Indonesian Biotechnology Research Institute for Estate Crops

Bogor, Indonesia

Indonesian Biotechnology Research Institute for Estate Crops

Bogor, Indonesia
SEARCH FILTERS
Time filter
Source Type

PubMed | Indonesian Rubber Research Institute, CAS Beijing Institute of Genomics, Indonesian Biotechnology Research Institute for Estate Crops, Rubber Research Institute and Unite mixte de recherche Amelioration Genetique et Adaptation des Plantes mediterraneennes et tropicales
Type: Journal Article | Journal: PloS one | Year: 2014

The AP2/ERF superfamily encodes transcription factors that play a key role in plant development and responses to abiotic and biotic stress. In Hevea brasiliensis, ERF genes have been identified by RNA sequencing. This study set out to validate the number of HbERF genes, and identify ERF genes involved in the regulation of latex cell metabolism. A comprehensive Hevea transcriptome was improved using additional RNA reads from reproductive tissues. Newly assembled contigs were annotated in the Gene Ontology database and were assigned to 3 main categories. The AP2/ERF superfamily is the third most represented compared with other transcription factor families. A comparison with genomic scaffolds led to an estimation of 114 AP2/ERF genes and 1 soloist in Hevea brasiliensis. Based on a phylogenetic analysis, functions were predicted for 26 HbERF genes. A relative transcript abundance analysis was performed by real-time RT-PCR in various tissues. Transcripts of ERFs from group I and VIII were very abundant in all tissues while those of group VII were highly accumulated in latex cells. Seven of the thirty-five ERF expression marker genes were highly expressed in latex. Subcellular localization and transactivation analyses suggested that HbERF-VII candidate genes encoded functional transcription factors.


Iskandar H.M.,CSIRO | Iskandar H.M.,University of Queensland | Iskandar H.M.,Indonesian Biotechnology Research Institute for Estate Crops | Casu R.E.,CSIRO | And 7 more authors.
BMC Plant Biology | Year: 2011

Background: The ability of sugarcane to accumulate high concentrations of sucrose in its culm requires adaptation to maintain cellular function under the high solute load. We have investigated the expression of 51 genes implicated in abiotic stress to determine their expression in the context of sucrose accumulation by studying mature and immature culm internodes of a high sucrose accumulating sugarcane cultivar. Using a sub-set of eight genes, expression was examined in mature internode tissues of sugarcane cultivars as well as ancestral and more widely related species with a range of sucrose contents. Expression of these genes was also analysed in internode tissue from a high sucrose cultivar undergoing water deficit stress to compare effects of sucrose accumulation and water deficit.Results: A sub-set of stress-related genes that are potentially associated with sucrose accumulation in sugarcane culms was identified through correlation analysis, and these included genes encoding enzymes involved in amino acid metabolism, a sugar transporter and a transcription factor. Subsequent analysis of the expression of these stress-response genes in sugarcane plants that were under water deficit stress revealed a different transcriptional profile to that which correlated with sucrose accumulation. For example, genes with homology to late embryogenesis abundant-related proteins and dehydrin were strongly induced under water deficit but this did not correlate with sucrose content. The expression of genes encoding proline biosynthesis was associated with both sucrose accumulation and water deficit, but amino acid analysis indicated that proline was negatively correlated with sucrose concentration, and whilst total amino acid concentrations increased about seven-fold under water deficit, the relatively low concentration of proline suggested that it had no osmoprotectant role in sugarcane culms.Conclusions: The results show that while there was a change in stress-related gene expression associated with sucrose accumulation, different mechanisms are responding to the stress induced by water deficit, because different genes had altered expression under water deficit. © 2011 Iskandar et al; licensee BioMed Central Ltd.


Piyatrakul P.,Unite Mixte de Rech. Amelioration Genetique et Adaptation des Plantes Mediterraneennes et Tropicales | Piyatrakul P.,Rubber Research Institute | Yang M.,CAS Beijing Institute of Genomics | Putranto R.-A.,Unite Mixte de Rech. Amelioration Genetique et Adaptation des Plantes Mediterraneennes et Tropicales | And 9 more authors.
PLoS ONE | Year: 2014

The AP2/ERF superfamily encodes transcription factors that play a key role in plant development and responses to abiotic and biotic stress. In Hevea brasiliensis, ERF genes have been identified by RNA sequencing. This study set out to validate the number of HbERF genes, and identify ERF genes involved in the regulation of latex cell metabolism. A comprehensive Hevea transcriptome was improved using additional RNA reads from reproductive tissues. Newly assembled contigs were annotated in the Gene Ontology database and were assigned to 3 main categories. The AP2/ERF superfamily is the third most represented compared with other transcription factor families. A comparison with genomic scaffolds led to an estimation of 114 AP2/ERF genes and 1 soloist in Hevea brasiliensis. Based on a phylogenetic analysis, functions were predicted for 26 HbERF genes. A relative transcript abundance analysis was performed by real-time RT-PCR in various tissues. Transcripts of ERFs from group I and VIII were very abundant in all tissues while those of group VII were highly accumulated in latex cells. Seven of the thirty-five ERF expression marker genes were highly expressed in latex. Subcellular localization and transactivation analyses suggested that HbERF-VII candidate genes encoded functional transcription factors.


