Indonesian Center for Agricultural Biotechnology

Bogor West Java, Indonesia

Indonesian Center for Agricultural Biotechnology

Bogor West Java, Indonesia
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Purnamaningsih R.,Indonesian Center for Agricultural Biotechnology | Hutami S.,Indonesian Center for Agricultural Biotechnology
Journal of Engineering and Applied Sciences | Year: 2016

Sugarcane is an important crop in Indonesia. Protocols were established to induce callus and treat with Ethyl Methane Sulphonate (EMS). Calli were induced and immersed in 0.1, 0.3 and 0.5% EMS solutions for 30, 60 and 120 min. PS 862 and VMC 7616 sugarcane varieties were used in this experiment. Mutant putative calli were selected on media with aluminium concentrations of 100, 200, 300, 400 and 500 ppm and then cultured on regeneration media. Sugarcane mutant plants were evaluated for its aluminum tolerance by planting them in acidic soil (pH of 4.1). This research showed that increasing EMS concentration reduced the regenerative capacity of sugarcane calli. Calli of PS 862 had a higher aluminium tolerance capacity compared to calli of VMC 7616. Mutant putative shoots could be induced to produce roots by treatment with 5 mg L-1 IBA. Field evaluation showed that mutant clones had higher agronomical characters value than mother plants which was due to the EMS-induced genetic mutation. Mutant clones had plant heights in the range of 2.8-4.3 m, the number of shoots 3-12, the number of nodes 9-16 and stem diameters 1.3-2.8 cm. Meanwhile, PS 862 and VMC 7616 (mother plants) had plant heights 2.9 m and 2.97 m, number of shoots 3.7 and 1.67; nodes number 8.14 and 7.33 and stem diameters 1.27 and 1.33 cm. The Brix values of mutant clones were in the range of 12-20% and fresh weights were 900-2610 gr while brix content of PS 862 and VMC 7616 (mother plants) were 16 and 15% and the fresh weight were 1419 and 1650 g. © Medwell Journals, 2016.


Fujita D.,International Rice Research Institute | Fujita D.,Japan International Research Center for Agricultural science | Fujita D.,Japan National Agriculture and Food Research Organization | Fujita D.,Kyushu University | And 21 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2013

Increasing crop production is essential for securing the future food supply in developing countries in Asia and Africa as economies and populations grow. However, although the Green Revolution led to increased grain production in the 1960s, no major advances have been made in increasing yield potential in rice since then. In this study, we identified a gene, SPIKELET NUMBER (SPIKE), from a tropical japonica rice landrace that enhances the grain productivity of indica cultivars through pleiotropic effects on plant architecture. Map-based cloning revealed that SPIKE was identical to NARROW LEAF1 (NAL1), which has been reported to control vein pattern in leaf. Phenotypic analyses of a near-isogenic line of a popular indica cultivar, IR64, and overexpressor lines revealed increases in spikelet number, leaf size, root system, and the number of vascular bundles, indicating the enhancement of source size and translocation capacity as well as sink size. The near-isogenic line achieved 13-36% yield increase without any negative effect on grain appearance. Expression analysis revealed that the gene was expressed in all cell types: panicles, leaves, roots, and culms supporting the pleiotropic effects on plant architecture. Furthermore, SPIKE increased grain yield by 18% in the recently released indica cultivar IRRI146, and increased spikelet number in the genetic background of other popular indica cultivars. The use of SPIKE in rice breeding could contribute to food security in indica- growing regions such as South and Southeast Asia.


Indrasumunar A.,University of Queensland | Indrasumunar A.,Indonesian Center for Agricultural Biotechnology | Gresshoff P.M.,University of Queensland
Plant Signaling and Behavior | Year: 2010

