Jurnal AgroBiogen
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Analisis Kekerabatan 50 Aksesi Kelapa Sawit (Elaeis guineensis Jacq.) Asal Kamerun Berdasarkan Marka Mikrosatelit
No full textGenetic diversity of theIndonesian oil palm collection remains low and collectionenrichness through exploration activities from the center oforigins is required. In 2009, 103 oil palm accessions fromCameroon were collected at the National Oil Palm GeneticResources Collection located at the District of Sijunjung,West Sumatera. The objectives of the present study were toanalayze the 50 Cameroon-originated oil palm accessions inorder to: (1) determine polymorphism levels of the SSRmarkers used; (2) understand diversity levels of the oil palmaccessions tested; and (3) analyze accessions potentiallyused for germ plasm collection. Fifty oil palm accessionswere used in this study. DNA was isolated from leaves of theselected individual plants representing each of theaccessions. DNA was analyzed with 12 SSR markers. Adendrogram was constructed using the UPGMA throughNumerical Taxonomy and Multivariate System programversion 2.1-pc. Results showed that SSR markers useddemonstrated the average number of alleles per locus of 3.6(2-6). The polymorphism level was 0.53 (0.21-0.73). Thephylogenetic analysis resulted nine clusters with geneticdiversity between two accessions ranged from 4-82%. Tenaccessions (20%) showed low genetic diversity (<10%) butthe accessions demonstrated high diversity in floweringtime. Eleven accessions showed medium diversity level (27-42%). Five accessions demonstrated high genetic diversitylevel (45-82%). A confirmation study using more SSRmarkers is recommended. This study finding may be usefulin planning the oil palm germ plasm collection activities
Manfaat Sekuen Genom Lengkap dalam Identifikasi Gen: Peranan Kelompok Gen Actin-myosin dalam Sistem Pertahanan Tanaman
Get PDFComplete genome sequencing of Arabidopsis thaliana and rice (Oryza sativa) were accomplished in 2000 and 2004, respectively. The availability of high quality genome sequences of A. thaliana and rice amenable for identification and understanding of the structure and functional genes in the plant genome. One of the genes family that have been investigated is the actin-myosin genes. This genes family contributes to signalling process of the plant defence mechanism. This paper focuses on phylogenetic characterization and activation of actin-myosin genes family with emphasis on involvement on the plant defence mechanism
Identitas dan Keragaman Genetik Begomovirus yang Berasosiasi dengan Penyakit Keriting pada Tomat Berdasarkan Teknik Polymerase Chain Reaction (PCR)- Restriction Fragment Length Polymorphism (RFLP)
Get PDFBegomoviruses, members of the Geminivirus,are considered as emerging plant viruses. This was due tothe increasing incidences and severities of the diseases in anumber of economically important crops, including tomato.Genetic diversities of the Begomovirus isolates infectingtomato (Lycopersicon esculentum) of several areas in Indonesiawere analyzed by using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP)technique. A 1500 base pairs of PCR fragments amplified byusing degenerate primers for Begomovirus was digestedusing four restriction enzymes, i.e., DraI, EcoRI, RsaI, andPstI. The pattern of RE digested fragments of 8 Begomovirusisolates and the predicted RFLP fragments of the Begomovirusisolates in the GeneBank database were used to determinethe genetic identities and diversities among the isolates.Positive results of the PCR amplifications proved thatdiseased tomato plant samples collected from 8 locations inJava and Sumatra were infected with at least one Begomovirusisolate. The PCR amplification products, which weredigested using the four restriction enzymes indicated thepresence of polimorfisms among the DNA fragments of theBegomovirus isolates. Identifications of the Begomovirusindicated that the Brastagi, Bogor, Sragen, Ketep, and Boyolaliisolates were Tomato Leaf Curl Virus (ToLCV); theisolates from Malang and Blitar isolates were AgeratumYellow Vein Virus (AYVV), while one isolate from Kaliurangwas Tomato Yellow Leaf Curl Virus (TYLCV). Results of thephylogenetic analysis of the 8 Begomovirus isolates basedon Begomoviruses from the DNA database indicated thatthey belonged to three different groups
Induksi dan Regenerasi Kalus Jagung yang Ditransformasi dengan Gen CsNitr1-L melalui Penembakan Partikel
