Publications of NIPGR Scientists
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Item Multi-environment phenotyping of ricebean (Vigna umbellata (Thunb.) Ohwi & Ohashi) germplasm and identification of core set for accelerating the crop improvement programs(Frontiers Media S.A., 2026) Gayacharan; Joshi, Dinesh C; Aravind, J; Wankhede, D P; Singh, Badal; Kumar, Prakash; Rajkumar, S; Parida, Swarup K; Semwal, D P; Sharma, Paras; Singh, Mohar; Chattopadhyay, Debasis; Singh, Kuldeep; Singh, G. P.; Singh, Amit KumarRicebean (Vigna umbellata) is a nutrient-rich rich underutilised legume crop. It is primarily grown in the uplands of India, Nepal and China. Despite its adaptation to a wide range of agroclimatic zones and resistance to various biotic and abiotic stresses, ricebean crop improvement efforts have been slow mainly because of the low levels of genetic diversity utilised in ricebean breeding. This study presents the first multi-environment phenotyping and core collection building in ricebean with 1,589 accessions maintained at the Indian National Gene Bank. The accessions were assessed in two diverse agro-ecological regions (New Delhi and Almora), indicating significant phenotypic variations for important economic traits such as days to flowering, pod length, number of seeds per pod, and seed weight. The core subsets were sampled using MStrat, PowerCore and PCSS, and CoreHunter algorithms. The sampled coresets were evaluated using diversity indices such as genetic distance, mean difference percentage (MD%), variance difference percentage (VD%), coincidence rate (CR) and variable rate of coefficient of variation. The E-EN100 approach of CoreHunter yielded the most effective representation, resulting in a final core set with 251 accessions (14.3% from the entire collection). Diversity indices, clustering methods, QQ-plots, and distributional comparisons confirmed the representativeness of the core set. Multi-environment GGE biplot analysis identified stable and high-performing accessions for early flowering, synchronous maturity, pod and seed traits, including promising genotypes such as IC351508 and IC352944 with determinate growth habit and high yield potential. The study provides a manageable subset of the entire collection, which may play a significant role in trait discovery and ricebean cultivar development.Item CBL1/9-CIPK6 complex negatively regulates respiratory burst oxidase homolog D in Arabidopsis thaliana(John Wiley & Sons, 2026) Vishwakarma, Niraj Kumar; Yadav, Shalini; Sardar, Atish; Choudhary, Megha; Chattopadhyay, DebasisPlant innate immune response is a well-balanced process with positive and negative regulations for the plants to survive. Calcium signaling is essential for pathogen-associated molecular pattern (PAMP)-driven respiratory burst oxidase homolog D (RBOHD)-mediated reactive oxygen species (ROS) burst. We show that calcium sensors calcineurin B like protein 1 (CBL1) and CBL9 and their interacting protein kinase CIPK6 negatively regulate RBOHD activity and immune response in Arabidopsis thaliana. Arabidopsis mutant cbl1cbl9, like cipk6, exhibited enhanced resistance and ROS production when infected with the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). CBL1 and CBL9 enhanced kinase activity of CIPK6. CBL1/9-CIPK6 module interacts with RBOHD at the plasma membrane. CIPK6 along with CBL1 reduces RBOHD activity in planta. CIPK6 phosphorylates the N-terminal cytoplasmic domain of RBOHD at a non-conserved (S33) and a conserved (S39) serine residue. While S39 phosphorylation increased RBOHD activity, S33 phosphorylation drastically reduced it and superseded the effect of S39 phosphorylation. We propose a model that CIPK6 phosphorylates RBOHD at S33 to suppress its activity to balance ROS generation in post-PTI situation in Arabidopsis. Our study reports a direct mechanism of negative regulation of ROS production and plant immune response by a calcium-signaling module in Arabidopsis thaliana.Item Unearthing the secrets of drought-driven root system architecture: Nutrient acquisition and rhizosphere microbe interplay(Elsevier B.V., 2026) Nayak, Jagatjeet; Chattopadhyay, Debasis; Giri, Mrunmay Kumar; Singh, NidhiDrought, a climatic occurrence that cyclically affects all climatic regions, is more prevalent in tropical and subtropical areas. This phenomenon inflicts physiological harm upon plants within ecosystems and agroecosystems. Apart from the direct scarcity of water, which severely impairs plant development and