Academic literature on the topic 'Analisi cDNA-AFLP'

AbstractLeaf fall disease caused by Corynespora cassiicola fungi is one of the most important diseases in rubber plant. Rubber clone AVROS 2037 is considered resistant to this pathogen while clone PPN 2444 is susceptible. These two rubberclones were used to identify genes or transcripts differentially expressed during interaction between rubber plants and the fungi, using cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) method. Induced genes/transcripts expression was examined to compare differencies between plants uninfected and infected with C. cassiicola at 24, 36, 48 and 72 hours after inoculation. cDNA-AFLP analysis was performed using restriction enzyme VspI and TaqI so the adapters and primers also have the recognition site of these enzymes. By using 29 specific primers, 35 out of approximately 1450 fragments were differentially expressed between AVROS and PPN 2444 clones. All of these fragments were cloned and sequenced. The homology-based grouping of these sequences resulted in 19 contigs and nine individual sequences. Among these, 10 contigs and five sequences have significant sequence homology with known genes in gene bank data base, such as Ran binding protein, protein transporter and transcriptional regulators of some organisms; arginase, GTP-binding protein, heat shock protein (HSP) and aconitase. Ran binding protein, GTPbinding protein and protein transporter were known as membrane proteins while arginase and HSP usually expressed as a response to wounding or toxin treatment. The present of arginase is usually related to the availability of nitric oxide (NO) in plant tissue. NO is well known as a signal molecule on plant defense response. AbstrakPenyakit gugur daun yang disebabkan oleh fungi Corynespora cassiicola merupakan salah satu penyakit penting tanaman karet. Klon karet AVROS 2037menunjukkan sifat resisten terhadap patogen tersebut sedangkan klon PPN 2444 merupakan klon yang rentan. Kedua klon karet tersebut digunakan untuk mengidentifikasi gen atau transkrip yang diekspresikan secara diferensial selama terjadi interaksi antara tanaman karet dengan C. cassiicola menggunakan teknik cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP). Ekspresi gen/transkrip dipelajari untuk membandingkan perbedaan antara tanaman yang tidak diinfeksi dengan yang diinfeksi patogen pada waktu 24, 36, 48 dan 72 jam setelah inokulasi. Analisis cDNA-AFLP dilaksanakan dengan menggunakan pasangan enzim restriksi VspI dan TaqI sehingga adapter dan primer memiliki sekuen pengenalan kedua enzim restriksi tersebut. Dengan menggunakan 29 pasang primer spesifik, sebanyak 35 dari sekitar 1450 fragmen memiliki ekspresi berbeda antara klon AVROS 2037 dan PPN 2444. Semua fragmen yang berbeda tersebut kemudian diklon pada vektor kloning dan disekuen. Hasil sekuensing dikelompokkan berdasarkan homologi sekuennya dan menghasilkan 19 contigs serta sembilan macam sekuen yang tidak mengelompok. Sebanyak 10 dari 19 contigs dan lima dari sembilan sekuen tersebut memiliki homologi dengan produk gen yang telah dikenal yang terdapat di pangkalan data GenBank, seperti putative Ran binding protein, protein transporter, regulator transkripsi, arginase, GTP-binding protein, heat shock protein (HSP) dan aconitase. Beberapa di antaranya seperti putative Ran binding protein, protein transporter dan GTP-binding protein dikenal sebagai protein membran, sedangkan arginase dan HSP merupakan protein atau enzim yang ekspresinya pada tanaman antara lain dipengaruhi oleh adanya pelukaan dan perlakuan toksin. Keberadaan arginase sering berhubungan dengan ketersediaan nitric oxide (NO) pada jaringan tanaman. NO dikenal sebagai salah satu sinyal molekul dalam mekanisme pertahanan tanaman.

