Publications of NIPGR Scientists

Permanent URI for this communityhttps://ndkr-library.nipgr.ac.in/handle/123456789/1

Browse

Subject: search.filters.subject.abiotic stress

Search Results

Now showing 1 - 10 of 49
  • Thumbnail Image
    Item
    Molecular and expression analyses indicate the role of fusion transcripts in mediating abiotic stress responses in chickpea
    (Frontiers Media S.A., 2025) Hamid, Fiza; Zahra, Shafaque; Kumar, Shailesh
    Understanding the transcriptome diversity is essential for deciphering the transcriptional level regulation. High-throughput sequencing technologies have facilitated the detection of fusion transcripts (FTs), which are chimeric mRNA molecules derived from gene fusions due to chromosomal rearrangements or via the splicing machinery at the RNA level. In this study, we investigated the transcriptome complexity in Cicer arietinum resulting from fusion events using high-throughput RNA-Seq datasets from five tissues, i.e., stem, leaves, buds, flowers, and pods, and two abiotic stress conditions, i.e., drought and salinity. Of the 328 unique FTs identified, 69% exhibited the presence of canonical splice sites at their junction, indicating their generation via trans-splicing. Functional annotation and enrichment analyses of fusion partners suggested that these transcripts may expand functional diversity. A total of 10 FTs were validated via RT-PCR followed by Sanger sequencing, which are the first FTs described in the important legume chickpea. Expression analysis of fusion transcripts across various tissues and under abiotic stress conditions revealed evidence of context-dependent regulation. Furthermore, 120 fusion gene pairs were found to be conserved across 17 chickpea genotypes, highlighting their potential biological significance and stability within the species. Overall, these findings suggest that fusion transcripts may contribute to regulatory mechanisms underlying abiotic stress responses in chickpea.
  • Thumbnail Image
    Item
    TaCCS1-B expression modulates copper, enzymatic antioxidants and polyphenols contents and provides abiotic stress tolerance in transgenic Arabidopsis
    (John Wiley & Sons, 2024) Tyagi, Shivi; Shumayla; Singh, Samar; Pandey, Ashutosh; Upadhyay, Santosh Kumar
    Abiotic stress, including osmotic and salinity stress, significantly affects plant growth and productivity. Copper chaperone for superoxide dismutase (CCS) is essential for copper homeostasis and oxidative stress management. In this study, we investigated the role of the TaCCS1-B gene of bread wheat in enhancing stress tolerance in yeast and transgenic Arabidopsis. Expression of TaCCS1-B increased abiotic stress tolerance in recombinant yeast cells. Phenotypic analysis of Arabidopsis TaCCS1-B expressing lines demonstrated that they exhibited significantly higher germination rates, increased root length and better growth under osmotic and salinity stress than wild type. Additionally, the transgenic lines exhibited higher copper accumulation and enhanced photosynthetic pigments and proline level, coupled with reduced hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) contents. They also showed higher enzymatic antioxidants' activities, indicating reduced oxidative stress in transgenic lines, resulting in reduced flavonoid content. Gene expression analysis indicated modulated expression of stress-responsive genes in the transgenic lines under stress conditions. These findings suggested the role of TaCCS1-B in enhancing stress tolerance by improving copper homeostasis and regulating key stress-responsive genes. This study highlights the potential of TaCCS1-B for the development of better stress resilience crops, which is critical for sustaining agricultural productivity for food security under adverse environmental conditions.
  • Thumbnail Image
    Item
    Genomic and transcriptomic approaches to developing abiotic stress-resilient crops
    (MDPI AG, 2023) Kamali, Saravanappriyan; Singh, Amarjeet
    In the realm of agriculture, a pressing concern remains the abiotic stresses, such as temperature fluctuation, drought, soil salinity, and heavy metal contamination. These adverse growth conditions hamper crop yields and global food security. In this review, we present a comprehensive examination of the recent advancements in utilizing genomics and transcriptomics, tools to enhance crop resilience against these stress factors. Genomics aids in the identification of genes responsive to stress, unravels regulatory networks, and pinpoints genetic variations linked to stress tolerance. Concurrently, transcriptomics sheds light on the intricate dynamics of gene expression during stress conditions, unearthing novel stress-responsive genes and signaling pathways. This wealth of knowledge shapes the development of stress-tolerant crop varieties, achieved through conventional breeding programs and state-of-the-art genetic engineering and gene editing techniques like CRISPR-Cas9. Moreover, the integration of diverse omics data and functional genomics tools empowers precise manipulation of crop genomes to fortify their stress resilience. In summary, the integration of genomics and transcriptomics holds substantial promise in elucidating the molecular mechanisms behind crop stress tolerance, offering a path towards sustainable agriculture and safeguarding food security amidst shifting environmental challenges.
  • Thumbnail Image
    Item
    When two negatives make a positive: The favorable impact of the combination of abiotic stress and pathogen infection on plants
    (Oxford University Press, 2024) Pandey, Prachi; Patil, Mahesh; Priya, Piyush; Senthil-Kumar, Muthappa
