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APLIKASI TEKNIK MOLEKULER UNTUK ANALISIS GENETIK TOMATO LEAF CURL VIRUS Santoso, Tri Joko
Jurnal Penelitian dan Pengembangan Pertanian Vol 32, No 4 (2013): Desember 2013
Publisher : Pusat Perpustakaan dan Penyebaran Teknologi Pertanian

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Tomato leaf curl virus (ToLCV) merupakan salah satu virus dalamgenus Begomovirus, famili Geminiviridae, yang menyebabkanpenyakit keriting daun pada tomat. Informasi tentang keragamangenetik ToLCV bermanfaat dalam perakitan tanaman tahan. Kemajuandi bidang biologi molekuler telah menghasilkan beberapa teknikyang dapat digunakan untuk analisis genetik Begomovirus. Teknikmolekuler yang banyak diaplikasikan ialah polymerase chainreaction (PCR). Teknik ini sangat sensitif dan spesifik untukmendeteksi Begomovirus pada tingkat DNA. PCR juga dapatdigunakan untuk mengidentifikasi tingkat keragaman genetik virus.Teknik PCR telah digunakan untuk mendeteksi Begomovirus padatomat (ToLCV) dari sentra produksi di Jawa Timur, Jawa Tengah,Jawa Barat, DI Yogyakarta, dan Sumatera. Kombinasi teknik PCRdengan restriction fragment length polymorphism (RFLP) jugadapat digunakan untuk mengidentifikasi keragaman genetik Begomovirus.Selain itu, teknik sekuensing DNA dapat diaplikasikanuntuk mempelajari identitas dan keragaman genetik isolat-isolatToLCV atau anggota Begomovirus lainnya. Analisis sekuen asamamino menunjukkan adanya keragaman genetik dari isolat-isolatToLCV Indonesia. Isolat-isolat tersebut homolog dengan Ageratumyellow vein virus (AYVV). Dengan teknik modifikasi gen (rekayasagenetik) telah berhasil memanfaatkan gen AV1 (coat protein) dariToLCV untuk menghasilkan tanaman tembakau tahan terhadapToLCV. Teknik modifikasi gen memberikan peluang yang besaruntuk mengembangkan tanaman tomat tahan ToLCV dan berperanpenting dalam pembangunan pertanian modern di masa mendatang.

EFEKTIVITAS DAN EFISIENSI TEKNIK ISOLASI DAN PURIFIKASI DNA PADA JAMBU METE ., Syafaruddin; Randriani, Enny; Santoso, Tri Joko
Jurnal Tanaman Industri dan Penyegar Vol 2, No 2 (2011): Buletin Riset Tanaman Rempah Dan Aneka Tanaman Industri
Publisher : Pusat Penelitian dan Pengembangan Perkebunan

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Effectivity and efficiency of DNA isolation and purification technique on cashew plant. Cashew well known as a potential industrial plant to be expanded due to of kernel price and cashew can also be used as conservation plant. As a potential plant, so needed informationmore detail including the molecular information. There are many techniques to conduct DNA isolation depend on kind of plants or plant tissue thatwill be used. The experiment had been conducted at Molecular Biology Laboratory of Indonesian Center for Agricultural Biotec hnology and GeneticResources Research and Development (BB BIOGEN), Bogor on May-July 2011. Young leaf of cashew used as genetic materials which is took fromexperimental station Cikampek, Indonesian Spice and Industrial Crops Research Institute (BALITTRI). While some chemicals were used as the other material. The activities following step: DNA extraction and purification, measurement of DNA concentration and amplification of DNA. Deletion ofresistor enzyme-polysacharide, especially for perennial plant. DNA isolation can be done by breaking down of cell wall, cell membrane and nuclearmembrane. The aim of this experiment was to find the effectivity and efficiency technique of DNA isolation and purification so can be reducing costand time consuming while working in the laboratory. The results shows that conscientiousness of DNA isolation and purification denotes an importantstep to obtain clean and contaminant free of DNA, so banding pattern will be clear. In this technique did not used polypinilpolypirolidone (PVPP)and mercapto-ethanol such as antioxidant, liquid nitrogen, neither over night storage of leaf extraction before used for purification which is often used for perennial plant. In addional, the results shows that band pattern of DNA was very thick and clear, therefore, this techni que can be used for DNA isolation on cashew.

