Papers by Viswanathan Chinnusamy
Plant Signaling & Behavior, 2015
Steroidogenic acute regulatory related transfer (StART) proteins that are involved in transport o... more Steroidogenic acute regulatory related transfer (StART) proteins that are involved in transport of lipid molecules, play a myriad of functions in insects, mammals and plants. These proteins consist of a modular START domain of approximately 200 amino acids which binds and transfers the lipids. In the present study we have performed a genome-wide search for all START domain proteins in chickpea. The search identified 36 chickpea genes belonging to the START domain family. Through a phylogenetic tree reconstructed with Arabidopsis, rice, chickpea, and soybean START proteins, we were able to identify four transmembrane START proteins in chickpea. These four proteins are homologous to the highly conserved mammalian phosphatidylcholine transfer proteins. The multiple sequence alignment of all the transmembrane containing START proteins from Arabidopsis, rice, chickpea, and soybean revealed that the amino acid residues to which phosphatidylcholine binds in mammals, is also conserved in all these plant species, implying an important functional role and a very similar mode of actionof all these proteins across dicots and monocots. This study characterises a few of the not so well studied transmembrane START superfamily genes that may be involved in stress signalling.The expression analysis in various tissues showed that these genes are predominantly expressed in flowers and roots of chickpea. Three of the chickpea TM START genes showed induced expression in response to drought, salt, wound and heat stress, suggesting their role in stress respopnse.
OMICS: A Journal of Integrative Biology, 2015
Wheat is a staple food worldwide and provides 40% of the calories in the diet. Climate change and... more Wheat is a staple food worldwide and provides 40% of the calories in the diet. Climate change and global warming pose a threat to wheat production, however, and demand a deeper understanding of how heat stress might impact wheat production and wheat biology. However, it is difficult to identify novel heat stress associated genes when the genomic information is not available. Wheat has a very large and complex genome that is about 37 times the size of the rice genome. The present study sequenced the whole transcriptome of the wheat cv. HD2329 at the flowering stage, under control (22° ± 3°C) and heat stress (42°C, 2 h) conditions using Illumina HiSeq and Roche GS-FLX 454 platforms. We assembled more than 26.3 and 25.6 million high-quality reads from the control and HS-treated tissues transcriptome sequences respectively. About 76,556 (control) and 54,033 (HS-treated) contigs were assembled and annotated de novo using different assemblers and a total of 21,529 unigenes were obtained. Gene expression profile showed significant differential expression of 1525 transcripts under heat stress, of which 27 transcripts showed very high (>10) fold upregulation. Cellular processes such as metabolic processes, protein phosphorylation, oxidations-reductions, among others were highly influenced by heat stress. In summary, these observations significantly enrich the transcript dataset of wheat available on public domain and show a de novo approach to discover the heat-responsive transcripts of wheat, which can accelerate the progress of wheat stress-genomics as well as the course of wheat breeding programs in the era of climate change.
Jenks/Plant Abiotic Stress, 2013
Frontiers in Plant Science, 2015
MYB transcription factor (TF) is one of the largest TF families and regulates defense responses t... more MYB transcription factor (TF) is one of the largest TF families and regulates defense responses to various stresses, hormone signaling as well as many metabolic and developmental processes in plants. Understanding these regulatory hierarchies of gene expression networks in response to developmental and environmental cues is a major challenge due to the complex interactions between the genetic elements. Correlation analyses are useful to unravel co-regulated gene pairs governing biological process as well as identification of new candidate hub genes in response to these complex processes. High throughput expression profiling data are highly useful for construction of co-expression networks. In the present study, we utilized transcriptome data for comprehensive regulatory network studies of MYB TFs by "top-down" and "guide-gene" approaches. More than 50% of OsMYBs were strongly correlated under 50 experimental conditions with 51 hub genes via "top-down" approach. Further, clusters were identified using Markov Clustering (MCL). To maximize the clustering performance, parameter evaluation of the MCL inflation score (I) was performed in terms of enriched GO categories by measuring F-score. Comparison of co-expressed cluster and clads analyzed from phylogenetic analysis signifies their evolutionarily conserved co-regulatory role. We utilized compendium of known interaction and biological role with Gene Ontology enrichment analysis to hypothesize function of coexpressed OsMYBs. In the other part, the transcriptional regulatory network analysis by "guide-gene" approach revealed 40 putative targets of 26 OsMYB TF hubs with high correlation value utilizing 815 microarray data. The putative targets with MYB-binding cis-elements enrichment in their promoter region, functional co-occurrence as well as nuclear localization supports our finding. Specially, enrichment of MYB binding regions involved in drought-inducibility implying their regulatory role in drought response in rice. Thus, the co-regulatory network analysis facilitated the identification of complex OsMYB regulatory networks, and candidate target regulon genes of selected guide MYB genes. The results contribute to the candidate gene screening, and experimentally testable hypotheses for potential regulatory MYB TFs, and their targets under stress conditions.
Current science
Thermotolerance is required in crop plants in order to maintain productivity under heat stress. A... more Thermotolerance is required in crop plants in order to maintain productivity under heat stress. At the cellular level, thermotolerance is linked with the induction of heat shock proteins (HSPs), a response conserved from prokaryotes to eukaryotes. HSPs belong to six families and each family has several members, of which only a few may be involved in acquired thermotolerance. Molecular approaches may help to assign specific role to HSPs involved in thermotolerance. Thermotolerant genotypes show adaptations at various levels of organization besides showing qualitative and quantitative differences in HSPs as compared to the thermosensitive genotypes. In future, HSPs and enzymes with broader thermal kinetic windows may be the desired selection criteria at molecular level for breeding thermotolerant crop plants.
