Publications of NIPGR Scientists

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Author: search.filters.author.Sahu, Pranav PankajSubject: search.filters.subject.Gene expression

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    Dynamics of defense related components in two contrasting genotypes to tomato upon infection with tomato leaf curl New Delhi virus
    (Springer, 2012) Sahu, Pranav Pankaj; Rai, Neeraj Kumar; Puranik, Swati; Roy, Anirban; Khan, Moinuddin; Prasad, Manoj
    Tomato leaf curl virus (ToLCV) disease is a serious threat for tomato cultivation in the tropics and subtropics. Despite serious efforts no immune commercial varieties or F(1) hybrids are available till date. In this study, the interaction between Solanum lycopersicum and ToLCV was characterized on molecular and biochemical basis. RNA silencing mediated by short interfering RNA (siRNA) and reactive oxygen species (ROS) has been proposed as central components of plant adaptation to several stresses. A comparative RNA interference study between two contrasting tomato genotypes, LA1777 (tolerant) and 15SBSB (susceptible) infected with Tomato Leaf Curl New Delhi Virus (ToLCNDV) revealed relatively higher accumulation of siRNA in the leaves of tolerant genotype. In LA1777, ToLCNDV produced chlorotic as well as necrotic areas at the inoculation sites 5-10 days post-inoculation. Caspase-9- and caspase-3-like activities were significantly increased in response to ToLCNDV infection in LA1777 at inoculated region. Activities of antioxidant enzymes involved in the detoxification of ROS were examined in both systemic and localized area of infection, and their expression level was further validated through quantitative real-time PCR of the corresponding transcripts. Expression patterns of three genes encoding pathogenesis-related proteins showed higher accumulation in tolerant genotype. Tolerance against the ToLCNDV in LA1777 can be attributed to the higher siRNA accumulation, localized cell death, altered levels of antioxidant enzymes and activation of pathogenesis-related genes at different durations of virus infection. Based on these direct and indirect evidences, we have proposed a putative mechanism for ToLCNDV tolerance in the tolerant genotype.
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    Tomato cultivar tolerant to tomato leaf curl New Delhi Virus infection induces virus-specific siRNA accumulation and defense associated host gene expression
    (Wiley-Blackwell, 2010) Sahu, Pranav Pankaj; Rai, Neeraj K.; Chakraborty, Supriya; Singh, Major; Chandrappa, Prasanna H.; Ramesh, Bandarupalli; Chattopadhyay, Debasis; Prasad, Manoj
    Tomato leaf curl New Delhi virus (ToLCNDV) infection causes significant yield loss in tomato. The availability of a conventional tolerance source against this virus is limited in tomato. To understand the molecular mechanism of virus tolerance in tomato, the abundance of viral genomic replicative intermediate molecules and virus-directed short interfering RNAs (siRNAs) by the host plant in a naturally tolerant cultivar H-88-78-1 and a susceptible cultivar Punjab Chhuhara at different time points after agroinfection was studied. We report that less abundance of viral replicative intermediate in the tolerant cultivar may have a correlation with a relatively higher accumulation of virus-specific siRNAs. To study defence-related host gene expression in response to ToLCNDV infection, the suppression subtractive hybridization technique was used. A library was prepared from tolerant cultivar H-88-78-1 between ToLCNDV-inoculated and Agrobacterium mock-inoculated plants of this cultivar at 21 days post-inoculation (dpi). A total of 106 nonredundant transcripts was identified and classified into 12 different categories according to their putative functions. By reverse Northern analysis and quantitative real-time polymerase chain reaction (qRT-PCR), we identified the differential expression pattern of 106 transcripts, 34 of which were up-regulated (>2.5-fold induction). Of these, eight transcripts showed more than four fold induction. qRT-PCR analysis was carried out to obtain comparative expression profiling of these eight transcripts between Punjab Chhuhara and H-88-78-1 on ToLCNDV infection. The expression patterns of these transcripts showed a significant increase in differential expression in the tolerant cultivar, mostly at 14 and 21 dpi, in comparison with that in the susceptible cultivar, as analysed by qRT-PCR. The probable direct and indirect relationship of siRNA accumulation and up-regulated transcripts with the ToLCNDV tolerance mechanism is discussed.
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    Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress
    (Elsevier B.V., 2010) Lata, Charu; Sahu, Pranav Pankaj; Prasad, Manoj
    hydration stress is one of the most important abiotic stresses that adversely influence crop growth and productivity. With the aim to understand the molecular mechanisms underlying dehydration stress tolerance in foxtail millet (Setaria italica L.), a drought tolerant crop, we examined its transcriptome changes at two time points (early and late) of dehydration stress. Two suppression subtractive hybridization (SSH) forward libraries were constructed from 21-day old seedlings of tolerant cv. Prasad at 0.5 and 6h PEG-induced dehydration stress. A total of 327 unique ESTs were identified from both libraries and were classified into 11 different categories according to their putative functions. The plant response against dehydration stress was complex, representing major transcripts involved in metabolism, stress, signaling, transcription regulation, translation and proteolysis. By Reverse Northern (RN) technique we identified the differential expression pattern of 327 transcripts, 86 (about 26%) of which showed > or = 1.7-fold induction. Further the obtained results were validated by quantitative real-time PCR (qRT-PCR) to have a comparative expression profiling of randomly chosen 9 up-regulated transcripts (> or =2.5 fold induction) between cv. Prasad (tolerant) and cv. Lepakshi (sensitive) upon dehydration stress. These transcripts showed a differential expression pattern in both cultivars at different time points of stress treatment as analyzed by qRT-PCR. The possible relationship of the identified transcripts with dehydration tolerance mechanism is discussed.
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    cDNA-AFLP analysis reveals differential gene expression in response to salt stress in foxtail millet (Setaria italica L.)
    (Springer, 2008) Jayaraman, Ananthi; Puranik, Swati; Rai, Neeraj Kumar; Vidapu, Sudhakar; Sahu, Pranav Pankaj; Lata, Charu; Prasad, Manoj
    Plant growth and productivity are affected by various abiotic stresses such as heat, drought, cold, salinity, etc. The mechanism of salt tolerance is one of the most important subjects in plant science as salt stress decreases worldwide agricultural production. In our present study we used cDNA-AFLP technique to compare gene expression profiles of a salt tolerant and a salt-sensitive cultivar of foxtail millet (Seteria italica) in response to salt stress to identify early responsive differentially expressed transcripts accumulated upon salt stress and validate the obtained result through quantitative real-time PCR (qRT-PCR). The expression profile was compared between a salt tolerant (Prasad) and susceptible variety (Lepakshi) of foxtail millet in both control condition (L0 and P0) and after 1 h (L1 and P1) of salt stress. We identified 90 transcript-derived fragments (TDFs) that are differentially expressed, out of which 86 TDFs were classified on the basis of their either complete presence or absence (qualitative variants) and 4 on differential expression pattern levels (quantitative variants) in the two varieties. Finally, we identified 27 non-redundant differentially expressed cDNAs that are unique to salt tolerant variety which represent different groups of genes involved in metabolism, cellular transport, cell signaling, transcriptional regulation, mRNA splicing, seed development and storage, etc. The expression patterns of seven out of nine such genes showed a significant increase of differential expression in tolerant variety after 1 h of salt stress in comparison to salt-sensitive variety as analyzed by qRT-PCR. The direct and indirect relationship of identified TDFs with salinity tolerance mechanism is discussed.