Institutional Publications
Permanent URI for this collectionhttps://ndkr-library.nipgr.ac.in/handle/123456789/11
Browse
13 results
Search Results
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 Chickpea (Cicer arietinum) PHO1 family members function redundantly in Pi transport and root nodulation(Elsevier B.V., 2024) Mani, Balaji; Maurya, Kanika; Kohli, Pawandeep Singh; Giri, JitenderPhosphorus (P), a macronutrient, plays key roles in plant growth, development, and yield. Phosphate (Pi) transporters (PHTs) and PHOSPHATE1 (PHO1) are central to Pi acquisition and distribution. Potentially, PHO1 is also involved in signal transduction under low P. The current study was designed to identify and functionally characterize the PHO1 gene family in chickpea (CaPHO1s). Five CaPHO1 genes were identified through a comprehensive genome-wide search. Phylogenetically, CaPHO1s formed two clades, and protein sequence analyses confirmed the presence of conserved domains. CaPHO1s are expressed in different plant organs including root nodules and are induced by Pi-limiting conditions. Functional complementation of atpho1 mutant with three CaPHO1 members, CaPHO1, CaPHO1;like, and CaPHO1;H1, independently demonstrated their role in root to shoot Pi transport, and their redundant functions. To further validate this, we raised independent RNA-interference (RNAi) lines of CaPHO1, CaPHO1;like, and CaPHO1;H1 along with triple mutant line in chickpea. While single gene RNAi lines behaved just like WT, triple knock-down RNAi lines (capho1/like/h1) showed reduced shoot growth and shoot Pi content. Lastly, we showed that CaPHO1s are involved in root nodule development and Pi content. Our findings suggest that CaPHO1 members function redundantly in root to shoot Pi export and root nodule development in chickpea.Item Dissecting chickpea genomic loci associated with the root penetration responsive traits in compacted soil(Springer Nature Publishing AG, 2024) Donde, Ravindra; Kohli, Pawandeep Singh; Pandey, Mandavi; Sirohi, Ujjwal; Singh, Bhagat; Giri, JitenderSoil compaction is a major concern for modern agriculture, as it constrains plant root growth, leading to reduced resource acquisition. Phenotypic variation for root system architecture (RSA) traits in compacted soils is present for various crops; however, studies on genetic associations with these traits are lacking. Therefore, we investigated RSA traits in diferent soil compaction levels and identifed signifcant genomic associations in chickpea. We conducted a Genome-Wide Association Study (GWAS) of 210 chickpea accessions for 13 RSA traits under three bulk densities (BD) (1.1BD, 1.6BD, and 1.8BD). Soil compaction decreases root exploration by reducing 12 RSA traits, except average diameter (AD). Further, AD is negatively correlated with lateral root traits, and this correlation increases in 1.8BD, suggesting the negative efect of AD on lateral root traits. Interestingly, we identifed probable candidate genes such as GLP3 and LRX for lateral root traits and CRF1-like for total length (TL) in 1.6BD soil. In heavy soil compaction, DGK2 is associated with lateral root traits. Reduction in laterals during soil compaction is mainly due to delayed seedling establishment, thus making lateral root number a critical trait. Interestingly, we also found a higher contribution of the GxE component of the number of root tips (Tips) to the total variation than the other lateral traits. We also identifed a pectin esterase, PPE8B, associated with Tips in high soil compaction and a signifcantly associated SNP with the relative change in Tips depicting a trade-of between Tips and AD. Identifed genes and loci would help develop soil-compaction-resistant chickpea varieties.Item Abiotic stress impact on the interaction between Macrophomina phaseolina and crop plants(Springer Nature Publishing AG, 2024) Ranjan, Shubhashish; Mirchandani, Rishabh; Senthil-Kumar, MuthappaMacrophomina phaseolina (Tassi.) Goid is an emerging pathogen that causes diseases like dry root rot and charcoal rot in more than 100 plant families. Abiotic stresses such as drought, salinity, and heat exacerbate this fungal effect and predispose crops to pathogen attacks. Importantly, these combined stresses lead to significant crop yield losses under field conditions. In this, we review the interaction between the devastating pathogen M. phaseolina and several abiotic stresses that are more likely to occur in scenarios of climate change. Drought, heat, and salinity are the major stresses that interact with M. phaseolina in the field. We discuss several field studies, unique physiological and molecular responses, and their mechanisms of control in response to combined stress. The net effect of these interactions depends on a multitude of factors; thus, these interactions modify the impact of biotic stresses on plants by altering their susceptibility. The aim of this review is to provide an overview of what is currently known about M. phaseolina and abiotic stress interactions, as well as several other edaphic factors that interact with plants. We briefly discuss the role of drought, salinity, heat stress, and edaphic factors (such as