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HUBUNAGN KEMAMPUAN PERGANTIAN INANG DENGAN PLASTISITAS GENETIKA PADA CENDAWAN BLAS PADI (PYRICULARIA GRISEA) Listiyowati, Sri; Widyastuti, Utut; Rahayu, Gayuh; Hartana, Alex; Jusuf, Muhammad
Jurnal Ilmu Pertanian Indonesia Vol. 14 No. 2 (2009): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

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Abstract

The Digitaria ciliaris, wild grass grown around rice field, was a host for Pyricularia grisea (Cooke) Sacc., the fungi caused blast disease of rice. This fungi have a specific mechanism to regenerate new genetic variation in its life cycle. The aim of this research is to study the relation between the ability of the fungi to infect different species of host with its genetic plasticity. It was used three SCAR molecular markers Cutl, Pwl 1 and Erg2. P. grisea isolates (Dc4J1) originated from D. ciliaris at Jasinga-Bogor were able to infect rice cultivars Kencana Bali and Cisokan. The original Dc4Jl, from D. ciliaris, and the Dc4Jl that were reisolated from the infected rice cultivars (reisolates-1) had the same ability to infect Kencana Bali and Cisokan. Molecular technique showed that there was a different molecular marker genotype between the original Dc4J1, from D. ciliaris, and the Dc4Jl reisolated from infected rice cultivars. The original Dc4J1 owned Cutl but did not Pwl2 in contrary the reisolates Dc4J1 from rice cultivars (reisolates-1) had Pwl2 but did not Cutl. The Erg2 presented in both the original and the reisolated Dc4Jl. These results indicated that there were a change of genotype of P. grisea at the same time with the change of host species. The Dc4Jl isolates originated from Kencana Bali and Cisokan (reisolates-2) that were infected by reisolate-1, had the same genotype with the reisolates-1.
KERAGAMAN GENETIK KELAPA SAWIT (ELAEIS GUINEENSIS JACQ.) ASAL ANGOLA MENGGUNAKAN MARKA SSR Sayekti, Urip; Widyastuti, Utut; Toruan-Mathius, Nurita
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 43 No. 2 (2015): Jurnal Agronomi Indonesia
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (479.461 KB) | DOI: 10.24831/jai.v43i2.10420

Abstract

ABSTRACTEffort to increase productivity and other elite characters in Indonesia oil palm breeding program is facing a problem because of the narrow genetic diversity. To broaden the genetic diversity, germplasm exploration has been done in Angola, Central Africa. The objective of this research was to assess the genetic diversity and population structure of Angola originated oil palm germplasm based on 20 SSR markers. The plant materials used were 27 accessions consisted of 136 palms planted in Riau, Sumatera. The DNA was isolated and amplified using PCR. Phylogeny analysis was constructed using Unrooted Neighbor-Joining by DARwin software 6.0.8. The result showed that polymorphic information content (PIC) value is 0.55 (0.17 to 0.75 for each locus) with 102 total number of alleles. Genetic diversity between individuals was higher compared to the genetic diversity within accessions or regions and between accessions or regions. Phylogenetic analysis of 27 accessions showed that accessions were divided into three main groups. Every group containing individuals originated from 5 spatial distribution regions. Principal coordinates analysis (PCoA) showed that accessions were distributed in one structure. Using more primers and samples to get more representative data is recommended for the following research.Keywords: allele, locus, germplasm, molecular marker, polymorphic
IMPROVEMENT METHOD OF GENE TRANSFER IN KAPPAPHYCUS ALVAREZII Triana, St. Hidayah; Alimuddin, .; Widyastuti, Utut; Suharsono, .; Suryati, Emma; Parenrengi, Andi
Jurnal Ilmu dan Teknologi Kelautan Tropis Vol. 8 No. 1 (2016): Elektronik Jurnal Ilmu dan Teknologi Kelautan Tropis
Publisher : Department of Marine Science and Technology, Faculty of Fisheries and Marine Science, IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jitkt.v8i1.13087