productivity, there can be consequential issues related to mineral nutrition. These secondary effects can arise and further impact plant development. Amidst drought conditions, roots play a critical role in shaping the growth and development of plants. During these circumstances, our understanding of the molecular mechanisms governing critical responses and interactions between plant roots and their surrounding rhizosphere is less comprehensive in comparison to other studies with well-characterized model species like Arabidopsis. This article examines the molecular mechanisms governing the adaptability of root system architecture (RSA) to drought stress in plants. It also explores how soil nutrients and microorganisms are regulated in response to these adaptive processes. We first give a general description of how plant hormones control RSA under water-scarce conditions. Additionally, we explore how nutrients, particularly phosphorus and nitrogen, affect the developmental responses of RSA to low water status. Additionally, this article delves into the existing understanding of the interactions between RSA and soil microbial niches under drought. Based on these understandings, our conclusion emphasizes that to achieve a more comprehensive grasp of the mechanisms underlying drought adaptation in plant roots, future research should adopt a holistic network perspective.Item Lighting the path: how light signaling regulates stomatal movement and plant immunity(Oxford University Press, 2025) Singh, Nidhi; Giri, Mrunmay Kumar; Chattopadhyay, DebasisStomata, the small pores on the surfaces of leaves and stems, are crucial for gas exchange in plants and also play a role in defense against pathogens. The stomatal movement is not only influenced by surrounding light conditions but also by the presence of foliar pathogens. To put it more crisply, certain light wavelengths such as blue or strong red light, cause stomatal opening, which tragically makes it easier for bacteria to enter through opened stomata and causes disease progression in plants. Illumination of blue or intense red light autophosphorylates phototropin, a blue light photoreceptor protein kinases that in turn activates signaling cascade to open stomata. Undoubtedly stomatal defense is a fascinating aspect of plant immunology, especially in plant-foliar pathogen interaction. During these interactions, stomata fundamentally serve as entry points for intrusive pathogens and initiate plant defense signaling cascade. The present review highlights how the light-activated photoreceptors like cryptochromes (CRYs), phytochromes (phys), and UV-receptors (UVRs) influence the stomatal movement and defense signaling after foliar pathogen intrusion. It also explores the link between stomatal defense, light signaling, and plant immunity, which is vital for safeguarding crops against pathogens.Item CaLAP1 and CaLAP2 orchestrate anthocyanin biosynthesis in the seed coat of Cicer arietinum(Springer Nature Publishing AG, 2024) Singh, Samar; Pal, Lalita; Rajput, Ruchika; Chhatwal, Himani; Singh, Nidhi; Chattopadhyay, Debasis; Pandey, AshutoshThe seed coat color is a major economic trait in leguminous crop chickpea (Cicer arietinum). Anthocyanins and proanthocyanidins (PAs) are two classes of flavonoids that mainly contribute to the flower, seed coat and color of Desi chickpea cultivars. Throughout the land plant lineage, the accumulation of anthocyanins and PAs is regulated by MYB and bHLH transcription factors (TFs), which form an MBW (MYB, bHLH, and WD40) complex. Here, we report two R2R3-MYB TFs in chickpea belonging to the anthocyanin-specific subgroup-6, CaLAP1 (Legume Anthocyanin Production 1), and CaLAP2 (Legume Anthocyanin Production 2), which are mainly expressed in the flowers and developmental stages of the seeds. CaLAP1 and CaLAP2 interact with TT8-like CabHLH1 and WD40, forming the MBW complex, and bind to the promoter sequences of anthocyanin- and PA biosynthetic genes CaCHS6, CaDFR2, CaANS, and CaANR, leading to anthocyanins and PA accumulation in the seed coat of chickpea. Moreover, these CaLAPs partially complement the anthocyanin-deficient phenotype in the Arabidopsis thaliana sextuple mutant seedlings. Overexpression of CaLAPs in chickpea resulted in significantly higher expression of anthocyanin and PA biosynthetic genes leading to a darker seed coat color with higher accumulation of anthocyanin and PA. Our findings show that CaLAPs positively modulate anthocyanin and PA content in seed coats, which might influence