Jurnal AgroBiogen
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Evaluasi Lapang dan Identifikasi Molekuler Plasma Nutfah Padi terhadap Keracunan Fe
Get PDFFe toxicity is one of the abiotic constraints thatcan significantly decrease rice production, especially inmarginal wetlands. The use of tolerant varieties can reducethe cost of soil processing and fertilizing. Many accessions ofrice germplasm have potential alleles that can be utilized tocreate new varieties tolerant to Fe toxicity. The objectives ofthis research were to evaluate the Fe toxicity tolerance ofrice germplasm and to analyze the genotype diversity usingSNP markers for OsIRT, Fe toxicity tolerant gene(s). Fetoxicity tolerant rice germplasms were screened in acidmarginal wetlands of Taman Bogo Experimental Station,Indonesian Soil Research Insitute, Lampung Province.Meanwhile, the genotypes performance analysis wasconducted on SNP genotyping analysis using SNP markersfor OsIRT gene(s). Based on phenotypic data of 97accessions, which were clustered into six groups, two ofthem (group 2 and group 5) consisted of the tolerantaccessions at both vegetative and generative stages. Theresults of grouping analysis of genotyping based on SNPmarkers were obtained that there were five genotypegroups: AGT, AAT, GAT, AAC, and GAC. The AGT genotypecluster was dominated by the accessions included in group1. Meanwhile, the GAT genotype cluster consisted of mixedtolerant and untolerant accessions to Fe toxicity. The GACgenotype cluster was dominated by the accessions includedin group 2. The accessions which were included in the besttolerant group, group 5, were separated in differentgenotype cluster. Based on association analysis, among thethree SNP markers, OsIRT1 was the most significant SNPmarker (P value = 0.01) which correlated to Fe toxicitytolerant on vegetative stage. Some of the selectedaccessions that were tolerant to Fe toxicity and had goodagronomic performance on acid soil with high Fe contentwere Ketan Alay, Markuti, Arias Halus, Komas a, Lantiak,and Utri Deli. These local rice accessions have the potentialalleles of OsIRT genes
Isolasi Identifikasi Bakteri Penghasil Xilanase serta Karakterisasi Enzimnya
Get PDFXylanase is an extracellular enzyme produced bymicroorganisms. This enzyme is able to hydrolise xylane(hemicellulose) to produce xylooligosaccharide and xylose.Thermoalkaliphilic xylanase is an agent that can be used asa substitute in the pulp whitening process instead of chlorine.A study was done to isolate, identificate of bacteria andcharacterize xylanase. The isolation of xylanase producingbacteria has been done from soil and waste of starch industry.Colonies which produced clearing zone were presumedas xylanolytic bacteria and chosen for further screening.Identification of potential isolate in xylanase production wasdone using 16S ribosomal RNA sequencing. Isolate Bacilluspumilus RXA-III5 originated from lime or alkaline soil wasmore potential isolate in xylanase production than other 24isolates. Precipitation of xylanase, that was done usingammonium sulphate followed by dialyzes produced xylanaseof a higher specific activity (267.1 U.mg-1) than that usingacetone (131.1 U.mg-1) and ethanol (186.65 U.mg-1). Xylanasewas done at purification produced three fractions of xylanase.Xylanase characteristics consist of pH and temperature(9 and 50oC), Km and Vmaks value 6 mg.ml-1 and 0.2mol.minute-1, respectively. The Fe2+ was the strongest activetorand Mg2+ was the strongest inhibitor activity. This enzymewas detected as a cellulose-free xylanase. Xylanase is aprospective agent for bio-bleaching of paper
Keragaman Genetika Empat Belas Aksesi Kentang (Solanum tuberosum L.) Berdasarkan Marka SSR dan STS (Genetic Diversity of Fourteen Potato Accessions Based on SSR and STS Markers)
Get PDFPotato is one of high economically horticultural plant. The increasing of national consumption of potato becomes a challenge forpotato breeders. The success of breeding programs is depending on availability of genetic diversity. The aim of this research wasto analyze the genetic diversity of fourteen accessions of potato by using SSR and STS markers. PCR analysis was scored as binerdata and the collected data was analyzed using NTSYS and PowerMarker. The result showed that there were 63% polymorphic(12 markers) of total markers. As many as 60 alleles with the size of 200–500 bp were identified by a range of 2–9 alleles perlocus. The polymorphism level was 0.59 (0.36–0.74). Result also showed the average of major allele frequency was 49.42%(35.71–63.64%). Nine markers which have polymorphism level more than 0.5 could be used to detect genetic diversity of potato.The average of genetic diversity index was 0.65. Cluster analysis showed that 14 accessions of potato were split in two groups(coefficient 0.70). The first groups consisted of Atlantik, GM 05, Granola Kembang Merbabu 17, and the second groups consist ofRepita, Maglia, Medians, CIP397078.7, CIP392781.1, Margahayu, Granola, CIP394613.139, Amabile, and Tenggo. The informationof genetic diversity of this germplasm could be used as a preliminary basis for choosing crossing parents in potato breeding inIndonesia