EFEKTIVITAS DAN EFISIENSI TEKNIK ISOLASI DAN PURIFIKASI DNA PADA JAMBU METE ., Syafaruddin; Randriani, Enny; Santoso, Tri Joko
Jurnal Tanaman Industri dan Penyegar Vol 2, No 2 (2011): Buletin Riset Tanaman Rempah Dan Aneka Tanaman Industri
Publisher : Pusat Penelitian dan Pengembangan Perkebunan

Show Abstract | Download Original | Original Source | Check in Google Scholar

Effectivity and efficiency of DNA isolation and purification technique on cashew plant. Cashew well known as a potential industrial plant to be expanded due to of kernel price and cashew can also be used as conservation plant. As a potential plant, so needed informationmore detail including the molecular information. There are many techniques to conduct DNA isolation depend on kind of plants or plant tissue thatwill be used. The experiment had been conducted at Molecular Biology Laboratory of Indonesian Center for Agricultural Biotec hnology and GeneticResources Research and Development (BB BIOGEN), Bogor on May-July 2011. Young leaf of cashew used as genetic materials which is took fromexperimental station Cikampek, Indonesian Spice and Industrial Crops Research Institute (BALITTRI). While some chemicals were used as the other material. The activities following step: DNA extraction and purification, measurement of DNA concentration and amplification of DNA. Deletion ofresistor enzyme-polysacharide, especially for perennial plant. DNA isolation can be done by breaking down of cell wall, cell membrane and nuclearmembrane. The aim of this experiment was to find the effectivity and efficiency technique of DNA isolation and purification so can be reducing costand time consuming while working in the laboratory. The results shows that conscientiousness of DNA isolation and purification denotes an importantstep to obtain clean and contaminant free of DNA, so banding pattern will be clear. In this technique did not used polypinilpolypirolidone (PVPP)and mercapto-ethanol such as antioxidant, liquid nitrogen, neither over night storage of leaf extraction before used for purification which is often used for perennial plant. In addional, the results shows that band pattern of DNA was very thick and clear, therefore, this techni que can be used for DNA isolation on cashew.

Pengembangan Identitas Spesifik Berbasis Marka SSR pada 29 Varietas Kedelai Lokal Indonesia Lestari, Puji; Risliawati, Andari; Utami, Dwinita Wikan; Hidayatun, Nurul; Santoso, Tri Joko; Chaerani, Chaerani
JURNAL BIOLOGI INDONESIA Vol 12, No 2 (2016): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

ABSTRACTSoybean is an important legume crop in Indonesia and local varieties from different regions are diversed. Accurate identification of local varieties is needed to determine the genetic identity in order to protect them to indicate the geographical origin and registration purpose. This study aimed to analyze DNA fingerprints of local varieties of soybean in Indonesia to develop a specific identity using SSR markers along with the marker set. A total of 29 local varieties/accessions was analyzed using 9 selected SSR markers with semi automated genetic analyzer on the basis of capillary electrophoresis. Total markers successfully detected 50 alleles in all varieties, with the average polymorphism information content (PIC) of each locus (0.579) and the genetic diversity index (0.629) were quite high as a reflection of diversity of the local varieties. Based on the analysis of the genetic diversity index, PIC, rare alleles, dominant allele frequency, analysis of genetic distance, 6 SSRs (Satt009, Satt038, Satt177, Satt242, Satt308 and Satt114) were selected as a set of markers for variety identification. Although three varieties can not be distinguished because of their close genetic relationship, but the digital coding indicates that local varieties of soybeans have possessed specific identities (ID) representing variation of SSR alleles. The selected SSR loci with additional identifier can be used to develop ID of Indonesian local soybean in the germplasm collection. Overall, the marker set is a powerful tool to complement morphological markers for the protection of local soybean varieties that contribute in accelerating local varieties improvement in the future agriculture.Keywords: specific identity, SSR, Indonesian local soybean variety, DNA fingerprint.

