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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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Journal : ANNALES BOGORIENSES

 1 
Genetic transformation of rice cv. Ciherang using double T-DNA vector harboring cry1Ab gene Sulistyowati, Yuli; Rachmat, Agus; Zahra, Fatimah; Rahmawati, Syamsidah; Nugroho, Satya
ANNALES BOGORIENSES Vol 15, No 1 (2011): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (383.64 KB) | DOI: 10.1234/37

Abstract

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.Keyword: double T-DNA, transgenic rice, Cry1Ab, transformation
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 : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.1234/32

Abstract

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 atempt 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.Keywords : Rice, stress tolerant
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; Widyajayantie, Dwi; Pantouw, Carla F.; Astuti, Dwi; Indrayani, Sri; Rahmawati, Syamsidah; Mulyaningsih, Enung Sri; Santoso, Tri Joko; Trijatmiko, Kurniawan Rudi
ANNALES BOGORIENSES Vol 15, No 1 (2011): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.1234/56

Abstract

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.   Keywords: rice, insertion mutant, gene discovery, drought, salinity
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 : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.1234/29

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 to characterize 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 varrying responds of the lines to the osmotic presure.  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.   Keywords:  Oryza sativa, insertion mutant, drought, PEG 6000, Degradation Index, Vigor Index.
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 : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1372.433 KB) | DOI: 10.1234/100

Abstract

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 undersanding 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.
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; Nena, Ade; Nugroho, Satya
ANNALES BOGORIENSES Vol 17, No 2 (2013): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.1234/77

Abstract

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. 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 precentages 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
Identification and Activity of The Retrotranposon Tos17 in Indonesian Javanica Rice CV.Rojolele And Japonica Rice CV. Gajahmungkur Nugroho, Satya; Loedin, Inez HS; Ouwerkerk, Pieter BF
ANNALES BOGORIENSES Vol 11, No 1 (2007): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (2649.41 KB) | DOI: 10.1234/20

Abstract

Retrotransposons arc  mobile  genetic  elements  that  transpose  via  an  RNA intermediate  that  is  reverse transcribed  before  integration  into  a  new  location  within  the  host  genome. They  are  ubiquitous  in  eukaryotic organism.  and constitute a major portion of the nuclear genome (often more than half of the total DNA) in plants .Tos17 is a  rice  endogenous  retrotransposon  on  that  has  been  studied  thoroughly. Tos17 has  been  shown  to  be  an efficient insertional mutagen and saturation mutagenesis tool for gene tagging and functional genomics in Japonicarice cv  Nipponbare.  In  lavanica rice however, the presence and activity of  Tos17 has not been described thus far. while in some Indica rice Tos17 has  been found  to be  inactive. Javanica rice, also known as tropical  Japonica rice,has many cultivars which may serve as pontetial genetic resources of great interest for breeding programmes. Here  , the presence and activities of retrotransposon Tos17 in  Javanica rice  cv Rojolele was described and compared  to those of Japonica rice and Japonica rice cv Gajahmungkur We  identified  five and theree copies of  Tos17 in Rojolele and Gajahmungkur, respeclively, with different activities.Keywords: Oryza  sativa, rice, javanica, retrotransposon, Tos17
Overexpression of OsHox-6 Gene Enhanced Tiller Number in Rice But Induced Yield Penalty Rahmawati, Syamsidah; Chairunnisa, Chairunnisa; Erdayani, Eva; Nugroho, Satya; Estiati, Amy
ANNALES BOGORIENSES Vol 23, No 1 (2019): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (712.857 KB) | DOI: 10.14203/ann.bogor.2019.v23.n1.30-40

Abstract

OsHox-6, belongs to the transcription factor homeodomain leucine zipper (HD-Zip) protein sub-family I, has unknown function. This study was aimed to characterize the phenotypes of two homozygous transgenic rice lines (S29-62-2 and S.40.4-158-1) containing an extra copy of OsHox-6 gene under the control of a rice constitutive promoter, OsLEA3, and to evaluate their tolerance to water stress. A real-time quantitative PCR (qRT-PCR) showed that the transcript expression of OsHox-6 gene in the transgenic lines increased 5-10 folds under a normal irrigation and 10-20 folds after exposure to water stress conditions as compared to its wild type control. Transgenic plants overexpressing OsHox-6 exhibited phenotypic alteration at the normal irrigation by inducing tiller formation, suggesting a decrease in the apical dominance. Transgenic plants also showed significant enhancement in the total grain number, however, the number of empty grains  also increased significantly (~16-22%).  After imposed to the water stress, the number of empty grains in the transgenic lines was even higher (up to 83% in average). Furthermore, observations on the water loss rates, relative water contents and drought resistance indices (DRI) suggested that the overexpression of OsHox-6 did not significantly increase tolerance to water stress.  Further research is required to reveal the detailed mechanisms of OsHox-6 in response to water and other abiotic stresses.
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