Pengaruh Media terhadap Produksi Prodigiosin Isolat Bakteri Entomopatogen Serratia marcescens Asal Wereng Batang Cokelat
Get PDFProdigiosin, the red pigment producedby the bacterium Serratia marcescens, is a secondarymetabolite of the family tripyrrole that has been widely usedas an antibiotic in the multifunction treatment ofantibacterial as well as antifungal. This study was aimed tostudy the effect of Luria-Bertani (LB) broth and nutrientbroth (NB) media suplemented with several concentrationsof FeSO4 and CaCO3 on the production and characteristic ofprodigiosin derived from S. marcescens. The study wasarranged in a completely randomized factorial design withfour replications. The LB and NB media were supplementedwith 0, 2.5, 5, and 10 mM CaCO3 and 0, 0.25, 0.5, and 1 mMFeSO4. Results showed a red pigment produced by S.marcescens when cultured on both LB and NB media. Redlikepigmentation was varied when supplemented withdifferent concentration of Fe2+ and Ca2+. The higher theconcentration of Fe2+, the more intense the red color,conversely, the higher the concentration of Ca2+, the lighterthe red color. The interaction was found between the mediaand concentrations of CaCO3 and FeSO4 on the productionof prodigiosin. The highest prodigiosin production wasobtained on NB media supplemented with FeSO4.Meanwhile, the addition of CaCO3 did not affect theprodigiosin production. An addition of 1 mM FeSO4 to LBand NB media produced crude prodigiosin of 486.0 mg/mland 489.0 mg/ml, respectively. Based on purification bycolumn chromatography using silica gel, the prodigiosinproduction on LB and NB media was 378 mg/ml and 450mg/ml, with the purity level of 77.8% and 92%, respectively.Detection of prodigiosin by thin-layer chromatography usingsilica gel showed the red pigment had Rf value of 0.83 andbioautography assay showed there was an antibacterialactivity against Xanthomanas oryzae pv. oryzae
Pendugaan Gen Bph1, bph2, Bph3, dan bph4 pada Galur-galur Padi Terpilih Tahan Hama Wereng Batang Cokelat (Nilaparvata lugens[Stål])
Get PDFPests are major constraints to increasingrice production and brown planthoppers/BPH (Nilaparvatalugens [Stål]) is one of the major pests of rice plant.Resistance cultivar is one of the strategies for BPHmanagement. The objective of this research was to analyzethe Bph1, bph2, Bph3, and bph4 gene existence on theselected rice lines using the molecular markers. Thephenotype of the rice lines were tested based on theirresponse to BPH population collected from West Java andCental Java. Molecular markers linked to Bph1, bph2, Bph3,and bph4 were used to characterize the genotypic profilebased on PCR analysis. The results showed that there are sixgenotypes resistant to one of the BPH populations fromWest Java or Central Java. The six rice varieties weredetected to have not only allele of Bph3 gene, but also otherdifferent allele genes. B12344-2D-PN-42-1 and Inpari 13 weredetected to have the alleles of Bph3 dan Bph1 genes.B12512-18-SI-3-3-MR-3-PN-1, B12512-18-SI-3-3-MR-3-PN-1,BMIP46-4-1, and PTB33 were detected to have the alleles ofBph3 and bph2 genes. Meanwhile, B11007E-MR-3-2-PN-2-1-MR-1-2 was detected to have alleles of three genes: Bph3,bph2, and bph4. Nevertheless, this last line had mediumresistance to both BPH populations invested. There is apossibility that the interaction between two genes, Bph3 andbph4, occured which may affect the resistance responses ofrice varieties tested to BPH
Analisis Keragaman Genetik Acremonium yang Berasosiasi dengan Tanaman Gaharu Menggunakan Teknik Random Amplified Polymorphic DNA (RAPD)
Get PDFAgarwoodor gaharu is a plant that has a high economic value in Asia,due to its use for production of incense and traditionalmedicines. The agarwood formation occurs in the trunk androots of trees that have been infected by a fungus, such asAcremonium spp. Various fungi were associated with theagarwood formation. Acremonium is generally considered ashighly polyphyletic, contains distantly related fungi. A studywas done to identify genetic diversities in 10 isolates ofAcremonium spp. from four different areas in Indonesia thatare associated with Aquilaria and Gyrinops verstigii using theRandom Amplified Polymorphic DNA (RAPD) technique.Eight RAPD primers, i.e., OPA 02, OPB 04, OPB 07, OPB 17,OPC 11, OPD 03, OPD 05, and OPE 07 were used in theanalyses. The results indicated that similarity index values ofthe genetic variation ranged from 0.21 to 0.97. Based on theNei and Li’s similarity coefficients, these values indicatingthe presence of high degree of genetic variability. The lowestdegree of genetic similarity were found between isolates F(Acremonium spp., which is associated with G. verstigii fromMataram, Nusa Tenggara Barat), and LM2 from south coastalarea of West Sumatra. The highest genetic similarity value(0.97) was found between isolates Sr2 and Sr4 from Sorong,Papua. Results from the cluster analysis indicated that theisolates could be grouped into two major clusters that wereassociated with their geographical locations