Hernandez-Moreno D.,Wageningen University | Hernandez-Moreno D.,University of Extremadura | Soffers A.E.M.F.,Wageningen University | Wiratno,Wageningen University | And 4 more authors.
Food and Chemical Toxicology | Year: 2013

This study presents a consumer and farmer safety evaluation on the use of four botanical pesticides in pepper berry crop protection. The pesticides evaluated include preparations from clove, tuba root, sweet flag and pyrethrum. Their safety evaluation was based on their active ingredients being eugenol, rotenone, β-asarone and pyrethrins, respectively.Botanical pesticides from Acorus calamus are of possible concern because of the genotoxic and carcinogenic ingredient β-asarone although estimated margins of exposure (MOE) for consumers indicate a low priority for risk management.For the other three botanical pesticides the margin of safety (MOS) between established acute reference doses and/or acceptable daily intake values and intake estimates for the consumer, resulting from their use as a botanical pesticide are not of safety concern, with the exception for levels of rotenone upon use of tuba root extracts on stored berries. Used levels of clove and pyrethrum as botanical pesticides in pepper berry crop production is not of safety concern for consumers or farmers, whereas for use of tuba root and sweet flag some risk factors were defined requiring further evaluation and/or risk management. It seems prudent to look for alternatives for use of sweet flag extracts containing β-asarone. © 2013 Elsevier Ltd.


Putranto R.-A.,CIRAD - Agricultural Research for Development | Putranto R.-A.,Indonesian Biotechnology Research Institute for Estate Crops | Sanier C.,CIRAD - Agricultural Research for Development | Leclercq J.,CIRAD - Agricultural Research for Development | And 8 more authors.
Plant Science | Year: 2012

Three types of roots (taproots, first order laterals and second order laterals) were functionally characterized on 7-month-old in vitro plantlets regenerated by somatic embryogenesis in Hevea brasiliensis. A histological analysis revealed different levels of differentiation depending on root diameter. A primary structure was found in first and second order lateral roots, while taproots displayed a secondary structure. The expression of 48 genes linked to some of the regulatory pathways acting in roots was compared in leaves, stems and the different types of roots by real-time RT-PCR. Thirteen genes were differentially expressed in the different organs studied in plants grown under control conditions. Nine additional other genes were differentially regulated between organs under water deficit conditions. In addition, 10 genes were significantly regulated in response to water deficit, including 8 regulated mainly in lateral roots types. Our results suggest that the regulation of gene expression in lateral roots is different than that in taproots, which have a main role in nutrient uptake and transport, respectively. © 2011 Elsevier Ireland Ltd.


Ratnadewi D.,Bogor Agricultural University | Satriawan D.,University of Bengkulu | Sumaryono,Indonesian Biotechnology Research Institute for Estate Crops
Biotropia | Year: 2013

Quinine is one of the major alkaloids in Cinchona spp., and it is used both as a medication and as a drink additive. The plant produces most of its alkaloids in the bark after 68 years of age. Repeated harvests can be performed until the plant dies, but only after every 35 years. We tested an improved method for culturing cell suspensions of Cinchona ledgeriana investigate the possibility of increasing production of quinine. The clone QRC 315 was treated with either a growth retardant (abscisic acid or paclobutrazol) or precursor feeding of L-tryptophan. To generate stress, we applied mannitol at 5.3 g/L combined with sucrose at a lower concentration (20 g/L), and we used sucrose at 30 g/L as the control. Paclobutrazol (7 mg/L) significantly suppressed cell growth and produced the highest level of quinine (11%) after 7 weeks of culture. L-tryptophan also reduced cell growth, but without any positive effect in the production of quinoline. The highest amount of quinine per culture flask, however, resulted from cells treated with 3 mg/L abscisic acid.


Goenadi D.H.,Indonesian Biotechnology Research Institute for Estate Crops | Santi L.P.,Indonesian Biotechnology Research Institute for Estate Crops
Agrivita | Year: 2013

The highest expense on sugarcane management is fertilization in which one of them is phosphate fertilizer produced by imported raw materials. An innovation was made by using the local phosphate deposits with low reactivity processed further to improve their effectiveness for sugarcane. The objective of this study was to investigate the growth, yield and quality of sugarcane as affected by bio-superphosphate (Bio-SP) application on a highly weathered tropical soil. A nine-month field experiment was conducted at Jatitujuh Sugar Mill area, West Java, Indonesia, comparing between sugarcane fertilized with Bio-SP to replace conventional single superphosphate (SP-36) and that fertilized with SP-36. Urea and MOP (Muriate of Potash) were applied at similar dosages as recommended by division of Jatitujuh Sugar Mill Agronomy Research. Bio-SP was formulated by reacting a Central Java Rock Phosphate with liquid culture supernatant (LCS) and phosphoric acid characterized by 33% total soluble P2O5, 23.1, and 10.7 % citric acid and water-soluble P2O5, respectively. The results indicated that Bio-SP at 50% dosage of SP-36 was as effective as the SP-36 in supporting sugarcane growth and improved yield up to 8% as crystal sugar. Further consequence of this finding is that the application of Bio-SP reduced 9.2% of fertilizer cost for sugarcane.