Get PDFThe success in development of transgenic plants is influenced by the regeneration system. The objective of the study was toassess the response of maize genotypes to regeneration system of organogenesis and embryogenesis, after transformed withCsNitr1-L gene through particle bombardment. Induction and callus regeneration of maize immature embryos of inbred linesUlt:cm.1#, ARC 178-123-112-XB3, and AZ2 were conducted through organogenesis, whereas those inbred lines AZ1, AZ2,P4G19(S)C2.59.3.3.1.3 and P4S3.29.4.4.1 were conducted through embryogenesis somatic. Transformation of CsNitr1-L gene wasdone with the distance of bombardment of 7 cm and 9 cm and calli were then selected using 10 mg/l hygromycin. All explants(100%) of inbred lines Ult:cm.1# formed organogenic callus, while callus formation of ARC 178-123-112-XB3 was 94.3% and AZ2was 60.5%. Ult:cm.1# was the most responsive line to the regeneration of organogenesis and produced 24 green shoots,compared with ARC 178-123-112-XB3 which produced one green shoot and AZ2 that did not produce green shoots. The highestpercentage of embryogenic calli formed through somatic embryogenesis was obtained on inbred lines AZ1 (85.4%) and thelowest was on P4S3.29.4.4.1 (18.9%). Inbred lines AZ1 had the highest percentage of regeneration (50.7%) and produced 62plants, followed by P4G19(S)C2.59.3.3.1.3 that produced 17 plants (2.8%) and P4S3.29.4.4.1 which produced two plants.Preliminary identification on 31 putative transgenic plants through PCR analysis produced 22 plants (70.96%) that contained nptIIgene
Pemanfaatan Markah Molekuler dalam Proses Seleksi Pemuliaan Tanaman
Get PDFDNA-based technology has dramatically enhanced the efficiency of plant breeding, especially when selections are to be done under unfavourable conditions. Although significant strides have been made in crop improvement trough phenotypic selections for ergonomically important traits, this often encounters considerable difficulties, particularly those posed by genotype x environment interactions. Besides testing procedure may be many times difficult, unreliable or expensive due to the nature of the target traits (e.g. abiotic and biotic stresses) or the target environment. The most widespread use of Marker Assisted Selection (MAS) to date is to assist backcrossing of major gene already proven elite cultivars. If individual genes or Quantitative Trait Loci (QTL) significantly influencing specific target traits can be identified based on their linkage to molecular markers, the efficiency of incorporating the desired traits in elite germplasm could be greatly enhanced. By combining QTL approach with backcrossing, useful genes that control quantitative traits have been identified in plant germplasm that are not for agriculture and have successfully been transferred to danced breeding lines. Indonesian molecular breeders should have a research program on DNA marker work that leads to application of useful selection tools and valuable germplasm. As molecular breeders adopt more rigorous experimental guidelines and ambitious goals, they also need to integrate the growing body of knowledge from genomics and bioinformatics
Penentuan Alergenisitas Protein Gen RB pada Kentang Produk Rekayasa Genetika Berdasarkan Studi Bioinformatika
Get PDFGenetically modified products (GMP) of Katahdin potato event SP951 containing RB gene resistant to late blight diseasescaused by Phytophtora infestans has been developed in the USA. This Katahdin SP951 potato has been crossed with localvarieties Atlantic and Granola for its development in Indonesia. In the release process, the GMP potato should be tested forenvironmental and food safety. One of the food safety assessment needs to be done by determining allergenicity of RB proteinwhether it is potential as allergen. This research aims to translate the RB gene sequence into RB protein sequence andinvestigate the potential RB protein as an allergen through bioinformatic studies. This study was performed based on thealignment with available protein allergens from available database websites. The predicted RB protein obtained from 2,913amino acids RB gene was a 971 amino acids length protein with ATG as a start codon and TAA as a stop codon. Bioinformaticsstudies of RB protein were performed using www.allergenonline.com, consisted of three searches, i.e. full-length search byFASTA, 80 amino acids search by FASTA, and 8 amino acid exact matches. For full-length alignment search, there are threeallergen proteins similar with RB protein sequence with the percentage identity of <35%, while for alignment with 80 aminoacids and 8 amino acids did not show similarity with any allergen protein in the database. It can be concluded that RB proteindid not have any potential as an allergen, as according to Codex Alimentarius guidelines for full-length alignment search, onlyprotein with identity greater than >50% indicating possible cross reactivity with protein allergen
Identifikasi Molekuler Hawar Daun Bakteri (Xanthomonas oryzae pv. oryzae) dan Uji Patogenisitasnya pada Galur-galur Padi Isogenik