    Combined abiotic and biotic stresses modify plant defense signaling, leading to either the activation or suppression of defense responses. Although the majority of combined abiotic and biotic stresses reduce plant fitness, certain abiotic stresses reduce the severity of pathogen infection in plants. Remarkably, certain pathogens also improve the tolerance of some plants to a few abiotic stresses. While considerable research focuses on the detrimental impact of combined stresses on plants, the upside of combined stress remains hidden. This review succinctly discusses the interactions between abiotic stresses and pathogen infection that benefit plant fitness. Here, we discuss various factors that govern the positive influence of combined abiotic stress and pathogen infection on plant performance. We also provide a brief overview of the role of pathogens, mainly viruses, in improving plant responses to abiotic stresses. We further highlight the critical nodes in defense signaling that guide plant responses during abiotic stress towards enhanced resistance to pathogens. Studies on antagonistic interactions between abiotic and biotic stressors can uncover candidates in host plant defense that may shield plants from combined stresses.
  • Thumbnail Image
    Item
    Lactate dehydrogenase superfamily in rice and Arabidopsis: Understanding the molecular evolution and structural diversity
    (MDPI AG, 2023) Chatterjee, Yajnaseni; Bhowal, Bidisha; Gupta, Kapuganti Jagadis; Pareek, Ashwani; Singla-Pareek, Sneh Lata
    Lactate/malate dehydrogenases (Ldh/Maldh) are ubiquitous enzymes involved in the central metabolic pathway of plants and animals. The role of malate dehydrogenases in the plant system is very well documented. However, the role of its homolog L-lactate dehydrogenases still remains elusive. Though its occurrence is experimentally proven in a few plant species, not much is known about its role in rice. Therefore, a comprehensive genome-wide in silico investigation was carried out to identify all Ldh genes in model plants, rice and Arabidopsis, which revealed Ldh to be a multigene family encoding multiple proteins. Publicly available data suggest its role in a wide range of abiotic stresses such as anoxia, salinity, heat, submergence, cold and heavy metal stress, as also confirmed by our qRT-PCR analysis, especially in salinity and heavy metal mediated stresses. A detailed protein modelling and docking analysis using Schrodinger Suite reveals the presence of three putatively functional L-lactate dehydrogenases in rice, namely OsLdh3, OsLdh7 and OsLdh9. The analysis also highlights the important role of Ser-219, Gly-220 and His-251 in the active site geometry of OsLdh3, OsLdh7 and OsLdh9, respectively. In fact, these three genes have also been found to be highly upregulated under salinity, hypoxia and heavy metal mediated stresses in rice.
  • Thumbnail Image
    Item
    AtSWEET11 and AtSWEET12 transporters function in tandem to modulate sugar flux in plants
    (John Wiley & Sons, 2023) Fatima, Urooj; Balasubramaniam, D.; Khan, Wajahat Ali; Kandpal, Manu; Vadassery, Jyothilakshmi; Arockiasamy, Arulandu; Senthil-Kumar, Muthappa
    The sugar will eventually be exported transporter (SWEET) members in Arabidopsis, AtSWEET11 and AtSWEET12 are the important sucrose efflux transporters that act synergistically to perform distinct physiological roles. These two transporters are involved in apoplasmic phloem loading, seed filling, and sugar level alteration at the site of pathogen infection. Here, we performed the structural analysis of the sucrose binding pocket of AtSWEET11 and AtSWEET12 using molecular docking followed by rigorous molecular dynamics (MD) simulations. We observed that the sucrose molecule binds inside the central cavity and in the middle of the transmembrane (TM) region of AtSWEET11 and AtSWEET12, that allows the alternate access to the sucrose molecule from either side of the membrane during transport. Both AtSWEET11 and AtSWEET12, shares the similar amino acid residues that interact with sucrose molecule. Further, to achieve more insights on the role of these two transporters in other plant species, we did the phylogenetic and the in-silico analyses of AtSWEET11 and AtSWEET12 orthologs from 39 economically important plants. We reported the extensive information on the gene structure, protein domain and cis-acting regulatory elements of AtSWEET11 and AtSWEET12 orthologs from different plants. The cis-elements analysis indicates the involvement of AtSWEET11 and AtSWEET12 orthologs in plant development and also during abiotic and biotic stresses. Both in silico and in planta expression analysis indicated AtSWEET11 and AtSWEET12 are well-expressed in the Arabidopsis leaf tissues. However, the orthologs of AtSWEET11 and AtSWEET12 showed the differential expression pattern with high or no transcript expression in the leaf tissues of different plants. Overall, these results offer the new insights into the functions and regulation of AtSWEET11 and AtSWEET12 orthologs from different plant species. This might be helpful in conducting the future studies to understand the role of these two crucial transporters in Arabidopsis and other crop plants.
  • Thumbnail Image
    Item
    Tweaking the small non-coding RNAs to improve desirable traits in plant
    (MDPI AG, 2023) Halder, Koushik; Chaudhuri, Abira; Abdin, Malik Z; Datta, Asis