In symbiosis with Bradyrhizobium japonicum, soybean (Glycine max L.) forms nitrogen-fixing nodules in its roots after mitogenic stimulation from a bacterial lipo-oligosaccharide (the 'Nodfactor'). In our recent paper in Plant and Cell Physiology we utilize two recessive loss-of-function plant mutants with a non-nodulation phenotype, and comparative genomics to clone and functionally analyze relevant soybean genes of the LysM receptor kinase family which are needed for perception of Nod-factor released by its microsymbiont B. japonicum. Two highly related lipo-oligochitin LysM type receptor kinase genes were cloned; they are presumed to be the critical nodulation inducing (Nod) factor receptor. These duplicated receptor genes were called GmNFR5α and GmNFR5β. Non-sense mutations in GmNFR5α and GmNFR5β were functionally complemented by both wild-type GmNFR5α and GmNFR5β in transgenic roots, indicating that both genes are functional. Both genes are wild-type in some soybean cultivars; however, non-functional NFR5β alleles were discovered in several others, which harbored an identical 1,407 bp retroelement-type insertion. GmNFR5α but not GmNFR5β was expressed in tap and lateral root portions at about 10-25% of GmATS1 (ATP synthase subunit 1), but not in trifoliate leaves and shoot tips. In general, inoculation treatment downregulated GmNFR5α/β transcripts in tap and lateral root portions. © 2010 Landes Bioscience.


Indrasumunar A.,University of Queensland | Indrasumunar A.,Indonesian Center for Agricultural Biotechnology | Searle I.,University of Queensland | Searle I.,Australian National University | And 7 more authors.
Plant Journal | Year: 2011

Two allelic non-nodulating mutants, nod49 and rj1, were characterized using map-based cloning and candidate gene approaches, and genetic complementation. From our results we propose two highly related lipo-oligochitin LysM-type receptor kinase genes (GmNFR1α and GmNFR1β) as putative Nod factor receptor components in soybean. Both mutants contained frameshift mutations in GmNFR1α that would yield protein truncations. Both mutants contained a seemingly functional GmNFR1β homeologue, characterized by a 374-bp deletion in intron 6 and 20-100 times lower transcript levels than GmNFR1α, yet both mutants were unable to form nodules. Mutations in GmNFR1β within other genotypes had no defects in nodulation, showing that GmNFR1β was redundant. Transgenic overexpression of GmNFR1α, but not of GmNFR1β, increased nodule number per plant, plant nitrogen content and the ability to form nodules with restrictive, ultra-low Bradyrhizobium japonicum titres in transgenic roots of both nod49 and rj1. GmNFR1α overexpressing roots also formed nodules in nodulation-restrictive acid soil (pH 4.7). Our results show that: (i) NFR1α expression controls nodule number in soybean, and (ii) acid soil tolerance for nodulation and suppression of nodulation deficiency at low titre can be achieved by overexpression of GmNFR1α. © 2010 Blackwell Publishing Ltd.


Indrasumunar A.,Indonesian Center for Agricultural Biotechnology | Indrasumunar A.,University of Queensland | Menzies N.W.,University of Queensland | Dart P.J.,University of Queensland
Soil Biology and Biochemistry | Year: 2012

A glasshouse experiment studied the role of calcium and pH on competitiveness of acid-sensitive and acid-tolerant Bradyrhizobium japonicum strains with similar N 2-fixation effectiveness in nodulating two soybean (Glycine max L. Merr) cultivars selected for tolerance of aluminium (PI416937) or for manganese (Manta). Liming provides calcium (Ca) as well as increasing soil pH. Thus the effect of Ca and pH of soil are difficult to separate. We examined the effects of Ca per se by comparing the response to gypsum and lime amendment on the competitiveness of acid-tolerant and acid-sensitive strains in nodulating soybean in an acid soil. Acid soil was treated with either CaSO 4 or CaCO 3 and incubated for 2 weeks before sowing soybean seed. Two acid-sensitive and two acid-tolerant B.japonicum strains were mixed with each other (one acid-sensitive plus one acid-tolerant) and were inoculated onto soybean seeds at the rate of 10 6cfuseed -1. Soil pH, as amended by lime addition, had more effect on nodulation than Ca addition in the form of gypsum. The response was affected by cultivar and strain in a complicated fashion with a marked strain×cultivar interaction. One acid-tolerant strain formed most nodules with both cultivars in the unamended soil of pH 4.36 in competition with one acid-sensitive strain. The same acid-tolerant strain was not competitive against the second acid-sensitive strain with Manta but was with PI416937. The second acid-tolerant strain was not competitive with either acid-sensitive strain in unamended and gypsum treated soils. It was only competitive with PI416937 in limed soil, a rather surprising result. Inoculation of this soil with no native soybean nodulating strains, increased shoot weight, %N, N uptake. N 2-fixation was greatly increased by inoculation and lime addition, and to a lesser extent by gypsum addition for Manta. This experiment indicates that addition of Ca per se as gypsum to an acid soil has little effect on symbiotic performance, but changing pH by liming has a major effect, that both soybean cultivar and B.japonicum strain influence the competitiveness of strains in acid soil and that acid-tolerance does not necessarily increase a strain's competitiveness. © 2011 Elsevier Ltd.


