Publications of NIPGR Scientists
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Item Plant responses to concurrent abiotic and biotic stress: unravelling physiological and morphological mechanisms(Springer Nature Publishing AG, 2024) Dixit, Shikha; Sivalingam, Palaiyur Nanjappan; Baskaran, R. K. Murali; Senthil-Kumar, Muthappa; Ghosh, Probir KumarWith the increasing impact of climate change and global warming, not only abiotic stress factors have gained prominence, but their infuence on plant–biotic interaction has also increased. Plants respond diferently to abiotic factors compared to pests and pathogens, which thrive under intense climatic conditions, leading to higher disease susceptibility and potential epidemic outbreaks. Therefore, a comprehensive understanding of the efects of concurrent biotic and abiotic stress on plants is essential. Despite its signifcance, there have been limited studies on the physiological and morphological responses of plants to combined stress, and the underlying molecular mechanisms remain elusive. While model crops like rice and maize have been explored under the context to some extent there is a scarcity of research on other crops. Furthermore, the impact of environmental factors on physiological changes in plants remains largely unknown. This review aims to consolidate existing literature on this topic, with a focus on interaction between abiotic stresses (drought, heat, and salinity) and biotic stresses (pathogens and pests). Additionally, it highlights agriculturally important morpho-physiological traits that can be utilized to identify genotypes with combined stress tolerance. Moreover, the review will outline the potential role of recent techniques and genomic tools in unravelling combined stress tolerance in plants. The fndings of this review will help physiologists and molecular biologists to design agronomically relevant strategies for developing broad-spectrum stress-tolerant crops.Item Genomic & structural diversity and functional role of potassium (K+) transport proteins in plants(Elsevier B.V., 2022) Ankit, Ankit; Kamali, Saravanappriyan; Singh, AmarjeetPotassium (K+) is an essential macronutrient for plant growth and productivity. It is the most abundant cation in plants and is involved in various cellular processes. Variable K+ availability is sensed by plant roots, consequently K+ transport proteins are activated to optimize K+ uptake. In addition to K+ uptake and translocation these proteins are involved in other important physiological processes like transmembrane voltage regulation, polar auxin transport, maintenance of Na+/K+ ratio and stomata movement during abiotic stress responses. K+ transport proteins display tremendous genomic and structural diversity in plants. Their key structural features, such as transmembrane domains, N-terminal domains, C-terminal domains and loops determine their ability of K+ uptake and transport and thus, provide functional diversity. Most K+ transporters are regulated at transcriptional and post-translational levels. Genetic manipulation of key K+ transporters/channels could be a prominent strategy for improving K+ utilization efficiency (KUE) in plants. This review discusses the genomic and structural diversity of various K+ transport proteins in plants. Also, an update on the function of K+ transport proteins and their regulatory mechanism in response to variable K+ availability, in improving KUE, biotic and abiotic stresses is provided.Item Heavy metal stress in rice: uptake, transport, signaling and tolerance mechanisms(John Wiley & Sons, 2021) Kaur, Ravneet; Das, Susmita; Bansal, Sakshi; Singh, Gurbir; Sardar, Shaswati; Dhar, Hena; Ram, HasthiHeavy metal contamination of agricultural fields has become a global concern as it causes a direct impact on human health. Rice is the major food crop for almost half of the world population and is grown under diverse environmental conditions, including heavy metal-contaminated soil. In recent years, the impact of heavy metal contamination on rice yield and grain quality has been shown through multiple approaches. In this review article, different aspects of heavy metal stress, i.e. uptake, transport, signalling and tolerance mechanisms, are comprehensively discussed with special emphasis on rice. For uptake, some of the transporters have specificity to one or two metal ions, whereas many other transporters are able to transport many different ions. After uptake, the intercellular signalling is mediated through different signaling pathways involving the regulation of various hormones, alteration of calcium levels and the activation of Mitogen-Activated Protein kinases. Heavy metal stress signals from various intermediate molecules activate various transcription factors, which triggers the expression of various antioxidant enzymes. Activated antioxidant enzymes then scavenge various reactive oxygen species, which eventually leads to stress tolerance in plants. Non-enzymatic antioxidants, such as ascorbate, metalloids and even metal-binding peptides (metallothionein and phytochelatin) can also help to reduce metal toxicity in plants. Genetic engineering has been successfully used in rice and many other crops to increase metal tolerance and reduce heavy metals accumulation. A comprehensive understanding of uptake, transport, signalling and tolerance mechanisms will help to grow rice plants in agricultural fields with less heavy metal accumulation in grains.