grass biomass. Therefore, the total lignin contents of thirty Indonesian rice accessions using Thioglycolic Acid Lignin (TGAL) method and their correlation to seven agromorphological characters using Pearson correlation analysis were investigated. Variation of lignin content ranged from 8.38 to 20.75% (of cell wal residue, CWR), and the average value was 13.55%. Correlation analysis showed that lignin total positively correlated with plant height, stem length, panicle length, stem diameter, total fresh weight, and panicle weight per tiller. On the other hand, the number of tillers had a significantly negative correlation to lignin contents.
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.
Co-Authors Agus Rachmat Anky Zannati Apriadi Situmorang Aris Hairmansis Chairunnisa Chairunnisa Dewi Sukma Didy Sopandie DINI NURDIANI Dwi Astuti Dwi Widyajayantie Enung Sri Mulyaningsih Erdayani, Eva Estiati, Amy Estiati, Amy Fatimah Zahra Fendiyanto, Miftahul Huda HAJRIAL ASWIDINNOOR Hery Widijanto Juandy Jo Kurniawan Rudi Trijatmiko, Kurniawan Rudi Loedin, Inez Hortenza Slamet Loedin, Inez HS Marbun, Kristin Talia Miftahudin Muchamad Joko Budianto, Muchamad Joko Nena, Ade Nurhasanah, Ade Nena Ouwerkerk, Pieter B. F. Ouwerkerk, Pieter BF Pantouw, Carla F. Pantouw, Carla Frieda Pantouw, Carla Frieda Rachmawati, Syamsidah Satrio, Rizky Dwi Sintho Wahyuning Ardie SRI HENDRASTUTI HIDAYAT Sri Indrayani, Sri Sudarsono Suryo Wiyono Swastika, Maria Swastika, Maria Syamsidah Rahmawati, Syamsidah TRI JOKO SANTOSO TRI KOESOEMANINGTYAS Trikoesoemaningtyas Vincentia Esti Windiastri, Vincentia Esti Widyajayanti, Dwi Widyajayanti, Dwi Yuli Sulistyowati