Abstract

Method of foreign gene transfer in red seaweed Kappaphycus alvarezii has been reported, however, li-mited number of transgenic F0 (broodstock) was obtained. This study was conducted to improve the method of gene transfer mediated by Agrobacterium tumefaciens in order to obtain high percentage of K. alvarezii transgenic. Superoxide dismutase gene from Melastoma malabatrichum (MmCu/Zn-SOD) was used as model towards increasing adaptability of K. alvarezii to environmental stress. The treat-ments were the culture media and recovery duration, and each treatment consisted of three replica-tions. The best method was co-cultivation using liquid media, then recovery was conducted in liquid media for 10 days. That treatment allowed higher transformation percentage (90%), regeneration effi-ciency (90%), putative bud efficiency (100%), number of buds and explants sprouted (100%) and transgenic explants (100%). The transgenic explants showed an amplification PCR product of Mm-Cu/Zn-SOD gene fragment, whereas the non-transgenic explants showed no amplification product.  All results revealed that suitable method of transgenesis for K. alvarezii has been developed. Keywords:       Agrobacterium tumefaciens, culture media, Kappaphycus alvarezii, recovery duration, transformation
ANDROGYNOMONOECIOUS JATROPHA CURCAS: CHROMOSOMES, ISOZYMES, AND FLOWERS GENDER Triadiati, Triadiati; Kurniati, Kurniati; Widyastuti, Utut; Dasumiati, Dasumiati
HAYATI Journal of Biosciences Vol. 26 No. 3 (2019): July 2019
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (356.606 KB) | DOI: 10.4308/hjb.26.3.%x

Abstract

Jatropha curcas (J. curcas) is usually monoecious plants, which have male and female flowers on the same inflorescence. However, J. curcas can be found as an androgynomonoecious plant (have male, female, and hermaphrodite flowers), even though very rare. Androgynomonoecious J. curcas can be identified after six months of planting when it had started flowering. Therefore, it is important to identify the characteristics of androgynomonoecious J. curcas that can differentiate between androgynomonoecious and monoecious plants in earlier stages of growth. The objectives of the research were to observe isozymes, chromosome and flowers gender of androgynomonoecious and monoecious J. curcas Banten and Lampung accessions. Seeds from five genotypes of J. curcas were used in the research. The observation was carried out on the chromosome and isozymes (Peroxidase and Esterase isozymes) could be used as markers to differentiate androgynomonoecious and monoecious plants. Observations about the flower gender from offsprings derived from different seeds were important to know the inheritance of flower gender. The androgynomonoecious and monoecious J. curcas were diploid with number of chromosomes 2n=2x=22. The chromosomes of androgynomonoecious have longer than that of monoecious J. curcas. The isozymes of androgynomonoecious J. curcas had four alleles and monoecious J. curcas (Banten female monoecious) had three alleles. The flower inflorescence and gender derived from androgynomonoecious plants were unstable, due to androgynomonoecious is intermediate state.
Pertumbuhan Tunas Nenas Lokal Bangka Secara In-Vitro pada Media Murashige-Skoog dengan Penambahan Thidiazuron Syafarudin, .; Widyastuti, Utut; Mustikarini, Eries Dyah; Rosa, Yanti
ENVIAGRO Vol 3, No 1 (2010): ENVIAGRO, APRIL 2010
Publisher : Universitas Bangka Belitung

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Abstract

The aim is to find out the best combination of Murashige-Skoog (MS) media and Thidiazuron (TDZ) concentrations for promoting pineapple shoot growth. Planting material used in this research is a piece of axillar shoots from the Bangka local pineapple  that has been sub-cultured four times on media 2 mg/l BAP.  Research used the completely randomized design in factorial that consists of 3 levels of MS media (50%,75% and 100%) combined with 4 levels of TDZ (2 mg/l BAP (control), 0.1 mg/l TDZ, 0.01 mg/l TDZ and 0.001 mg/l TDZ).  Results showed that the use of 75% MS medium concentration gave the best effect on the variable of shoots appearing time (1.45 MST) and the shoots length (22.35 mm); the tabulation gives the highest average score on the variable number of shoots (6.44 shoots), explants percentage germination (97.22%) and number of leaves (8.6 pieces). The concentration of 0.01 mg/l TDZ gave the best effect of time for emerging shoots (1.51 MST) and the number of shoots (8.16 shoots). At concentrations 0.001 mg/l TDZ gave the best effect on the shoots length (28.07 mm) and number of leaves (11.12 pieces). The combination treatment of 75% MS medium and 0.01 mg/l TDZ provided the highest value for the time of emerging shoots (1.77 MST) and number of shoots at 8 MST (10.49 buds). The combination treatment of 75% MS medium with 0001 mg/l TDZ provided the highest value for the shoot length (31.22 mm) and number of leaves (11.88 pieces).
Method development for detection of E545A mutation PIK3CA gene in breast cancer patients using Tm Shift SYBR Green I qPCR Al Ahwani, Fuad; Desriani, Desriani; Widyastuti, Utut; Suharsono, Suharsono
Indonesian Journal of Biotechnology Vol 21, No 1 (2016)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (987.933 KB) | DOI: 10.22146/ijbiotech.26815