plant development and resistance to various biotic and abiotic stresses.Item Identification of a stable drought-tolerant high-yielding line for chickpea crop improvement(Springer Nature Publishing AG, 2025) Gupta, Santosh Kumar; Dwivedi, Vikas; Kute, Nandakumar Surendra; Francis, Philip; Parida, Swarup K.; Chattopadhyay, DebasisChickpea (Cicer arietinum L.) is grown in marginal land with low input and is, therefore, drought-prone. In order to develop a drought-tolerant line, a bi-parental recombinant inbred line (RIL) mapping population was generated by inter-crossing between two varieties JGK3 (ICCV 95334) and Himchana1 (ICCX-810800) having contrasting root traits. Ninety-two genetically diverse RILs of F8 generation were selected based on their total root length to root dry weight ratio (RL/DW). The leaf relative water content of these RILs under low soil moisture did not show any strong correlation with the RL/DW. Twenty RILs having high RL/DW were evaluated for seed yield in a field under rainfed condition without any supplementary irrigation. The best performing RIL, which performed better than the check varieties, was reevaluated for a further year under rainfed condition. The genotypic constitution of this superior low soil moisture tolerant individual RIL was determined by constructing its recombination map using genome-wide SNPs obtained through genotyping-by-sequencing. The RIL possesses the superior alleles of the genomic QTL region known to govern drought tolerance in chickpea. The phenotypic and genotypic characterization of RILs in our study identified a chickpea pre-breeding line that can be used as a genetic donor for developing drought-tolerant high-yielding chickpea varieties and our results provide an evidence that total root length to root dry weight ratio can be used as a quantitative trait for assessing drought tolerance.Item Transcriptome-wide association mapping provides insights into the genetic basis and candidate genes governing flowering, maturity and seed weight in rice bean (Vigna umbellata)(BioMed Central Ltd, 2024) Sahu, Tanmaya Kumar; Verma, Sachin Kumar; Gayacharan; Singh, Nagendra Pratap; Joshi, Dinesh Chandra; Wankhede, D. P.; Singh, Mohar; Bhardwaj, Rakesh; Singh, Badal; Parida, Swarup K.; Chattopadhyay, Debasis; Singh, Gyanendra Pratap; Singh, Amit KumarBackground: Rice bean (Vigna umbellata), an underrated legume, adapts to diverse climatic conditions with the potential to support food and nutritional security worldwide. It is used as a vegetable, minor food crop and a fodder crop, being a rich source of proteins, minerals, and essential fatty acids. However, little effort has been made to decipher the genetic and molecular basis of various useful traits in this crop. Therefore, we considered three economically important traits i.e., flowering, maturity and seed weight of rice bean and identified the associated candidate genes employing an associative transcriptomics approach on 100 diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank. Results: The transcriptomics-based genotyping of one-hundred diverse rice bean cultivars followed by pre-processing of genotypic data resulted in 49,271 filtered markers. The STRUCTURE, PCA and Neighbor-Joining clustering of 100 genotypes revealed three putative sub-populations. The marker-trait association analysis involving various genome-wide association study (GWAS) models revealed significant association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The transcript annotation provided information on the putative candidate genes for the considered traits. The candidate genes identified for flowering include HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A. Further, the WRKY1 and DEAD-box-RH27 were found to be associated with seed weight. Furthermore, the associations of PIF3 and pentatricopeptide-repeat-containing-gene with maturity and seed weight, and aldo–keto-reductase with flowering and maturity were revealed. Conclusion: This study offers insights into the genetic basis of key agronomic traits in rice bean, including flowering, maturity, and seed weight. The identified markers and associated candidate genes provide valuable resources for future exploration and targeted breeding, aiming to enhance the agronomic performance of rice bean cultivars. Notably, this research represents the first transcriptome-wide association study in pulse crop, uncovering the candidate genes for agronomically useful traits.Item Uncovering DNA methylation landscapes to decipher