Unrevealing the molecular details of plant response and defense against abiotic stress factors su... more Unrevealing the molecular details of plant response and defense against abiotic stress factors such as drought, salt and temperature extremes is a crucial and challenging issue in plant research. Functional genomics and computational biology enhance pace of molecular dissection of abiotic stress response mechanisms. During the past two decades several QTLs associated with abiotic stress responses of plants have been mapped. A QTL is a chromosomal region that contains a gene or genes that influence a quantitative trait. QTL mapping approach is applied frequently to map chromosomal regions that contribute significantly to a complex trait. The availability of complete genome sequence of important model plants namely Arabidopsis and rice, QTL databases and mapping tools facilitate genomics-based strategies for gene discovery, coupled with high-throughput techniques speed-up gene discovery for abiotic stress tolerance.
: Leaf area index (LAI) of vegetation influences radiation interception, latent and sensible heat... more : Leaf area index (LAI) of vegetation influences radiation interception, latent and sensible heat fluxes, and CO2 exchange between terrestrial ecosystems and atmosphere. LAI is used as a key input parameter in many crop growth simulation and radiative transfer models. Conventional LAI measurements are usually time-consuming, and is taken at few representative sample sites only.Alternately, non invasiveestimation of LAIfrom digital image can be an inexpensive and reliable and faster option.The present study attempts to develop an approach for estimation of LAI using top-of canopy digital colour photography over wheat canopy. Different colour based vegetation indices such as Excess Green (ExG), Excess Red (ExR),Normalized Difference(NDI) and Excess Green minus Excess Red (ExG-ExR) Indices were developed from digital images. A histogram-based threshold technique was used to separate green vegetation tissues from background soil in order to derive the canopy vertical gap fraction. The i...
Frontiers in Plant Science, 2015
Small non-coding RNAs (sRNAs) namely microRNAs (miRNAs) and trans-acting small interfering RNAs (... more Small non-coding RNAs (sRNAs) namely microRNAs (miRNAs) and trans-acting small interfering RNAs (tasi-RNAs) play a crucial role in post-transcriptional regulation of gene expression and thus the control plant development and stress responses. In order to identify drought-responsive miRNAs and tasi-RNAs in sorghum, we constructed small RNA libraries from a drought tolerant (M35-1) and susceptible (C43) sorghum genotypes grown under control and drought stress conditions, and sequenced by Illumina Genome Analyzer IIx. Ninety seven conserved and 526 novel miRNAs representing 472 unique miRNA families were identified from sorghum. Ninety-six unique miRNAs were found to be regulated by drought stress, of which 32 were up-and 49 were down-regulated (fold change ≥ 2 or ≤ −2) at least in one genotype, while the remaining 15 miRNAs showed contrasting drought-regulated expression pattern between genotypes. A maximum of 17 and 18 miRNAs was differentially regulated under drought stress condition in the sensitive and tolerant genotypes, respectively. These results suggest that genotype dependent stress responsive regulation of miRNAs may contribute, at least in part, to the differential drought tolerance of sorghum genotypes. We also identified two miR390-directed TAS3 gene homologs and the auxin response factors as tasi-RNA targets. We predicted more than 1300 unique target genes for the novel and conserved miRNAs. These target genes were predicted to be involved in different cellular, metabolic, response to stimulus, biological regulation, and developmental processes. Genome-wide identification of stress-responsive miRNAs, tasi-RNAs and their targets identified in this study will be useful in unraveling the molecular mechanisms underlying drought stress responses and genetic improvement of biomass production and stress tolerance in sorghum.
Plant Molecular Biology Reporter
Carotenoid metabolism is regulated by several genes encoding carotenoid biosynthetic pathway enzy... more Carotenoid metabolism is regulated by several genes encoding carotenoid biosynthetic pathway enzymes. In the present study, a fruit transcriptome in tomato (Solanum lycopersicum) was compared between high lycopene accumulating genotype EC-521086 and low lycopene accumulating genotype VRT-32-1 at three different stages (green, breaker and red) of fruit ripening. This analysis led to the identification of 2,558 differentially expressed genes at three stages of fruit ripening. Among these genes, 123 were carotenoid-correlated genes. Quantitative RT-PCR analysis revealed high expression of genes encoding enzymes involved in lycopene biosynthesis like IPP isomerase, phytoene synthase, phytoene desaturase, z-carotene desaturase; and comparatively lower expression of genes encoding enzymes involved in lycopene catabolism like lycopene cyclase, carotenoid e-ring hydroxylase, zeaxanthin epoxidase, violaxanthin de-epoxidase and neoxanthin synthase in EC-521086, thereby possibly explaining the...
The objective of this study was to examine the role of ethylene, aerenchyma formation and express... more The objective of this study was to examine the role of ethylene, aerenchyma formation and expression of xyloglucan endotransglycosylase (XET) in the waterlogging tolerance of contrasting mung bean (Vigna radiata) genotypes viz., T 44 (tolerant) and Pusa Baisakhi (susceptible), and a highly tolerant wild Vigna species Vigna luteola under pot-culture condition. Waterlogging resulted in decrease in relative water content (RWC) and chlorophyll (Chl) content in leaves, and membrane stability index (MSI) in root and leaf tissues. Waterlogging induced decline in RWC, MSI, and Chl was greater in Pusa Baisakhi (PB) than V. luteola and T 44. Ethylene production in the roots increased in all the genotypes, however, the concentration was higher in V. luteola and T 44 than Pusa Baisakhi. Though the waterlogging induced XET expression in the roots was observed in case of V. luteola and T 44, aerenchyma formation was observed only in the roots of V. luteola. PCR band products were cloned and seque...
Plant Breeding Reviews: Volume 38, 2014
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Papers by Viswanathan Chinnusamy