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E545A is one of the point mutations, and its frequency is high in PIK3CA gene (3.8%), particularly breast cancer patients in Singapore (13.8%) and Mexico (11.5%). In addition to induce breast cancer, the mutation also caused resistance of anti-HER2 in HER2 cancer subtype. The tremendous effect of this mutation was not supported by affordable detection method. This study aimed to develop a feasible and sensitive method of E545A detection. The developing method used Tm and Ct to identify samples. Based on optimization, the best condition was obtained at optimization 2 at annealing temperature of 65°C. At this condition, Tm and Ct of each sample were (a) exon 9 (78.4°C and 13.005±0.007) and (b) E5454A (80.4°C and 10.07±0.1). This method also demonstrated good precision as observed in variance coefficient of intra and inter assay (0). Thus, method for E5454A detection mutation was successfully developed.
Evaluation of different promoters driving the GFP reporter gene in seaweed Kappaphycus alvarezii Rajamuddin, Muh. Alias L.; Alimuddin, A.; Widyastuti, Utut; Faizal, Irvan
Indonesian Journal of Biotechnology Vol 19, No 2 (2014)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (366.674 KB) | DOI: 10.22146/ijbiotech.9304

Abstract

Promoter regulates expression level of foreign gene in transgenic organism. This study was performed to select asuitable promoter as the fi rst step towards production of valuable trait-enhanced seaweed by transgenic technology. Greenfl uorescent protein (GFP) gene was used as a reporter to determine the activity of promoter in seaweed Kappaphycusalvarezii. GFP gene constructs driven by cytomegalovirus (pCMV-GFP), caulifl ower mosaic virus (pCaMV-GFP),medaka β-actin (pmBA-GFP) and Japanese fl ounder keratin (pJfKer-GFP) promoters were introduced by electroporationmethod. Electroporation was performed using a gene pulser (BIORAD) with voltage of 300 V, pulse length of 0.5 ms,pulse numbers of 4, and pulse interval of 0.1 s. Promoter activity was determined by analyzing GFP gene expressionlevel using a fl uorescent microscope. The results showed that CMV regulated highest number of fi lament callus(34.10%±1.49) expressing GFP at medium to strong fl uorescence levels. CaMV promoter had relatively similar activitywith CMV, but lower number of fi lament callus expressing GFP (10.48%±0.25). mBA promoter drove GFP expressionat medium level and similar number of fi lament callus (8.85%±2.31) expressing GFP with CaMV, while JfKer promoterhad lowest activity by means in number of fi lament callus expressing GFP (4.79%±0.26) and GFP expression level. PCRanalysis for transgenic confi rmation showed a DNA band of PCR product from pCMV-GFP and pCaMV-GFP expressingfi lament callus in the same size (about 0.6 kb) with positive control of plasmid. Thus, CMV and CaMV promoters wasan appropriate promoter and foreign gene could be transferred to fi lament callus by electroporation method. Combiningthis achievement with developing a culture method of fi lament callus to be thallus, stable transgenic breeding in K.alvarezii can be feasible.
CONSTRUCTION OF RNA INTERFERENCE VECTOR TO SILENCE ALUMINUM TOLERANCE GENE CANDIDATE IN RICE CV HAWARA BUNAR Wahyuningtyas, Windarti; Miftahudin, Miftahudin; Widyastuti, Utut; Tjahjoleksono, Aris
HAYATI Journal of Biosciences Vol. 23 No. 2 (2016): April 2016
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1366.677 KB) | DOI: 10.4308/hjb.23.2.79

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One of the aluminum (Al) tolerance gene candidates, namely B11 gene, has been successfully isolated from Al-tolerant rice cv Hawara Bunar. However, the role of the gene in Al tolerance in rice has not been known. RNA interference (RNAi) technique is an effective tool to examine the biological function of the target gene in plant. The objective of the research was to construct RNAi recombinant vector carrying untranslated region of the B11 gene. RNAi recombinant vector carrying 195 bp sized 3?UTR_B11 fragment as a double-stranded RNA (dsRNA) trigger has been successfully constructed using GATEWAY? cloning technology, pENTR?/D-TOPO® as a shuttle vector, and pANDA vector as a destination vector. RNAi construct was successfully introduced into Agrobacterium tumefaciens AgL0, and has been infected to rice cv Hawara Bunar. Analysis of putative transgenic rice showed eight of 20 plants were transgenic carrying the B11-RNAi construct.
DETECTION OF LUMINOUS VIBRIO HARVEYI IN PENAEID SHRIMP THROUGH NESTED PCR USING HAEMOLYSIN GENE PRIMER SETIAWAN, WAWAN ABDULLAH; WIDYASTUTI, UTUT; YUHANA, MUNTI
HAYATI Journal of Biosciences Vol. 22 No. 2 (2015): April 2015
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1909.736 KB) | DOI: 10.4308/hjb.22.2.60