Piyatrakul P.,CIRAD - Agricultural Research for Development | Piyatrakul P.,Rubber Research Institute | Putranto R.-A.,CIRAD - Agricultural Research for Development | Putranto R.-A.,Indonesian Biotechnology Research Institute for Estate Crops | And 7 more authors.
BMC Plant Biology | Year: 2012

Background: Ethylene production and signalling play an important role in somatic embryogenesis, especially for species that are recalcitrant in in vitro culture. The AP2/ERF superfamily has been identified and classified in Hevea brasiliensis. This superfamily includes the ERFs involved in response to ethylene. The relative transcript abundance of ethylene biosynthesis genes and of AP2/ERF genes was analysed during somatic embryogenesis for callus lines with different regeneration potential, in order to identify genes regulated during that process.Results: The analysis of relative transcript abundance was carried out by real-time RT-PCR for 142 genes. The transcripts of ERFs from group I, VII and VIII were abundant at all stages of the somatic embryogenesis process. Forty genetic expression markers for callus regeneration capacity were identified. Fourteen markers were found for proliferating calli and 35 markers for calli at the end of the embryogenesis induction phase. Sixteen markers discriminated between normal and abnormal embryos and, lastly, there were 36 markers of conversion into plantlets. A phylogenetic analysis comparing the sequences of the AP2 domains of Hevea and Arabidopsis genes enabled us to predict the function of 13 expression marker genes.Conclusions: This first characterization of the AP2/ERF superfamily in Hevea revealed dramatic regulation of the expression of AP2/ERF genes during the somatic embryogenesis process. The gene expression markers of proliferating callus capacity to regenerate plants by somatic embryogenesis should make it possible to predict callus lines suitable to be used for multiplication. Further functional characterization of these markers opens up prospects for discovering specific AP2/ERF functions in the Hevea species for which somatic embryogenesis is difficult. © 2012 Piyatrakul et al.; licensee BioMed Central Ltd.


Agustin F.,Bogor Agricultural University | Agustin F.,Andalas University | Toharmat T.,Bogor Agricultural University | Evvyernie D.,Bogor Agricultural University | And 2 more authors.
Media Peternakan | Year: 2013

The research was designed to evaluate chromium incorporation by Ganoderma lucidum in rice straw substrate supplemented with chromium chloride. Treatments were combination of Cr level (0, 500, 1000, 1500, 2000, 25000, and 3000 ppm) and fermentation time (0, 2, 3, and 4 wk). The treatments were arranged in a factorial 7 × 4 and allocated in completely randomized design with three replica¬tions. G. lucidum was grown in potato dextrose agar (PDA) medium for 10 days and was inoculated to the substrate which have been sterilized and mixed with CrCl3.6H2O. The moisture of substrate was maintained at 70%. Fiber and protein components of growth media of G. lucidum was determined and analyzed for their Cr content. The finding result showed that addition of Cr up to 3000 ppm into the substrate stimulated the G. lucidum growth. Chromium was incorporated into the fiber and protein components of the growth substrate of G. lucidum during fermentation. Incorporation of Cr into the protein of substrate containing 3000 ppm Cr was highest when fermented for 4 wk. Protein component of substrate contained 9.29% Cr while in NDF and ADF was 27.20% and 10.55% Cr, respectively. It is concluded that Cr was incorporated into the G. lucidum cells during fermentation.


PubMed | Indonesian Biotechnology Research Institute for Estate Crops
Type: Journal Article | Journal: Plant cell reports | Year: 2013

The effect of humic acid on shoot development from nodal segments in tissue culture was tested. The species wereGnetum gnemon, Elletaria cardamomum, andPogostemon cablin. Humic acids were extracted from a peat soil sampled from South Sumatra, Indonesia. Alkaline extraction was conducted on two series of 12-hour agitations followed by centrifugation and sedimentation at pH below 2. Explants were 1-cm long single nodes ofG. gnemon andP. cablin, and lateral buds ofE. cardamomum on MS medium. Benzyladenine was added at 0.1 mg/L for the first two and at 0.3 mg/L for the latter. The treatments included six, seven, and eight levels of humic acid concentrations for the respective species in a completely randomized design with 10 replicates. Effect of the treatment was evaluated on the basis of the initiation period of shoots and/or roots, and the number and height of the shoots. The initiation period of the shoots was significantly shortened in the presence of humic acids. Root initiation was significantly induced especially when humic acids were used in liquid medium. In combinations with BA, the addition of humic acids at 400 mg/L, 40 mg/L, and 300 mg/L yielded the fastest growth ofG. gnemon, E. cardamomum, andP. cablin, respectively.

Loading Indonesian Biotechnology Research Institute for Estate Crops collaborators
Loading Indonesian Biotechnology Research Institute for Estate Crops collaborators