Interaksi AtMEK1-EXGT pada Arabidopsis thaliana pada Saat Terjadi Pelukaan
Get PDFProteininteractions occur within cellular level of stimulated plantcells to relay signals from receptors to production of response.AtMEK1-EXGT interaction had been detected in nontreatedArabidopsis. In this research, interaction betweenAtMEK1, a mitogen-activated protein kinase kinase ofArabidopsis thaliana, and EXGT, endoxyloglucan transferase,after the plant was wounded was examined usingco-immunoprecipitation and in vitro phosphorylation assay.The results demonstrated that EXGT interact with AtMEK1soon after and 10 minutes after wounding. In addition,AtMEK1 phosphorylation activity increased when increasedlevel of EXGT was incorporated into the reaction mixture.These indicate that EXGT amplifies wound-caused phosphorylationactivity of AtMEK1. The results elucidate part ofthe AtMEKK1-AtMEK1-AtMPK4 cascade which is stimulatedby wounding. How the complex interaction between EXGT,AtMEK1 and AtMPK4 fits within the cascade is remained tobe uncovered
Survei Polimorfisme Tetua untuk Pengembangan Panel CSSL Padi (Oryza sativa L.) dan Identifikasi Tanaman F1
Get PDFRaising yield potential of modernindica varieties is essential to meet the increased demand ofrice production. This is due to increased human population,threats of climate change and degradation of agriculturalresources. The use of chromosome segment substitutionlines (CSSL) is more effective for identification of genesthose are useful for improvement of yield potential. The aimsof this study were to observe the morphological traitdifferences between recipient parent (var. Ciherang) andthree candidates of donor parent (var. Fatmawati and newplant type lines, i.e. B12743 and B11143D), to identifypolymorphic SSR markers among them and to verify F1individuals. Ciherang and B11143D showed significantdifferences on flowering time, plant height, flag leaf area,tiller number, productive tiller number, panicle length,spikelet number per panicle and 1,000 grain weight. The rateof SSR marker polymorphisms between Ciherang andB11143D was the highest, where 155 of 513 markers (30.2%)were polymorphic. Marker genotyping using threepolymorphic markers showed that 26 of 27 plants resultedfrom the cross of Ciherang х B11143D were F1. These F1plants could become the basis of CSSL panel that facilitatethe mapping of genes responsible for increasing the yieldpotential
Seleksi dan Konfirmasi Alel Gen-gen Hd pada Padi Berumur Genjah dan Produktivitas Tinggi Persilangan Code x Nipponbare
Get PDFTo support the IP 300 program rice varietieswith both early maturity and high productivity are needed.The objective of the research was to improve those traits inCode variety using RIL (recombinant inbreed line) methods.The research was conducted in the year 2009-2011 at thegreenhouse and laboratory of Molecular Biology, IndonesianCenter for Agricultural Biotechnology and GeneticResources Research and Development. Materials consistedof 600 individuals of F2 derived from one of F1 Code xNipponbare crossed plants and they were planted up to F4with seed-to-seed, then confirmed by 8 microsatelitemarkers linked to loci of Hd genes. The molecular analysisshowed that 84 of 600 F2 plants produced. The F4 plants have50% of flowering time shorter than F2 and F3 plants. Twolines (CdNb_388 and CdNb_270) have higher productivitycompared to Code by the number of productive tillers (20)and the number of tiller grains (2240 and 1740) and haveclosely 50% of 60 days flowering time of Nipponbare. Threelines of F4 plants (CdNb_270, 364, and 388) were predictedto have allele of Hd7 gene, and CdNb_472 was predicted tohave alelle of Hd14 gene
Pengembangan Set Multipleks Penanda DNA Mikrosatelit untuk Analisis Variasi Genetik Padi dan Kedelai
Get PDFDetection of multiplex microsatellite markers in asingle capillary array on a laser detection system is traditionallyconducted with specific primers that are labelled withfluorescent dyes. An alternative method using fluorescentlabels that are appended to 5’ end of universal primer M13instead of to the specific primers offers flexibility indesignning multiplex panels and a less expensive method.Allele size range of microsatellite loci that can be grouped inmultiplex panels can be accurately estimated by pooling andanalyzing DNA samples from several genotypes simultaneously.This paper describes the procedure in developmentof microsatellite multiplex panels using M13 fluorescentlylabelledand estimation of allele size range based on pooledDNA strategies. Two multiplex panels of PCR amplificationproducts for rice consisting of 15 loci and three panels forsoybean consisting of 10 loci have been designed. Thepanels have been applied to 50 accessions of rice and soybeanwith fairly good results. Further characterization ofallele size range, however, is required prior to the applicationof these panels to diverse genotypes. The proceduredescribed here should be applicable in the development ofmultiplex panels of other species