Publications of NIPGR Scientists
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Item Reference gene identification for gene expression analysis in rice under different metal stress(Elsevier B.V., 2021) Soni, Praveen; Shivhare, Radha; Kaur, Amandeep; Bansal, Sakshi; Sonah, Humira; Deshmukh, Rupesh; Giri, Jitender; Lata, Charu; Ram, HasthiReal-time quantitative polymerase chain reaction (RT-qPCR) is the most common approach to quantify changes in gene expression. Appropriate internal reference genes are essential for normalization of data of RT-qPCR. In the present study, we identified suitable reference genes for gene expression analysis in rice seedlings subjected to different heavy metal stresses such as deficiencies of iron and zinc and toxicities of cobalt, cadmium and nickel. First, from publically available RNA-Seq data we identified 10 candidate genes having stable expression. We also included commonly used house-keeping gene OsUBQ5 (Ubiquitin 5) in our analysis. Expression stability of all the 11 genes was determined by two independent tools, NormFinder and geNorm. Our results show that selected candidate reference genes have higher stability in their expression compared to that of OsUBQ5. Genes with locus ID LOC_Os03g16690, encoding an oxysterol-binding protein (OsOBP) and LOC_Os01g56580, encoding Casein Kinase_1a.3 (OsCK1a.3) were identified to be the most stably expressed reference genes under most of the conditions tested. Finally, the study reveals that it is better to use a specific reference gene for a specific heavy metal stress condition rather than using a common reference gene for multiple heavy metal stress conditions. The reference genes identified here would be very useful for gene expression studies under heavy metal stresses in rice.Item Genome-wide investigation of GRAM-domain containing genes in rice reveals their role in plant-rhizobacteria interactions and abiotic stress responses(Elsevier B.V., 2020) Tiwari, Shalini; Shweta; Prasad, Manoj; Lata, CharuA comprehensive genome-wide survey of GRAM-domain containing genes in rice identified total 64 genes which were grouped into six classes and were physically mapped onto different rice chromosomes. GRAM domain-containing genes showed total 8 segmental and 3 tandem duplications. Comparative physical mapping between rice OsGRAM and its orthologs in related C4-crops depicted evolutionary insights into this gene family. Expression analyses of OsGRAM genes in rice roots subjected to salt stress with or without Bacillus amyloliquefaciens (SN13) inoculation revealed significant differential expression patterns suggesting their crucial role in beneficial plant-rhizobacteria interactions under stress. Further, expression analyses of selected 15 candidate genes with ≥3.0-fold induction in salt + SN13 treated samples indicated their precise and overlapping expression patterns under various abiotic stresses and phytohormones at early (1 h) and late (24 h) durations which might be ultimately responsible for functional divergence and beneficial plant-microbe interactions. Furthermore, OsGRAM27 and OsGRAM47 could be considered as potential candidate genes for further functional characterization and application in crop improvement since these genes showed positive modulation in stress under the influence of SN13. This study provides new dimensions into the evolution and divergence of OsGRAM and their role in plant-rhizobacteria interactions that could be utilized for improving stress tolerance in crops.Item A functional genomic perspective on drought signalling and its cross talk with phytohormone-mediated signalling pathways in plants(Bentham Science, 2017) Tiwari, S; Lata, Charu; Chauhan, PS; Prasad, V; Prasad, ManojINTRODUCTION: Drought stress is one of the most important abiotic stresses that negatively influence crop performance and productivity. Plants acclimatize to drought stress conditions through altered molecular, biochemical and physiological responses. Gene and/or protein expression and regulation are thought to be modulated upon stress perception and signal transduction for providing requisite endurance to plants.Plant growth regulators or phytohormones are important molecules required for various biological processes in plants and are also central to stress signalling pathways. Among various phytohormones, Abscisic Acid (ABA) and Ethylene (ET) are considered to be the most vital growth regulators implicated in drought stress signalling and tolerance. Besides the above two known classical phytohormones, Salicylic Acid (SA) and Jasmonic Acid (JA) have also been found to potentially enhance abiotic stress tolerance particularly that of drought, salinity, and heat stress tolerance in plants. Apart from these several other growth regulators such as Cytokinins (CKs), Auxin (AUX), Gibberellic Acid (GA), Brassinosteroids (BRs) and Strigolactones (SLs) have also been reported to actively participate in abiotic stress responses and tolerance in plants. The abiotic stress signalling in plants regulated by these hormones further depends upon the nature, intensity, and duration of exposure to various environmental stresses. It has been reported that all these phytohormones are also involved in extensive crosstalk and signal transduction among themselves and/or with other factors. CONCLUSION: This review thus summarizes the molecular mechanism of drought signalling and its crosstalk with various phytohormone signalling pathways implicated in abiotic stress response and tolerance.Item Integrative analysis and expression profiling of secondary cell wall genes in C4 biofuel model Setaria italica reveals targets for lignocellulose bioengineering(Frontiers Media S.A., 2015) Muthamilarasan, Mehanathan; Khan, Yusuf; Jaishankar, Jananee; Shweta, Shweta; Lata, Charu; Prasad, ManojSeveral underutilized grasses have excellent potential for use as bioenergy feedstock due to their lignocellulosic biomass. Genomic