Sianipar N.F.,Binus University | Purnamaningsih R.,Indonesian Center for Agricultural Biotechnology | Gumanti D.L.,Pelita Harapan University | Rosaria,Pelita Harapan University | Vidianty M.,Pelita Harapan University
Jurnal Teknologi | Year: 2016

Rodent tuber (Typhonium flagelliforme Lodd.) is an herbal medicinal plant with anticancer activity. The genetic diversity of rodent tuber is low due to vegetative propagation. Somatic cell population of rodent tuber from Bogor had been irradiated with gamma ray to increase genetic diversity. There were 37 clones of first generation putative mutant (MV1) which had been analyzed based on morphological and RAPD markers. Out of those 37 MV1 clones, there were 17 clones which had undergone genetic mutation and had a diversified genetic profile. MV1 had been regenerated to fourth generation putative mutant clones (MV4). This research was aimed to analyze the mutation stability of MV4 based on morphological and RAPD markers. Clone 6-1-2 had the highest increase of the number of shoots and leaves than control and the other MV4 clones, with 4.7 and 19.7 shoots and leaves, respectively. Clone 6-1-1-6 obtained the highest increase in plant height than control and the other MV4 clones, i.e. 25.2 cm. Clone 6-9-5 had the weightiest fresh and dry weight, i.e. 41.67 gram and 12.01 gram respectively. RAPD molecular marker analysis of MV4 by using 15 primers had produced 64 polymorphic DNA bands out of 146 total bands. OPD-10 primer produced the highest number of polymorphic bands, i.e. 15 polymorphic bands out of 17 total bands with sizes 200-2000 bp. RAPD profile of MV4 had showed 5 main clusters at similiarity coefficient cut-off 0.91. Morphological characterization and RAPD analysis had proved the stability of genetic mutation of MV4. © 2016 Penerbit UTM Press. All rights reserved.


Waki T.,Tochigi Prefectural Agricultural Experiment Station | Horita M.,Japan National Institute for Agro - Environmental Sciences | Kurose D.,Japan National Institute for Agro - Environmental Sciences | Mulya K.,Indonesian Center for Agricultural Biotechnology | Tsuchiya K.,Kyushu University
Japan Agricultural Research Quarterly | Year: 2013

Asia-Pacific region was assessed by examining their biochemical properties, discriminating the phylogeny by polymerase chain reaction (PCR), and analyzing the egl and mutS gene sequences. These data were compared with those of reference strains covering the known diversity within the R. solanacearum species complex. Fifty-two of the Zingiberaceae plant isolates belong to either biovar 3 or biovar 4. Multiplex PCR analyses indicated that these strains belong to phylotype I. Phylogenetic analyses revealed that the investigated strains could be further divided into five or more groups and three major groups, based on the egl and mutS gene sequences, respectively. These groups were closely correlated with the host species and/or geographical origin. Our findings suggest that R. solanacearum strains affecting Zingiberaceae plants have multiple origins from within the Asia-Pacific region, and may have been disseminated with seed rhizomes.