No full textIdentification of Xanthomonas oryzae pv.oryzae (Xoo) based on molecular analysis has beenintroduced just few years ago. This method used somespecific primers for Xoo and can be done quickly. Thepurposes of this research were to identify isolate Xoooriginated from five locations in Indonesia and to determinethe level of pathogenicity of these bacteria. Studies wereconducted in the greenhouse and the Molecular BiologyLaboratory of ICABIOGRAD, from 2011 to 2012. Bacterialisolates were taken from five regions in Indonesia, namely:West Sumatra, West Java, Central Java, South Sulawesi, andWest Kalimantan. The specific primers of Xoo wereXoo2967, Xoo80, and Xoo. Results showed that 216 isolatescould be grown to form yellow colored colonies, whichbelongs to a criterian for Xoo. Molecular analysisdemonstrated that 189 isolates were Xoo and 27 isolateswere not. Amplification of DNA of the isolates resulted a 337bp PCR product for primer Xoo2976, 700 bp for primerXoo80 and 534 bp for primer Xoo. Pathogenicity tests of theXoo isolates showed xa5, Xa7, and Xa21 resistance geneswere still effective againts BLB pathogens originated fromthose five regions, with percentage of resistance were 93.57,77.49, and 85.37%, respectively
Pemurnian Parsial dan Karakterisasi Kitinase Asal Jamur Entomopatogen Beauveria bassiana Isolat BB200109
Get PDFBeauveria bassiana is one of theentomopathogenic fungus that produces chitinase wheninfecting its host. This study was aimed to purify, isolate andcharacterize chitinase of B. bassiana isolate BB200109.Pathogen identity was determined both morphologically andmolecularly using ITS primer, whilst characterization wasdone at various conditions i.e. temperature, pH, metal ionand incubation time. Results showed that the BB200109isolate belonged to B. bassiana. The isolate producedextracellular chitinase with chitinolytic index of 1.035. Partialpurification of three saturated ammonium sulphateprecipitation (10, 30, and 70%) showed maximum purity of1.2 times, while dialysis could increase the purity of 1.9times compared to that of crude enzyme extract.Characterization results showed that the chitinase isolatedfrom B. bassiana isolate BB200109 had an optimum activityat pH 4, temperature 50oC, and optimum incubation time of90 minutes. The effect of metal ions (60 mM) Mn2+ served asactivator, while EDTA, K+, Mg2+, Cu2+, Fe2+, Zn2+, and Na+acted as inhibitors. The chitinase demonstrated loweraffinity to chitin substrate as indicated by high Km value of0.266 mg/l and a Vmax of 0.067 mg/l sec. Based on SDS-PAGE,chitinase from B. bassiana isolate BB200109 had molecularweight of 60.25 kDa. The study implied the potency ofB. bassiana isolate BB200109 as extracellular chitinaseproducer with its enzyme charateristics seems to bedeveloped as an insect biocontrol agent
Keragaman Genetik Inbrida Jagung QPM dan Normal Berbasis Marka Mikrosatelit dan Hubungannya dengan Penampilan Hibrida
Get PDFInformation on genetic divergence ofinbred lines and performance of the hybrids developed fromthe lines is a great value in maize hybrid program. A studywas conducted to evaluate genetic diversity of six QPM andfive normal maize inbred lines, to determine the relationshipbetween genetic distance based on SSR markers and thegrain yield of single cross hybrid, and to get informationpromising hybrid from the single cross of QPM hybrid.Twenty four polymorphic primers that covered the 10 maizechromosomes were used to fingerprint the lines, detectingin 94 alleles (average of 3.9 and a range of 2-6 alleles perlocus). Genetic divergences were determined using theJaccard’s similarity coefficient, and a dendrogram wasconstructed using the UPGMA. Cluster analysis divided theinbreds into two clusters that were confirmed by principalcoordinate analysis. Two promising QPM hybrids that arecrossed from different heterotic group were found. Theestimated value of simple correlations (r) of GDs with thegain yield of single cross hybrid was negatif (-0.07). There isa need to conduct more field trials to obtain more accuratecorrelations, particularly in a practical utility for predictingmaize hybrid performance for grain yield
Perkecambahan dan Perbanyakan Gaharu secara In Vitro
Get PDFAgarwood (Aquilaria malaccensis Lank) is one of the forest wood that are continously exploited. Currently, the Indonesian export of agarwood is decreasing because its population is endangered by excessive logging. Agarwood propagations need technology for reproduction of agarwood seedlings and their fungal inoculum. In vitro technique for germination of recalsitrant seeds and micropropagation are technologies that can be used for propagation of agarwood seedlings. An experiment was done to develop techniques for in vitro germination and micropropagation of agarwood. The in vitro germination was done using two different techniques. Firstly, sterile seeds were germinated on an MS medium + 50 mg/l PVP, 50 mg/l GA, and 1 mg/l BA or kinetin. Secondly, sterile seeds were germinated on basal medium of MS, 1/2 MS medium, MS medium without vitamins, as well as on MS medium without pyridoxine, nicotinic acid and WPM. Shoot initiations and multiplications were done on MS and 1/2 MS media containing 1, 3, or 5 mg/l BA. The explants used were cotyledone nodes, terminal shoots, single node with leaf, and sinle node without leaf. The results showed that the seed germination rate on the different media ranged from 7,14 to 50%. The seed germination rate on the MS medium without vitamis was the highest. The best explants for shoot induction and multiplication was single node with leaf which was cultured on MS + 1 mg/l BA