tools have enabled identification of lignocellulose biosynthesis genes in several sequenced plants. However, the non-availability of whole genome sequence of bioenergy grasses hinders the study on bioenergy genomics and their genomics-assisted crop improvement. Foxtail millet (Setaria italica L.; Si) is a model crop for studying systems biology of bioenergy grasses. In the present study, a systematic approach has been used for identification of gene families involved in cellulose (CesA/Csl), callose (Gsl) and monolignol biosynthesis (PAL, C4H, 4CL, HCT, C3H, CCoAOMT, F5H, COMT, CCR, CAD) and construction of physical map of foxtail millet. Sequence alignment and phylogenetic analysis of identified proteins showed that monolignol biosynthesis proteins were highly diverse, whereas CesA/Csl and Gsl proteins were homologous to rice and Arabidopsis. Comparative mapping of foxtail millet lignocellulose biosynthesis genes with other C4 panicoid genomes revealed maximum homology with switchgrass, followed by sorghum and maize. Expression profiling of candidate lignocellulose genes in response to different abiotic stresses and hormone treatments showed their differential expression pattern, with significant higher expression of SiGsl12, SiPAL2, SiHCT1, SiF5H2, and SiCAD6 genes. Further, due to the evolutionary conservation of grass genomes, the insights gained from the present study could be extrapolated for identifying genes involved in lignocellulose biosynthesis in other biofuel species for further characterization.Item Drought stress responses and signal transduction in plants(Springer, 2015) Lata, Charu; Muthamilarasan, Mehanathan; Prasad, ManojNature provides all necessary components for healthy growth and development of plants in the form of air, water, light, nutrients, and soil. Any imbalance in the environmental harmony may cause stress to them. Stresses encountered by plants can broadly be categorized into biotic and abiotic stresses. Biotic stresses are mainly caused by pathogens and herbivory, whereas abiotic stresses include the threat imposed by drought, salinity, and extremes of temperature, heavy metals, and pollution. Drought stress is a major cause of yield instability in crops across diverse eco-geographic regions worldwide. A variety of biochemical, molecular, and physiological changes are manifested by plants in response to drought stress. The cellular abscisic acid (ABA) concentration increases on water deficit leading to the activation of a number of stress-responsive genes and the patterns of expression of these genes are very complex, with some genes being induced early while others respond slowly. In general, drought-responsive genes respond to salt and cold stresses as well as to exogenous ABA treatment. However, there are several genes, which express themselves in an ABA-independent manner suggesting that both ABA-dependent and -independent signal transduction cascades exist for drought stress perception, response, and adaptation. Drought stress response and adaptation in plants involves an array of pathways for signal perception, transduction, gene expression and synthesis of proteins, and other stress metabolites. Drought-responsive genes can mainly be classified into two groups. First group constitutes genes whose products provide osmotolerance and protection to plants thus directly functioning in tolerance to stress, while the second group includes genes playing a role in signal transduction as well as regulation of gene expression. This chapter summarizes the complex molecular mechanisms of drought stress response and adaptation in plants, highlighting the transcriptional regulation of stress-responsive gene expression. It also focuses on the recent advances in analyzing various stress-responsive pathways with prime emphasis on ABA-dependent and -independent pathways.Item Association of an allele-specific marker with dehydration stress tolerance in foxtail millet suggests SiDREB2 to be an important QTL(Springer, 2014) Lata, Charu; Prasad, ManojDehydration-responsive element binding (DREB) genes assist in improving stress tolerance of plants by activating the expression of several stress-responsive genes. Therefore, development of functional markers for useful alleles utilizing DREB genes is crucial for crop improvement strategies. Earlier we reported a synonymous single nucleotide polymorphism (SNP) associated with dehydration tolerance at 558th bp (an A/G transition) in the SiDREB2 gene of foxtail millet (Setaria italica L.) and developed an allele-specific marker (ASM) for SiDREB2. In the present study, we validated this ASM using a set of 122 foxtail accessions, of which 45 were investigated in an earlier study. The QTL associated with SiDREB2 contributed to ~20 % of the total phenotypic variation (PV) for relative water content (RWC) and this signified the importance of this QTL for dehydration tolerance in foxtail millet.Item Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in foxtail millet (Setaria italica L.)(PLOS, 2014) Lata, Charu; Mishra, Awdhesh Kumar; Muthamilarasan, Mehanathan; Bonthala, Venkata Suresh; Khan, Yusuf; Prasad, ManojThe APETALA2/ethylene-responsive element binding factor (AP2/ERF) family is one of the largest transcription factor (TF) families in plants that includes four major sub-families, namely AP2, DREB (dehydration responsive element binding), ERF (ethylene responsive factors) and RAV (Related to ABI3/VP). AP2/ERFs are known to play significant roles in various plant processes including growth and development and biotic and abiotic stress responses. Considering this, a comprehensive genome-wide study was conducted in foxtail millet (Setaria italica L.). A total of 171 AP2/ERF genes were identified by systematic sequence analysis and were physically mapped onto nine chromosomes. Phylogenetic analysis grouped AP2/ERF genes into six classes (I to VI). Duplication analysis revealed that 12 (∼7%) SiAP2/ERF genes