Safitri H.,Indonesian Center for Rice Research | Purwoko B.S.,Bogor Agricultural University | Dewi I.S.,Indonesian Center for Agricultural Biotechnology | Ardie S.W.,Bogor Agricultural University
Journal of the International Society for Southeast Asian Agricultural Sciences | Year: 2016

Salt accumulation in irrigated soil is one of the main factors limiting rice productivity. A greenhouse experiment was conducted at Cimanggu Experiment Station, Bogor, Indonesia from May to September 2014 using a completely randomized design in a factorial arrangement with three replications. Four salt tolerant and two salt sensitive genotypes of rice were used in this experiment. The treatments were five concentrations of NaCl (0, 20, 40, 60 and 80 mM) applied on 21 day-old seedlings and maintained until harvest time. The study sought to evaluate the response of several rice genotypes to various NaCl concentrations through observation of morphological and physiological characters. The study showed that the increase of NaCl concentrations in soil significantly reduced plant height, number of panicles plant-1, panicle length, leaf length, 1000 grain weight, and grain yield. On physiological characters, salinity increased [Na+], decreased [K+] and [Ca2+] concentrations, and reduced K+/Na+ and Ca2+/Na+ ratios in the leaf tissue. The addition of 40 mM NaCl can distinguish tolerant and sensitive genotypes. The grain yield of sensitive genotypes decreased 90-100% at 40 mM NaCl, while the tolerant genotypes showed <70% in grain yield reduction. © 2016, International Society for Southeast Asian Agricultural Sciences. All Rights Reserved.


Satyawan D.,Indonesian Center for Agricultural Biotechnology | Rijzaani H.,Indonesian Center for Agricultural Biotechnology | Tasma I.M.,Indonesian Center for Agricultural Biotechnology
Plant Genetic Resources: Characterisation and Utilisation | Year: 2014

Soybean is an important crop in Indonesia and its consumption has consistently surpassed local production in recent times. As the average yield is relatively low, a more efficient breeding programme that utilizes the latest technological developments in DNA analysis is required. To provide a genomic data resource for future breeding programmes, in this study, whole-genome sequencing was performed for five Indonesian soybean varieties, with an average sequencing depth of 34 reads. Comparison of these sequences with the Williams 82 reference sequence revealed 3,150,869 DNA variations, which averages to one variation in every 308 bases. Comparison of these variations with known single-nucleotide polymorphisms (SNPs) in the SoyKB database revealed that approximately 29% of them were novel SNPs unique to the Indonesian cultivars. Variations found within exons totalled 95,154. Of these, 57,171 were capable of causing mutations that would modify the amino-acid composition of the encoded proteins (nonsynonymous mutations). Phylogenetic analysis using a subset of these SNP data indicated that the cultivars had genetic similarities to landraces from China and Japan, which could provide clues to the origin of soybeans that were introduced into Indonesia. © NIAB 2014.


Lestari P.,Indonesian Center for Agricultural Biotechnology | Elfrida N.,Bogor Agricultural University | Suryani A.,Bogor Agricultural University | Suryadi Y.,Indonesian Center for Agricultural Biotechnology
Jordan Journal of Biological Sciences | Year: 2014

Bacterial cellulose (BC), produced by Acetobacter xylinum, has been given a great attention due to its high potency for many industrial applications. An optimized substrate is important for higher BC production; thus, an alternative natural product, as a carbon source, should be determined. This study aims at investigating the BC of A. xylinum cultured in coconut water and pineapple juice-based media and to predict its fermentation kinetics. The BC was produced on two stages of fermentation system, the shaking culture for propagation and the static culture fermentation for BC production. A. xylinum exhibited exponential phase at 48 h which showed BC production associated with its cell growth on both substrates. Fermentation kinetics of A. xylinum using coconut water and pineapple juice revealed Rp 0.117 and 0.051 g/l/h, Rx 0.309 and 0.133 g/l/h, Rs 0.079 and 0.215 g/l/h, Yx/s 1.408 and 0.240 g biomass/g glucose, Yp/s 3.612 and 0.599 g cellulose/g glucose, Yp/x 2.235 and 2.452 g cellulose/g biomass, μmax 0.0132 and 0.0082/h, σ 0.028 and 0.0173/h, respectively. Overall parameters of fermentation kinetics revealed a high rate of BC formation and efficient conversions of glucose to biomass and BC by A. xylinum on coconut water substrate. Thus, coconut water proved to be a more suitable substrate to produce BC in comparison with pineapple juice. © 2014 Jordan Journal of Biological Sciences.

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