RESPON PADI TRANSGENIK CV. NIPPONBARE GENERASI T1 YANG MENGANDUNG GEN Oryza sativa DEHYDRATION-RESPONSE ELEMENT BINDING 1A (OsDREB1A) TERHADAP CEKAMAN SALINITAS [Response of T1 Generation Transgenic Rice cv. Nipponbare Containing an Oryza sativa Dehydration-response Element Binding 1A (OsDREB1A) Gene to Salinity Stress] Santoso, Tri Joko; Apriana, Aniversari; Sisharmini, Atmitri; Trijatmiko, Kurniawan Rudi
BERITA BIOLOGI Vol 11, No 2 (2012)
Publisher : Research Center for Biology-Indonesian Institute of Sciences

Salinity is one of the abiotic constraints in the cultivation of rice crop. One of the reasons agricultural land becomes saline is due to the intrusion of seawater into the mainland as a result of global climate change. Dehydration-responsive element binding (DREB) gene is a plant -specific transcription factor gene that have important role in regulating plant responses to abiotic stresses, including high salinity. Transgenic rice plants cv. Nipponbare carrying OsDREB1A gene have been generated. However, study of the response of putative transgenic plants to salinity has not been done. The research objective is to study the response of T1 generation Nipponbare-OsDREB1A transgenic rice plants to salinity stress. The result showed that the response of putative transgenic rice Nipponbare-OsDREB1A to salinity stress 25 mM and 150 mM NaCl indicated a level of tolerance varies from highly sensitive to highly tolerance. These variations were possibly occurred because of the segregation state of the T1 generation transgenic rice. Based on damage symptom scoring and PCR analysis provided information that transgenic rice plant cv. Nipponbare-OsDREB1A which showed positive PCR had a very high tolerance to salinity stress 150 mM compared with non-transgenic rice cv. Nipponbare.

Phenotypic Screening of Ds transposon and Activation-tag Insertional Mutant Rice Population for Drought and Salinity Tolerant Related Traits Nugroho, Satya; Zannati, Anky; Situmorang, Apriadi; Windiastri, Vincentia Esti; Widyajayantie, Dwi; Pantouw, Carla F.; Astuti, Dwi; Indrayani, Sri; Rahmawati, Syamsidah; Mulyaningsih, Enung Sri; Santoso, Tri Joko; Trijatmiko, Kurniawan Rudi
ANNALES BOGORIENSES Vol 15, No 1 (2011): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.1234/56

The studies of rice genes through functional genomics are greatly facilitated by the availability of the complete genome sequences, including the complete physical map of the japonica rice cv. nipponbare. Using the Ac and Ds transposon, that are capable of transposition in various heterologous plants including the monocotyledon rice, Â combined with the enhancer element for generating activation taged lines, it is possible to discover and isolate functional genes involved in various important agronomical traits; such as those involved in abiotic stress tolerance (drought, high salt) and biotic stresses diseases and pests. We have developed 1,785 first (T0) generation of mutant nipponbare rice by transposons Ac/Ds insertions containing activation-tag, generated by transformation using Agrobacterium-mediated method. Currently, we have generated approximately 1,000 stable lines with transposon Ds and activation-tag insertion ready for screening. Efficient screening methods for mutant Nipponbare rice lines have been established for agronomically important mutant traits. Among the new phenotypes related to important agronomical traits observed were drought and salt tolerant or sensitive, stunted and robust growth, variable root penetration and other interesting traits such as reduced tillering, rolled leaf and thin tiller. Â Â Keywords: rice, insertion mutant, gene discovery, drought, salinity

PENGEMBANGAN IDENTITAS SPESIFIK BERBASIS MARKA SSR PADA 29 VARIETAS KEDELAI LOKAL INDONESIA Lestari, Puji; Risliawati, Andari; Utami, Dwinita Wikan; Hidayatun, Nurul; Santoso, Tri Joko; Chaerani, Chaerani
JURNAL BIOLOGI INDONESIA Vol 12, No 2 (2016): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v12i2.2888

ABSTRACTSoybean is an important legume crop in Indonesia and local varieties from different regions are diversed. Accurate identification of local varieties is needed to determine the genetic identity in order to protect them to indicate the geographical origin and registration purpose. This study aimed to analyze DNA fingerprints of local varieties of soybean in Indonesia to develop a specific identity using SSR markers along with the marker set. A total of 29 local varieties/accessions was analyzed using 9 selected SSR markers with semi automated genetic analyzer on the basis of capillary electrophoresis. Total markers successfully detected 50 alleles in all varieties, with the average polymorphism information content (PIC) of each locus (0.579) and the genetic diversity index (0.629) were quite high as a reflection of diversity of the local varieties. Based on the analysis of the genetic diversity index, PIC, rare alleles, dominant allele frequency, analysis of genetic distance, 6 SSRs (Satt009, Satt038, Satt177, Satt242, Satt308 and Satt114) were selected as a set of markers for variety identification. Although three varieties can not be distinguished because of their close genetic relationship, but the digital coding indicates that local varieties of soybeans have possessed specific identities (ID) representing variation of SSR alleles. The selected SSR loci with additional identifier can be used to develop ID of Indonesian local soybean in the germplasm collection. Overall, the marker set is a powerful tool to complement morphological markers for the protection of local soybean varieties that contribute in accelerating local varieties improvement in the future agriculture.Keywords: specific identity, SSR, Indonesian local soybean variety, DNA fingerprint.

