Publications of NIPGR Scientists

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    Temperature regulation of cell cycle and growth dynamics in Arabidopsis
    (Portland Press, 2026) Sundaravadivelu, Vasundara; Raipuria, Ritesh Kumar; Ranjan, Aashish
    The plant cell cycle is a highly coordinated and regulated process that integrates endogenous and environmental signals to control cell division, meristem maintenance, and cell fate specification for growth and development. Temperature is a critical environmental signal that regulates the cell cycle to manifest developmental plasticity in Arabidopsis roots and shoots. Arabidopsis plants exhibit either adaptive growth responses or arrested growth, depending on the temperature regime. The temperature-mediated growth dynamics in Arabidopsis involve altered cell-cycle regulation. While plant developmental and physiological responses to temperature have been extensively studied, the integration of temperature signalling cues with cell-cycle dynamics to regulate growth adaptation remains poorly understood. The present review not only compiles existing information on temperature-mediated regulation of cell-cycle dynamics but also provides a perspective on multidisciplinary approaches to investigate cell-cycle dynamics at spatiotemporal resolution in Arabidopsis adaptive growth responses.
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    Genome-wide identification, characterization, and expression analysis of Clavata3 Insensitive receptor Kinases (CIKs) on developmental tissues and under temperature stress conditions in Brassica oleracea
    (Springer Nature Publishing AG, 2025) Suresh, Gokul Babu; Baskar, Harssitha; Subramaniam, Geethanjali; Soundararajan, Prabhakaran
    Unprecedented climate changes are one of the major global threats to agriculture. Though cauliflower is grown worldwide in different conditions, it is sensitive to temperature fluctuation. Clavata3 Insensitive receptor Kinase (CIK) is one of the important co-receptors involved in WUS-CLV pathway for shoot apical meristem (SAM) maintenance, floral development and environment buffering. In this study we did genome-wide identification and characterization of CIKs in Brassica oleracea var. botrytis cv. Korso. Expression analysis was conducted on developmental tissues and short-term heat and cold stress conditions. Seven fulllength BolCIKs have been identified in the Korso genome through comparison against Arabidopsis thaliana CIKs. Gene structure and motifs are distinct between each sub-class. Ka/Ks ratios showed that all CIKs underwent purifying selection. Abundance of stress-responsive cis-elements, such as MYB and MYC recognition sites, showed the involvement of BolCIK in environmental stress regulation. Among the nine developmental tissues such as leaf, stem, root, curd, sepal, petal, stamen, pistil, and silique, except BolCIK4 and BolCIK5a, CIKs were merely detected in leaves. Contrastingly, expression of all BolCIKs was detected in stem, curd, and reproductive organs. Importantly, most of the BolCIKs were highly expressed in sepal, petal, pistil, and siliques. In SAM specific manner, BolCIK3 and BolCIK6 are upregulated in heat stress and cold stress, respectively. Other BolCIKs expressions are varying between tissues-types and stress conditions. Since CIKs can possibly be involved in thermomorphogenesis, results of this work may lead to further exploration of its function to improve climate resilience in cauliflower.
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    Delineation of genes for a major QTL governing heat stress tolerance in chickpea
    (Springer Nature Publishing AG, 2024) Mohanty, Jitendra K.; Thakro, Virevol; Yadav, Antima; Nayyar, Harsh; Dixit, Girish P.; Agarwal, Pinky; Parida, Swarup K.; Jha, Uday Chand
    Chickpea (Cicer arietinum) is a cool season grain legume experiencing severe yield loss during heat stress due to the intensifying climate changes and its associated gradual increase of mean temperature. Hence, understanding the genetic architecture regulating heat stress tolerance has emerged as an important trait to be addressed for enhancing yield and productivity of chickpea under heat stress. The present study is intended to identify the major genomic region(s) governing heat stress tolerance in chickpea. For this, an integrated genomics-assisted breeding strategy involving NGS-based high-resolution QTL-seq assay, QTL region-specifc association analysis and molecular haplotyping was deployed in a population of 206 mapping individuals and a diversity panel of 217 germplasm accessions of chickpea. This combinatorial strategy delineated a major 156.8 kb QTL genomic region, which was subsequently narrowed-down to a functional candidate gene CaHSFA5 and its natural alleles associated strongly with heat stress tolerance in chickpea. Superior natural alleles and haplotypes delineated from the CaHSFA5 gene have functional signifcance in regulating heat stress tolerance in chickpea. Histochemical staining, interaction studies along with diferential expression profling of CaHSFA5 and ROS scavenging genes suggest a cross talk between CaHSFA5 with ROS homeostasis pertaining to heat stress tolerance in chickpea. Heterologous gene expression followed by heat stress screening further validated the functional signifcance of CaHSFA5 for heat stress tolerance. The salient outcomes obtained here can have potential to accelerate multiple translational genomic analysis including marker-assisted breeding and gene editing in order to develop high-yielding heat stress tolerant chickpea varieties.
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    Non-coding RNAs (ncRNAs) in plant: Master regulators for adapting to extreme temperature conditions
    (Elsevier B.V., 2023) Jha, Uday Chand; Nayyar, Harsh; Roychowdhury, Rajib; Prasad, P. V. Vara; Parida, Swarup K.; Siddique, Kadambot H. M.