AbstractLeaf fall disease caused by Corynespora cassiicola fungi is one of the most important diseases in rubber plant. Rubber clone AVROS 2037 is considered resistant to this pathogen while clone PPN 2444 is susceptible. These two rubberclones were used to identify genes or transcripts differentially expressed during interaction between rubber plants and the fungi, using cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) method. Induced genes/transcripts expression was examined to compare differencies between plants uninfected and infected with C. cassiicola at 24, 36, 48 and 72 hours after inoculation. cDNA-AFLP analysis was performed using restriction enzyme VspI and TaqI so the adapters and primers also have the recognition site of these enzymes. By using 29 specific primers, 35 out of approximately 1450 fragments were differentially expressed between AVROS and PPN 2444 clones. All of these fragments were cloned and sequenced. The homology-based grouping of these sequences resulted in 19 contigs and nine individual sequences. Among these, 10 contigs and five sequences have significant sequence homology with known genes in gene bank data base, such as Ran binding protein, protein transporter and transcriptional regulators of some organisms; arginase, GTP-binding protein, heat shock protein (HSP) and aconitase. Ran binding protein, GTPbinding protein and protein transporter were known as membrane proteins while arginase and HSP usually expressed as a response to wounding or toxin treatment. The present of arginase is usually related to the availability of nitric oxide (NO) in plant tissue. NO is well known as a signal molecule on plant defense response. AbstrakPenyakit gugur daun yang disebabkan oleh fungi Corynespora cassiicola merupakan salah satu penyakit penting tanaman karet. Klon karet AVROS 2037menunjukkan sifat resisten terhadap patogen tersebut sedangkan klon PPN 2444 merupakan klon yang rentan. Kedua klon karet tersebut digunakan untuk mengidentifikasi gen atau transkrip yang diekspresikan secara diferensial selama terjadi interaksi antara tanaman karet dengan C. cassiicola menggunakan teknik cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP). Ekspresi gen/transkrip dipelajari untuk membandingkan perbedaan antara tanaman yang tidak diinfeksi dengan yang diinfeksi patogen pada waktu 24, 36, 48 dan 72 jam setelah inokulasi. Analisis cDNA-AFLP dilaksanakan dengan menggunakan pasangan enzim restriksi VspI dan TaqI sehingga adapter dan primer memiliki sekuen pengenalan kedua enzim restriksi tersebut. Dengan menggunakan 29 pasang primer spesifik, sebanyak 35 dari sekitar 1450 fragmen memiliki ekspresi berbeda antara klon AVROS 2037 dan PPN 2444. Semua fragmen yang berbeda tersebut kemudian diklon pada vektor kloning dan disekuen. Hasil sekuensing dikelompokkan berdasarkan homologi sekuennya dan menghasilkan 19 contigs serta sembilan macam sekuen yang tidak mengelompok. Sebanyak 10 dari 19 contigs dan lima dari sembilan sekuen tersebut memiliki homologi dengan produk gen yang telah dikenal yang terdapat di pangkalan data GenBank, seperti putative Ran binding protein, protein transporter, regulator transkripsi, arginase, GTP-binding protein, heat shock protein (HSP) dan aconitase. Beberapa di antaranya seperti putative Ran binding protein, protein transporter dan GTP-binding protein dikenal sebagai protein membran, sedangkan arginase dan HSP merupakan protein atau enzim yang ekspresinya pada tanaman antara lain dipengaruhi oleh adanya pelukaan dan perlakuan toksin. Keberadaan arginase sering berhubungan dengan ketersediaan nitric oxide (NO) pada jaringan tanaman. NO dikenal sebagai salah satu sinyal molekul dalam mekanisme pertahanan tanaman.