Screening and Integration Analysis of OsDREB1A BC4F2 and BC5F1 Generations of Transgenic Ciherang Rice (Oryza sativa L.) for High-Salinity Tolerance Priyono, Dika Migi; Santoso, Tri Joko; Salamah, Andi
Makara Journal of Science Vol. 17, No. 2
Publisher : UI Scholars Hub

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Salinity is one of a number of abiotic stresses that threaten rice production in Indonesia. To support food security programs, BB-Biogen has developed rice lines derived from OsDREB1A transformed Ciherang up to BC4F2 and BC5F1 generations. To verify the salinity tolerance and the stability of transgene integration, the BC4F2 and BC5F1 generations of Ciherang-OsDREB1A transgenic were screened to select high-salinity tolerant lines. Second, molecular analysis using the primers hptII-F/hptII-R and 35S-496-F/OsDREB1A-R was conducted to identify the existence and the stability of the transgene integration in the BC4F2 and BC5F1 generations. Screening 543 BC4F2 and BC5F1 Ciherang-OsDREB1A transgenic lines in a nutrient solution with a final electrical conductivity (EC) of approximately 18 mS/cm for 26 days yielded 134 putative transgenic plants. Integration analysis using the hptII-F/hptII-R primers showed that 73 of the 134 putative transgenic plants had positive PCR products, indicating the presence of the transgene in those plants. All the 73 plants also produced PCR products when tested with the specific primer 35S-496- F/OsDREB1A-R, indicating that transgene integration was maintained during the development of BC4F2 and BC5F1.

Morphological and Molecular Analysis and Flowering Time of T2 Generation Transgenic Rice cv. Nipponbare Carrying CONSTANS (CO) Gene Irshanty, Firdha Meidi; Salamah, Andi; Santoso, Tri Joko
Makara Journal of Science Vol. 8, No. 1
Publisher : UI Scholars Hub

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Flowering is an important process that initiates plant productivity. Rice (Oryza sativa cv. Nipponbare) was genetically engineered by introducing a CONSTANS (CO) gene from Arabidopsis thaliana (AtCO) to improve rice productivity. The CO gene is a gene responsible for inducing early flowering. The aims of the experiment were to use morphological and molecular analysis to study the integration of the AtCO gene and its influence on agronomic traits in the T2 generation of Nipponbare transgenic AtCO rice. Morphological observations showed that agronomic traits tended to be better in the transgenic plants than in the wild type (controls), although the transgenic plants flowered later than the wild type. Polymerase Chain Reaction (PCR) analysis showed that 169 out of 227 transgenic rice plants showed hpt and CO gene integration.

Morphological and Molecular Analysis and Flowering Time of T2 Generation Transgenic Rice cv. Nipponbare Carrying CONSTANS (CO) Gene Irshanty, Firdha Meidi; Salamah, Andi; Santoso, Tri Joko
Makara Journal of Science Vol. 18, No. 1
Publisher : UI Scholars Hub

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Flowering is an important process that initiates plant productivity. Rice (Oryza sativa cv. Nipponbare) was genetically engineered by introducing a CONSTANS (CO) gene from Arabidopsis thaliana (AtCO) to improve rice productivity. The CO gene is a gene responsible for inducing early flowering. The aims of the experiment were to use morphological and molecular analysis to study the integration of the AtCO gene and its influence on agronomic traits in the T2 generation of Nipponbare transgenic AtCO rice. Morphological observations showed that agronomic traits tended to be better in the transgenic plants than in the wild type (controls), although the transgenic plants flowered later than the wild type. Polymerase Chain Reaction (PCR) analysis showed that 169 out of 227 transgenic rice plants showed hpt and CO gene integration.

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