    Plant transcriptome contains an enormous amount of non-coding RNAs (ncRNAs) that do not code for proteins but take part in regulating gene expression. Since their discovery in the early 1990s, much research has been conducted to elucidate their function in the gene regulatory network and their involvement in plants' response to biotic/abiotic stresses. Typically, 20-30 nucleotide-long small ncRNAs are a potential target for plant molecular breeders because of their agricultural importance. This review summarizes the current understanding of three major classes of small ncRNAs: short-interfering RNAs (siRNAs), microRNA (miRNA), and transacting siRNAs (tasiRNAs). Furthermore, their biogenesis, mode of action, and how they have been utilized to improve crop productivity and disease resistance are discussed here.
  • Thumbnail Image
    Item
    Abiotic stress tolerance in plants: Brassinosteroids navigate competently
    (MDPI AG, 2022) Chaudhuri, Abira; Halder, Koushik; Abdin, Malik Z; Majee, Manoj; Datta, Asis
    Brassinosteroid hormones (BRs) multitask to smoothly regulate a broad spectrum of vital physiological processes in plants, such as cell division, cell expansion, differentiation, seed germination, xylem differentiation, reproductive development and light responses (photomorphogenesis and skotomorphogenesis). Their importance is inferred when visible abnormalities arise in plant phenotypes due to suboptimal or supraoptimal hormone levels. This group of steroidal hormones are major growth regulators, having pleiotropic effects and conferring abiotic stress resistance to plants. Numerous abiotic stresses are the cause of significant loss in agricultural yield globally. However, plants are well equipped with efficient stress combat machinery. Scavenging reactive oxygen species (ROS) is a unique mechanism to combat the deleterious effects of abiotic stresses. In light of numerous reports in the past two decades, the complex BR signaling under different stress conditions (drought, salinity, extreme temperatures and heavy metals/metalloids) that drastically hinders the normal metabolism of plants is gradually being untangled and revealed. Thus, crop improvement has substantial potential by tailoring either the brassinosteroid signaling, biosynthesis pathway or perception. This review aims to explore and dissect the actual mission of BRs in signaling cascades and summarize their positive role with respect to abiotic stress tolerance.
  • Thumbnail Image
    Item
    Physiological implications of SWEETs in plants and their potential applications in improving source-sink relationships for enhanced yield
    (John Wiley & Sons, 2023) Singh, Jitender; Das, Shubhashis; Gupta, Kapuganti Jagadis; Ranjan, Aashish; Foyer, Christine H; Thakur, Jitendra K.
    The SWEET (SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTERS) family of transporters in plants is identified as a novel class of sugar carriers capable of transporting sugars, sugar alcohols, and hormones. Functioning in intercellular sugar transport, SWEETs influence a wide range of physiologically important processes. SWEETs regulate the development of sink organs by providing nutritional support from source leaves, responses to abiotic stresses by maintaining intracellular sugar concentrations, and host-pathogen interactions through the modulation of apoplastic sugar levels. Many bacterial and fungal pathogens activate the expression of SWEET genes in species such as rice and Arabidopsis to gain access to the nutrients that support virulence. The genetic manipulation of SWEETs has led to the generation of Bacterial Blight (BB) resistant rice varieties. Similarly, while the overexpression of the SWEETs involved in sucrose export from leaves and pathogenesis led to growth retardation and yield penalties, plants overexpressing SWEETs show improved disease resistance. Such findings demonstrate the complex functions of SWEETs in growth and stress tolerance. Here, we review the importance of SWEETs in plant-pathogen and source-sink interactions and abiotic stress resistance. We highlight the possible applications of SWEETs in crop improvement programs aimed at improving sink and source strengths important for enhancing the sustainability of yield. We discuss how the adverse effects of the overexpression of SWEETs on plant growth may be overcome.
  • Thumbnail Image
    Item
    Characterization and expression profiling of PIN auxin efflux transporters reveal their role in developmental and abiotic stress conditions in rice
    (Frontiers Media S.A., 2022) Manna, Mrinalini; Rengasamy, Balakrishnan; Ambasht, Navin Kumar; Sinha, Alok Krishna
    The auxin efflux transporter proteins called PINs ferry auxin from its source to sinks in particular directions depending on their polar localizations in the plasma membrane, thus facilitating the development of the entire plant architecture. The rice genome has 12 PIN genes distributed over eight chromosomes. To study their roles in plant development, abiotic stress responsiveness, and shaping an auxin-dependent root architecture, a genome-wide analysis was carried out. Based on phylogeny, cellular localization, and hydrophilic loop domain size, the PINs were categorized into canonical and noncanonical PINs. PINs were found expressed in all of the organs of plants that emphasized their indispensable role throughout the plant's life cycle. We discovered that PIN5C and PIN9 were upregulated during salt and drought stress. We also found that regardless of its cellular level, auxin functioned as a molecular switch to turn on auxin biosynthesis genes. On the contrary, although PIN expression was upregulated upon initial treatment with auxin, prolonged auxin treatment not only led to their downregulation but also led to the development of auxin-dependent altered root formation in rice. Our study paves the way for developing stress-tolerant rice and plants with a desirable root architecture by genetic engineering