    Unusual daily temperature fluctuations caused by climate change and climate variability adversely impact agricultural crop production. Since plants are immobile and constantly receive external environmental signals, such as extreme high (heat) and low (cold) temperatures, they have developed complex molecular regulatory mechanisms to cope with stressful situations to sustain their natural growth and development. Among these mechanisms, non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), small-interfering RNAs (siRNAs), and long-non-coding RNAs (lncRNAs), play a significant role in enhancing heat and cold stress tolerance. This review explores the pivotal findings related to miRNAs, siRNAs, and lncRNAs, elucidating how they functionally regulate plant adaptation to extreme temperatures. In addition, this review addresses the challenges associated with uncovering these non-coding RNAs and understanding their roles in orchestrating heat and cold tolerance in plants.
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    Dry root rot disease: Current status and future implications for chickpea production
    (Springer Nature Publishing AG, 2023) Mirchandani, Rishabh; Irulappan, Vadivelmurugan; Chilakala, Aswin Reddy; Senthil-Kumar, Muthappa
    Chickpea is one of the most important food legumes in the world. Several abiotic and biotic factors limit chickpea yields, notably, heat, drought, and dry root rot (DRR) disease. The occurrence and severity of DRR are further magnified by abiotic stresses. This review highlights the current impact of DRR on chickpea production in India, the deepening of the economic losses caused by DRR owing to drought, and integrated management practices to curb DRR. Management strategies and research targeting this aspect are critical because the long-term consequences of this rapidly emerging disease could be severe owing to climate change.
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    Exploring the master regulator heat stress transcription factor HSFA1a-mediated transcriptional cascade of HSFs in the heat stress response of tomato
    (Springer Nature Publishing AG, 2021) Rao, Sombir; Das, Jaishri Rubina; Mathur, Saloni
    The tomato heat stress transcription factor A1a (Sly-HSFA1a) acts as the master regulator of the heat stress (HS) by directly regulating the transcription of Sly-HSFA2. However, it is unclear whether the activation of Sly-HSFA2 alone is sufficient to trigger the entire transcriptional cascade downstream of Sly-HSFA1a. Therefore, the present study aims to delineate the Sly-HSFA1a governed downstream HSFs cascade regulating the tomato heat stress response. The study identified several HSFs with common and specific roles in different HS regimes as well as in HS memory. Furthermore, the study established Sly-HSFA7, Sly-HSFA6b, Sly-HSFA4c, Sly-HSFB1 and Sly-HSFB2b as new downstream targets of SlyHSFA1a during heat stress by using virus-induced-gene-silencing (VIGS) of Sly-HSFA1a. Moreover, the silencing of downstream target Sly-HSFA7 and Sly-HSFB1 revealed the orchestration of downstream transcriptional cascade of HSFs regulated individually or in a synergistic manner by Sly-HSFA1a and Sly-HSFA7 along with co-activator Sly-HSFB1. This complex transcriptional cascade of HSFs sheds light on regulatory mechanisms that enable tomato plants to respond to various heat stress conditions to maintain cellular homeostasis.
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    Delineating the epigenetic regulation of heat and drought response in plants
    (Taylor & Francis Group, 2022) Singh, Roshan Kumar; Prasad, Manoj
    Being sessile in nature, plants cannot overlook the incursion of unfavorable environmental conditions, including heat and drought. Heat and drought severely affect plant growth, development, reproduction and therefore productivity which poses a severe threat to global food security. Plants respond to these hostile environmental circumstances by rearranging their genomic and molecular architecture. One such modification commonly known as epigenetic changes involves the perishable to inheritable changes in DNA or DNA-binding histone proteins leading to modified chromatin organization. Reversible epigenetic modifications include DNA methylation, exchange of histone variants, histone methylation, histone acetylation, ATP-dependent nucleosome remodeling, and others. These modifications are employed to regulate the spatial and temporal expression of genes in response to external stimuli or specific developmental requirements. Understanding the epigenetic regulation of stress-related gene expression in response to heat and drought would commence manifold avenues for crop improvement through molecular breeding or biotechnological approaches.
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    Population structure and association analysis of heat stress relevant traits in chickpea (Cicer arietinum L.)
    (Springer, 2018) Jha, Uday Chand; Jha, Rintu; Bohra, Abhishek; Parida, Swarup K.; Kole, Paresh Chandra; Thakro, Virevol; Singh, Deepak; Singh, Narendra Pratap
    Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.
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    Identification and characterization of high temperature stress responsive genes in bread wheat (Triticum aestivum L.) and their regulation at various stages of development
    (Springer Science, 2011) Chauhan, Harsh; Khurana, Neetika; Tyagi, Akhilesh K.; Khurana, Jitendra P.; Khurana, Paramjit
    To elucidate the effect of high temperature, wheat plants (Triticum aestivum cv. CPAN 1676) were given heat shock at 37 and 42°C for 2 h, and responsive genes were identified through PCR-Select Subtraction technology. Four subtractive cDNA libraries, including three forward and one reverse subtraction, were constructed from three different developmental stages. A total of 5,500 ESTs were generated and 3,516 high quality ESTs submitted to Genbank. More than one-third of the ESTs generated fall in unknown/no hit category upon homology search through BLAST analysis. Differential expression was confirmed by cDNA macroarray and by northern/RT-PCR analysis. Expression analysis of wheat plants subjected to high temperature stress, after 1 and 4 days of recovery, showed fast recovery in seedling tissue. However, even after 4 days, recovery was negligible in the developing seed tissue after 2 h of heat stress. Ten selected genes were analyzed in further detail including one unknown protein and a new heat shock factor, by quantitative real-time PCR in an array of 35 different wheat tissues representing major developmental stages as well as different abiotic stresses. Tissue specificity was examined along with cross talk with other abiotic stresses and putative signalling molecules.