pH, N, P, K, etc.) that influence pathogen infection in plants. Furthermore, we discuss possible management strategies to combat crop loss due to combined stress. Thus, we suggest the future aspect of combined stress breeding, along with the use of multi-omics techniques and genome editing approaches, to develop cultivars that exhibit stability in a combined stress environment.Item Genome-wide identification, characterization, and expression profiling of 14-3-3 genes in legumes(Springer Nature Publishing AG, 2022) Chakraborty, Srija; Soundararajan, Prabhakaran; Kumar, ShaileshIn plants, a large multigene family encodes 14-3-3 proteins, which are commonly found in eukaryotes. They are involved in plant development and environmental stress regulation. The current study aims to identify and characterize the 14-3-3 gene family in four important legumes, viz. Cicer arietinum, Cajanus cajan, Vigna radiata and Arachis hypogaea. The 14-3-3 proteins were clustered into ε and non-ε groups based on phylogenetic analysis, which was further confrmed by gene structure analysis, and motif composition analysis. Our study suggests that segmental duplication events played a pivotal role in the evolution and expansion of this gene family. Evidence of both stress-responsive, and hormone-responsive cis-regulatory elements in the promoter region of the 14-3-3 genes points to the possibility that they might be involved in the interplay between hormone and stress signalling pathways. The expression profling using RNA-seq data sets showed a variation in expression level in most 14-3-3 genes under multiple stress conditions, and in diferent developmental stages. Hence, this study afrms the participation of the 14-3-3 genes in multiple stress regulation, and in growth and development of the legumes. The results obtained from this study provide crucial information for improved understanding, and stress response analysis of the 14-3-3 gene family in C. arietinum, C. cajan, V. radiata and A. hypogaea.Item BURP domain-containing genes in legumes: genome-wide identification, structure, and expression analysis under stresses and development(Springer Nature Publishing AG, 2022) Chitkara, Pragya; Poddar, Nikita; Singh, Amarjeet; Kumar, ShaileshBURP domain-containing proteins are a plant-specific protein family which play an important role in plant metabolism and development. These proteins have also been involved in various abiotic and biotic stress responses. In this study, genome-wide identification and characterization of BURP domain protein encoding gene family is performed in four important legumes, Phaseolus vulgaris, Cicer arietinum, Cajanus cajan, and Vigna radiata. BURP genes were distributed randomly across chromosomes in all four legume plants. The phylogenetic analysis classified all BURP proteins into five major subfamilies, namely, USP-like, RD22-like, BNM2-like, PG1β-like, and BURPV. Our findings revealed that BURP gene family descended from common ancestors with segmental gene duplication events playing a critical role in their evolution and expansion in legumes. The intron–exon and conserved protein motifs analysis revealed that BURP genes are structurally conserved in legumes. The promoter analysis revealed the presence of hormone, and stress-responsive cis-regulatory elements in BURP promoters, implying that BURP functions in both hormone and abiotic stress signaling. Global expression analysis revealed that several BURP genes in all four legumes express differentially during plant development, and under biotic and abiotic stresses. This indicates crucial role of BURP proteins in regulating the development of legumes and adaptation to different abiotic/biotic stresses. This study will provide the starter for cloning and detail functional investigation of BURP proteins in legume crops.Item Quantitative phosphoproteomic analysis of legume using TiO2-based enrichment coupled with isobaric labeling(Springer Nature Publishing AG, 2020) Barua, Pragya; Lande, Nilesh Vikram; Kumar, Sunil; Chakraborty, Subhra; Chakraborty, NiranjanPhosphorylation of proteins is the most dynamic protein modification, and its analysis aids in determining the functional and regulatory principles of important cellular pathways. The legumes constitute the third largest family of higher plants, Fabaceae, comprising about 20,000 species and are second to cereals in agricultural importance on the basis of global production. Therefore, an understanding of the developmental and adaptive processes of legumes demands identification of their regulatory components. The most crucial signature of the legume family is the symbiotic nitrogen fixation, which makes this fascinating and interesting to investigate phosphorylation events. The research on protein phosphorylation in legumes has been focused primarily on two model species, Medicago truncatula and Lotus japonicus. The development of reciprocal research in other species, particularly the crops, is lagging behind which has limited its beneficial uses in agricultural productivity. In this chapter, we outline the titanium dioxide-based enrichment of phosphopeptides for nuclear proteome analysis of a grain legume, chickpea.Item