Downy mildew, caused by the oomycete Plasmopara viticola (B. et C.) Berl. et De Toni, is a common disease of grapevine. Although the exact mechanisms by which grapevine cells regulate the disease incidence upon P. viticola infection have largely lain undiscovered until now, it is known that a hypersensitive response (HR) occurs in American Vitis species. The HR to P. viticola was also associated with metabolic and transcriptional events, such as deposition of lignin and other phenolics, accumulation of stilbene phytoalexins, and activation of genes encoding for pathogenesis related proteins (Jeandet et al., 2002, Pezet et al., 2004, Kortekamp, 2006). Aim of this project was to test a possible correlation between the variability in the resistance to the fungus, in the stilbene content and in the gene expression by a targeted metabolite and transcriptional profiling of selected individuals of a population from Merzling (V. vinifera x V. rupestris x V. lincecumii) x V. vinifera ‘Teroldego’. The phenotypic characterization of the response to the fungus within the population allowed us to classify the individuals in classes from total resistance to total susceptibility. The HPLC-DAD-MS analysis performed on infected leaves collected at 6 days post infection (dpi) with the pathogen lead to three main results: it confirmed the stilbene accumulation upon P. viticola infection, it selected a 17% of individuals accumulating the five major viniferins in grapevine and it pointed our attention to the presence of a few oligostilbenes and stilbenoids still undiscovered, whose characterization was performed in the same project. The comparative transcriptional analysis was conducted on resistant and susceptible individuals by a combined approach of i) cDNA-Amplification Fragment Length Polymorphism (AFLP) and ii) oligo-array techniques. The first analysis lead to the isolation of more than 300 transcripts specifically modulated in a totally resistant offspring with respect to Merzling parental and to the discovery that these transcripts can be clustered in two groups according to their kinetics of activation. The “early modulated” were differentially expressed during the first 12 hours post infection, the “late modulated” were differentially expressed starting from 48 hpi. The second analysis allowed further investigation of these genes picking which ones were specific or common between resistant and susceptible individuals.

Exposure to higher than optimal temperatures - heat-stress (HS) - is becoming increasingly common to all crop plants worldwide. Heat stress coinciding with microgametogenesis, especially during the post-meiotic phase that is marked by starch biosynthesis, is often associated with starch-deficient pollen and male sterility and ultimately, greatly reduced crop yields. The molecular basis for the high sensitivity of developing pollen grains, on one hand, and factors involved in pollen heat-tolerance, on the other, is poorly understood. The long-term goal of this project is to provide a better understanding of the genes that control pollen quality under heat-stress conditions. The specific objectives of this project were: (1) Determination of the threshold heat stress temperature(s) that affects tomato and sorghum pollen quality whether: a) Chronic mild heat stress conditions (CMHS), or b) Acute heat stress (AHS). (2) Isolation of heat-responsive, microgametogenesis-specific sequences. During our one-year feasibility project, we have accomplished the proposed objectives as follows: Objectrive 1: We have determined the threshold HS conditions in tomato and sorghum. This was essential for achieving the 2nd objective, since our accumulated experience (both Israeli and US labs) indicate that when temperature is raised too high above "threshold HS levels" it may cause massive death of the developing pollen grains. Above-threshold conditions have additional major disadvantages including the "noise" caused by induced expression of genes involved in cell death and masking of the differences between heatsensitive and heat-tolerant pollen grains. Two different types of HS conditions were determined: a) Season-long CMHS conditions: 32/26°C day/night temperatures confirmed in tomato and 36/26°C day maximum/night minimum temperatures in sorghum. b) Short-term AHS: In tomato, 2 hour exposure to 42-45°C (at 7 to 3 days before anthesis) followed by transfer to 28/22±2oC day/night temperatures until flower opening and pollen maturation, caused 50% reduced germinating pollen in the heat-sensitive 3017 cv.. In sorghum, 36/26°C day/night temperatures 10 to 5 days prior to panicle emergence, occurring at 35 days after sowing (DAS) in cv. DeKalb28E, produced starch-deficient and sterile pollen. Objective 2: We have established protocols for the high throughput transcriptomic approach, cDNA-AFLP, for identifying and isolating genes exhibiting differential expression in developing microspores exposed to either ambient or HS conditions and created a databank of HS-responsivemicrogametogenesis-expressed genes. A subset of differentially displayed Transcript-Derived Fragments (TDFs) that were cloned and sequenced (35 & 23 TDFs in tomato and sorghum, respectively) show close sequence similarities with metabolic genes, genes involved in regulation of carbohydrate metabolism, genes implicated in thermotolerance (heat shock proteins), genes involved in long chain fatty acids elongation, genes involved in proteolysis, in oxidation-reduction, vesicle-mediated transport, cell division and transcription factors. T-DNA-tagged Arabidopsis mutants for part of these genes were obtained to be used for their functional analysis. These studies are planned for a continuation project. Following functional analyses of these genes under HS – a valuable resource of genes, engaged in the HS-response of developing pollen grains, that could be modulated for the improvement of pollen quality under HS in both dicots and monocots and/or used to look for natural variability of such genes for selecting heat-tolerant germplasm - is expected.