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 Millets genetic engineering: the progress made and prospects for the future(Springer Nature, 2019) Sood, Priyanka; Singh, Roshan Kumar; Prasad, ManojSustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on 'adaptive traits' that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping-genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated "omics-assisted" approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.Item Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes(Springer Nature, 2019) Jha, Uday Chand; Bohra, Abhishek; Jha, Rintu; Parida, Swarup K.Key message Sustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Abstract Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on ‘adaptive traits’ that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping–genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated “omics-assisted” approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.Item Biotechnology for drug discovery and crop improvement(Springer, 2017) Kamthan, Ayushi; Kamthan, Mohan; Datta, AsisGenomics has emerged as the single most powerful discipline for detailed analysis of organization expression, and interaction of an organism at the genome level. Pathogens like Candida albicans, Vibrio cholerae etc. are responsible for causing morbidity and mortality in human beings. Besides, phytopathogens like Magnaporthe oryzae can lead to potential loss of yield in staple crop of rice. Genes of N-Acetyl-d-glucosamine metabolic pathway has been found to be universal in the diverse pathogens like C. albicans, V. cholerae and M. oryzae, playing an important role in their virulence. Lack of optimal treatment and emergence of multi-drug resistance necessitate the designing of better/new drugs against these pathogens. Research on these pathogens has increased the understanding of virulence and pathogenicity factors which can serve as potential drug targets that can be efficiently utilized to design a successful therapy to combat various diseases. Agricultural biotechnology has provided new tools for effectively ensuring food and nutritional security that can overcome many of the technical roadblocks that limit the application of conventional biological techniques in agricultural research. Limitations of water resources, decreased fertility of arable land skyrocketing cost of energy and galloping increases in the population make it imperative that food supplies of the 21st century will depend on a new form of agriculture in which custom-made food plants will dominate the world market. The ultimate goal is to create crops that are tailored to provide better nutrition for humans, improved fruit shelf life and enhanced tolerance to various stresses.Item Genome-wide survey and expression analysis of F- box genes in chickpea(BioMed Central Ltd, 2015) Gupta, Shefali; Garg, Vanika; Kant, Chandra; Bhatia, SabhyataThe F-box genes constitute one of the largest gene families in plants involved in degradation of cellular proteins. F-box proteins can recognize a wide array of substrates and regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence, among others. However, little is known about the F-box genes in the important legume crop, chickpea. The available draft genome sequence of chickpea allowed us to conduct a genome-wide survey of the F-box gene family in chickpea.Item Generation of expressed sequence tags under cadmium stress for gene discovery and development of molecular markers in chickpea(Springer, 2014) Gaur, Rashmi; Bhatia, Sabhyata; Gupta, MeetuChickpea is the world's third most important legume crop and belongs to Fabaceae family but suffered from severe yield loss due to various biotic and abiotic stresses. Development of modern genomic tools such as molecular markers and identification of resistant genes associated with these stresses facilitate improvement in chickpea breeding towards abiotic stress tolerance. In this study, 1597 high-quality expressed sequence tags (ESTs) were generated from a cDNA library of variety Pusa 1105 root tissue after cadmium (Cd) treatment. Assembly of ESTs resulted in a total of 914 unigenes of which putative homology was obtained for 38.8 % of unigenes after BLASTX search. In terms of species distribution, majority of sequences found similarity with Medicago truncatula followed by Glycine max, Vitis vinifera and Populus trichocarpa and Pisum sativum sequences. Functional annotation was assigned using Blast2Go, and the Gene Ontology (GO) terms were categorized into biological process, molecular function and cellular component. Approximately 10.83 % of unigenes were assigned at least one GO term. Moreover, in the distribution of transcripts into various biological pathways, 20 of the annotated transcripts were assigned to ten pathways in KEGG database. A majority of the genes were found to be involved in sulphur and nitrogen metabolism. In the quantitative real-time PCR analysis, five of the transcription factors and three of the transporter genes were found to be highly expressed after Cd treatment. Besides, the utility of ESTs was demonstrated by exploiting them for the development of 83 genic molecular markers including EST-simple sequence repeats and intron targeted polymorphism that would assist in tagging of genes related to metal stress for future prospects.Item Molecular cloning and characterization of a membrane associated NAC family gene, SiNAC from foxtail millet [Setaria italica (L.) P. Beauv.](Springer Science, 2011) Puranik, Swati; Bahadur, Ranjit Prasad; Srivastava, Prem S.; Prasad, ManojThe plant-specific NAC (NAM, ATAF, and CUC) transcription factors have diverse role in development and stress regulation. A transcript encoding NAC protein, termed SiNAC was identified from a salt stress subtractive cDNA library of S. italica seedling (Puranik et al., J Plant Physiol 168:280-287, 2011). This single/low copy gene containing four exons and four introns within the genomic-sequence encoded a protein of 462 amino acids. Structural analysis revealed that highly divergent C terminus contains a transmembrane domain. The NAC domain consisted of a twisted antiparallel beta-sheet packing against N terminal alpha helix on one side and a shorter helix on the other side. The domain was predicted to homodimerize and control DNA-binding specificity. The physicochemical features of the SiNAC homodimer interface justified the dimeric form of the predicted model. A 1539 bp fragment upstream to the start codon of SiNAC gene was cloned and in silico analysis revealed several putative cis-acting regulatory elements within the promoter sequence. Transactivation analysis indicated that SiNAC activated expression of reporter gene and the activation domain lied at the C terminal. The SiNAC:GFP was detected in the nucleus and cytoplasm while SiNAC ΔC(1-158):GFP was nuclear localized in onion epidermal cells. SiNAC transcripts mostly accumulated in young spikes and were strongly induced by dehydration, salinity, ethephon, and methyl jasmonate. These results suggest that SiNAC encodes a membrane associated NAC-domain protein that may function as a transcriptional activator in response to stress and developmental regulation in plants.