Abstract

Whiteleg shrimp (Litopenaeus vannamei)  is one of the most important aquaculture commodity in Indonesia. However, the luminous disease primarily caused by Vibrio harveyi bacteria still becomes an obstacle in penaeid shrimp farming, especially in shrimp hatchery. This study was aimed to identify the presence of V. harveyi in L. vannamei through nested PCR using haemolysin gene primer. First, initial primers were designed using V. harveyi VIB 391 haemolysin gene sequence (accession number: DQ640264), flanking the position 133 to 756. This primer pairs were used to identify haemolysin gene in both V. harveyi MR5339 and V. harveyi 275 strain. Sequencing results from each sample showed 99% similarity with haemolysin gene sequence in Genebank. Furthermore, the sequence of V. harveyi MR5339 haemolysin gene was used to design the nested PCR primers. The first primer pairs of nested PCR have successfully amplified the haemolysin gene fragment of all V. harveyi strains samples from position 52 to 405. The second primer pairs of nested PCR have amplified position 204 to 405 where it can detect all of V. harveyi strains used as sample sources in this study. The application of nested PCR technique in this study was able to identify V. harveyi strains at serial dilution of cells density as low as 100 cfu/mL, which is equal to a single cell or at DNA concentration up to 101 fg/µL.
DIVERSITY OF ENDOPHYTIC FUNGI FROM RED GINGER (ZINGIBER OFFICINALE ROSC.) PLANT AND THEIR INHIBITORY EFFECT TO FUSARIUM OXYSPORUM PLANT PATHOGENIC FUNGI GINTING, ROHANI CINTA BADIA; SUKARNO, NAMPIAH; WIDYASTUTI, UTUT; DARUSMAN, LATIFAH KOSIM; KANAYA, SIHEGIKO
HAYATI Journal of Biosciences Vol. 20 No. 3 (2013): September 2013
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (74.046 KB) | DOI: 10.4308/hjb.20.3.127

Abstract

Indonesia has been known as a country with high medicinal plant diversity. One of the most common medicinal plant from Indonesia is red ginger (Zingiber officinale Rosc.). Nevertheless, limited studies of endophytic fungi associated with these medicinal plants are hitherto available. The objectives of this research were to study the diversity of endophytic fungi on red ginger and to analyze their potential as a source of antifungal agent. All parts of plant organs such as leaf, rhizome, root, and stem were subjected for isolation. Fungal identification was carried out by using a combination of morphological characteristic and molecular analysis of DNA sequence generated from ITS rDNA region. Thirty endophytic fungi were successfully isolated from leaf, rhizome, root, and stem of red ginger plant. Antagonistic activity was tested against Fusarium oxysporum, a pathogenic fungus on plants, using an antagonistic assay. Based on this approach, the fungi were assigned as Acremonium macroclavatum, Beltraniella sp., Cochliobolus geniculatus and its anamorphic stage Curvularia affinis, Fusarium solani, Glomerella cingulata, and its anamorphic stage Colletotrichum gloeosporoides, Lecanicillium kalimantanense, Myrothecium verrucaria, Neonectria punicea, Periconia macrospinosa, Rhizopycnis vagum, and Talaromyces assiutensis. R. vagum was found specifically on root whereas C. affinis, L. kalimantanense, and M. verrucaria were found on stem of red ginger plant.  A. macroclavatum was found specifically in red ginger plant?s organ which located under the ground, whereas C. affinis was found from shoot or organ which located above the ground. The antagonistic activity of isolated endophytic fungi against F. oxysporum varied with the inhibition value range from 1.4 to 68.8%. C. affinis (JMbt7), F. solani (JMd14), and G. cingulata (JMr2) had significantly high antagonistic activity with the value above 65%; and R. vagum (JMa4) and C. geniculatus (JMbt9) had significantly low antagonistic activity with the range value 0-10%.