evolutionary footprints of phenotypic diversity in chickpea(Oxford University Press, 2024) Daware, Anurag; Mohanty, Jitendra K.; Narnoliya, Laxmi; Singh, Akansha; Rathore, Deepanshi; Thakro, Virevol; Francis, Aleena; Singh, Nagendra Pratap; Francis, Philip; Tripathi, Shailesh; Chattopadhyay, Debasis; Parida, Swarup K.Genetic diversity and environmental factors are long believed to be the dominant contributor to phenotypic diversity in crop plants. However, it has been recently established that, besides genetic variation, epigenetic variation, especially variation in DNA methylation, plays a significant role in determining phenotypic diversity in crop plants. Therefore, assessing DNA methylation diversity in crop plants becomes vital, especially in the case of crops like chickpea, which has a narrow genetic base. Thus, in the present study, we employed whole-genome bisulfite sequencing to assess DNA methylation diversity in wild and cultivated (desi and kabuli) chickpea. This revealed extensive DNA methylation diversity in both wild and cultivated chickpea. Interestingly, the methylation diversity was found to be significantly higher than genetic diversity, suggesting its potential role in providing vital phenotypic diversity for the evolution and domestication of the Cicer gene pool. The phylogeny based on DNA methylation variation also indicates a potential complementary role of DNA methylation variation in addition to DNA sequence variation in shaping chickpea evolution. Besides, the study also identified diverse epi-alleles of many previously known genes of agronomic importance. The Cicer MethVarMap database developed in this study enables researchers to readily visualize methylation variation within the genes and genomic regions of their interest (http://223.31.159.7/cicer/public/). Therefore, epigenetic variation like DNA methylation variation can potentially explain the paradox of high phenotypic diversity despite the narrow genetic base in chickpea and can potentially be employed for crop improvement.Item Role of plant neurotransmitters in salt stress: A critical review(Elsevier B.V., 2024) Malakar, Paheli; Gupta, Santosh K.; Chattopadhyay, DebasisNeurotransmitters are naturally found in many plants, but the molecular processes that govern their actions still need to be better understood. Acetylcholine, γ-Aminobutyric acid, histamine, melatonin, serotonin, and glutamate are the most common neurotransmitters in animals, and they all play a part in the development and information processing. It is worth noting that all these chemicals have been found in plants. Although much emphasis has been placed on understanding how neurotransmitters regulate mood and behaviour in humans, little is known about how they regulate plant growth and development. In this article, the information was reviewed and updated considering current thinking on neurotransmitter signaling in plants' metabolism, growth, development, salt tolerance, and the associated avenues for underlying research. The goal of this study is to advance neurotransmitter signaling research in plant biology, especially in the area of salt stress physiology.Item Updating the impact of drought on root exudation: A strigolactones perspective(Springer Nature Publishing AG, 2023) Singh, Nidhi; Chattopadhyay, Debasis; Gupta, Santosh KumarWith the changing global climate, drought is considered one of the most devastating abiotic factors. Drought not only limits plant productivity by changing growth and development but also alters the microbiome in the rhizosphere. In addition to influencing the root microbes, drought modifies the root exudate's composition and profile in the rhizosphere. Plant health, root exudation, and abundance of soil microbes in the rhizosphere are inter-connected. The composition of root exudate is altered in terms of the abundance of primary metabolites such as sugar, amino acids, and organic acids and secondary metabolites like flavonoids, strigolactones, and terpenoids. Here, we discuss how a plethora of soil microbes may be involved in a feedback mechanism by utilizing root exudate constituents to promote drought tolerance in plants. Furthermore, plant drought tolerance is positively associated with strigolactones (SLs) exudation via coordination with ABA hormone signaling. Lastly, while the collection, sampling, and analysis of root exudates are all promising, we attempted to present advanced methodology and the development of novel processes in the review, which benefited greatly.