were tandem repeated and 22 (∼13%) were segmentally duplicated. Comparative physical mapping between foxtail millet AP2/ERF genes and its orthologs of sorghum (18 genes), maize (14 genes), rice (9 genes) and Brachypodium (6 genes) showed the evolutionary insights of AP2/ERF gene family and also the decrease in orthology with increase in phylogenetic distance. The evolutionary significance in terms of gene-duplication and divergence was analyzed by estimating synonymous and non-synonymous substitution rates. Expression profiling of candidate AP2/ERF genes against drought, salt and phytohormones revealed insights into their precise and/or overlapping expression patterns which could be responsible for their functional divergence in foxtail millet. The study showed that the genes SiAP2/ERF-069, SiAP2/ERF-103 and SiAP2/ERF-120 may be considered as potential candidate genes for further functional validation as well for utilization in crop improvement programs for stress resistance since these genes were up-regulated under drought and salinity stresses in ABA dependent manner. Altogether the present study provides new insights into evolution, divergence and systematic functional analysis of AP2/ERF gene family at genome level in foxtail millet which may be utilized for improving stress adaptation and tolerance in millets, cereals and bioenergy grasses.Item Validation of an allele-specific marker associated with dehydration stress tolerance in a core set of foxtail millet accessions(John Wiley & Sons, 2013) Lata, Charu; Prasad, ManojDehydration responsive element binding (DREB) genes play an important role in improving and enhancing stress tolerance of plants in response to abiotic stresses by interacting with DRE/CRT cis- element present in the promoter region of various stress-responsive genes. Thus, characterization of these genes and development of functional markers for effective alleles is important for crop improvement programmes. Identification of a synonymous single nucleotide polymorphism associated with dehydration tolerance at 558th bp (an A/G transition) in the SiDREB2 gene of foxtail millet (Setaria italica L.) and development of an allele-specific marker (ASM) has previously been reported by us. Here, we report on validation of the ASM in a core set of 170 foxtail millet accessions through single-marker regression analysis. The regression of lipid peroxidation (LP) on the ASM suggested that the SiDREB2 associated trait contributed to 27.18% of the total variation in LP among the 170 accessions indicating it to be a major QTL for dehydration tolerance. Thus, this ASM can be used for marker-aided breeding and allele-mining for dehydration tolerance in foxtail millet.Item Setaria genome sequencing: an overview(Springer, 2013) Lata, Charu; Prasad, ManojThe genus Setaria includes two important C4 Panicoid grass species, namely S. italica (cultivated) and S. viridis (weed; wild ancestor), which together represent an appropriate model system for architectural, physiological, evolutionary, and genomic studies in related grasses. It is a diploid, inbreeder, self-fertile annual cereal grass having short life cycle and minimal growth requirements. There close relatedness to biofuel crops like switch grass and napier grass further signifies their importance. Further, foxtail millet is an important food and fodder grain crop grown in arid and semi-arid regions in many parts of the world. Therefore, an increasing interest in these species has led to a gradual accumulation and development of genomic data and genetic resources. Setaria genome sequencing is an outcome of such endeavors. These sequencing efforts uncovered several distinctive attributes of Setaria genome that may help in understanding its physiology, evolution and adaptation. This will not only aid in comparative genomics studies of Setaria and related crops including bioenergy grasses but also help in rapid advancements of genomics information for developing varieties with superior traits either through marker-assisted selection (MAS) or using transgenic approaches in these crops.Item Foxtail millet: A model crop for genetic and genomic studies in bioenergy grasses(Informa UK Limited, an Informa Group Company (T&F Group), 2013) Lata, Charu; Gupta, Sarika; Prasad, ManojFoxtail millet is one of the oldest domesticated diploid C4 Panicoid crops having a comparatively small genome size of approximately 515 Mb, short life cycle, and inbreeding nature. Its two species, Setaria italica (domesticated) and Setaria viridis (wild progenitor), have characteristics that classify them as excellent model systems to examine several aspects of architectural, evolutionary, and physiological importance in Panicoid grasses especially the biofuel crops such as switchgrass and napiergrass. Foxtail millet is a staple crop used extensively for food and fodder in parts of Asia and Africa. In its long history of cultivation, it has been adapted to arid and semi-arid areas of Asia, North Africa, South and North America. Foxtail millet has one of the largest collections of cultivated as well as wild-type germplasm rich with phenotypic variations and hence provides prospects for association mapping and allele-mining of elite and novel variants to be incorporated in crop improvement programs. Most of the foxtail millet accessions can be primarily abiotic stress tolerant particularly to drought and salinity, and therefore exploiting these agronomic traits can enhance its efficacy in marker-aided breeding as well as in genetic engineering for abiotic stress tolerance. In addition, the release of draft genome sequence of foxtail millet would be useful to the researchers worldwide in not only discerning the molecular basis of biomass production in biofuel crops and the methods to improve it, but also for the introgression of beneficial agronomically important characteristics in foxtail millet as well as in related Panicoid bioenergy grasses.