Genotype-independent Agrobacterium rhizogenes-mediated root transformation of chickpea: a rapid and efficient method for reverse genetics studies(BioMed Central Ltd, 2018) Aggarwal, Pooja Rani; Nag, Papri; Choudhary, Pooja; Chakraborty, Niranjan; Chakraborty, SubhraBackground: Chickpea (Cicer arietinum L.), an important legume crop is one of the major source of dietary protein. Developing an efcient and reproducible transformation method is imperative to expedite functional genomics studies in this crop. Here, we present an optimized and detailed procedure for Agrobacterium rhizogenes-mediated root transformation of chickpea. Results: Transformation positive roots were obtained on selection medium after two weeks of A. rhizogenes inoculation. Expression of green fuorescent protein further confrmed the success of transformation. We demonstrate that our method adequately transforms chickpea roots at early developmental stage with high efciency. In addition, root transformation was found to be genotype-independent and the efcacy of our protocol was highest in two (Annigiri and JG-62) of the seven tested chickpea genotypes. Next, we present the functional analysis of chickpea hairy roots by expressing Arabidopsis TRANSPARENT TESTA 2 (AtTT2) gene involved in proanthocyanidins biosynthesis. Overexpression of AtTT2 enhanced the level of proanthocyanidins in hairy roots that led to the decreased colonization of fungal pathogen, Fusarium oxysporum. Furthermore, the induction of transgenic roots does not afect functional studies involving infection of roots by fungal pathogen. Conclusions: Transgenic roots expressing genes of interest will be useful in downstream functional characterization using reverse genetics studies. It requires 1 day to perform the root transformation protocol described in this study and the roots expressing transgene can be maintained for 3–4 weeks, providing sufcient time for further functional studies. Overall, the current methodology will greatly facilitate the functional genomics analyses of candidate genes in root-rhizosphere interaction in this recalcitrant but economically important legume crop.Item Legume proteomics: Progress, prospects and challenges(John Wiley & Sons, 2016) Rathi, Divya; Gayen, Dipak; Gayali, Saurabh; Chakraborty, Subhra; Chakraborty, NiranjanLegumes are the major sources of food and fodder with strong commercial relevance, and are essential components of agricultural ecosystems owing to their ability to carry out endosymbiotic nitrogen fixation. In recent years, legumes have become one of the major choices of plant research. The legume proteomics is currently represented by more than 100 reference maps and an equal number of stress-responsive proteomes. Among the 48 legumes in the protein databases, most proteomic studies have been accomplished in two model legumes, soybean, and barrel medic. This review highlights recent contributions in the field of legume proteomics to comprehend the defence and regulatory mechanisms during development and adaptation to climatic changes. Here, we attempted to provide a concise overview of the progress in legume proteomics and discuss future developments in three broad perspectives: (i) proteome of organs/tissues; (ii) subcellular compartments; and (iii) spatiotemporal changes in response to stress. Such data mining may aid in discovering potential biomarkers for plant growth, in general, apart from essential components involved in stress tolerance. The prospect of integrating proteome data with genome information from legumes will provide exciting opportunities for plant biologists to achieve long-term goals of crop improvement and sustainable agriculture.Item Genome-wide analysis of homeobox gene family in legumes: identification, gene duplication and expression profiling(PLOS, 2015) Bhattacharjee, Annapurna; Ghangal, Rajesh; Garg, Rohini; Jain, MukeshHomeobox genes encode transcription factors that are known to play a major role in different aspects of plant growth and development. In the present study, we identified homeobox genes belonging to 14 different classes in five legume species, including chickpea, soybean, Medicago, Lotus and pigeonpea. The characteristic differences within homeodomain sequences among various classes of homeobox gene family were quite evident. Genome-wide expression analysis using publicly available datasets (RNA-seq and microarray) indicated that homeobox genes are differentially expressed in various tissues/developmental stages and under stress conditions in different legumes. We validated the differential expression of selected chickpea homeobox genes via quantitative reverse transcription polymerase chain reaction. Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family. The Ka/Ks ratio of duplicated homeobox genes in soybean showed that several members of this family have undergone purifying selection. Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization. The genome-wide identification and comprehensive gene expression profiling of homeobox gene family members in legumes will provide opportunities for functional analysis to unravel their exact role in plant growth and development.