Browsing by Author "Chattopadhyay, Debasis"

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Adaptation of plants to salt stress: the role of the ion transporters
(Springer Nature Publishing AG, 2021) Malakar, Paheli; Chattopadhyay, Debasis
Adaptation to high salinity is achieved by cellular ion homeostasis which involves regulation of toxic sodium ion (Na+) and Chloride ion (Cl−) uptake, preventing the transport of these ions to the aerial parts of the plants and vacuolar sequestration of these toxic ions. Ion transporters have long been known to play roles in maintaining ion homeostasis. Na+ enters the cell through various voltage dependent selective and non-selective ion channels. High Na+ concentration in the plasma membrane is balanced either by uptake of potassium ion (K+) by various potassium importing channels, by salt exclusion mechanism or by sequestration of Na+ in the vacuoles. Therefore, the role of high-affinity potassium transporter, the salt overly sensitive pathway, the most well-defined Na+ exclusion pathway that exports Na+ from cell into xylem and tonoplast localized cation transporters that compartmentalizes Na+ in vacuoles need to be studied in detail and applied to make the plant adaptable to saline soil. Knowledge on the regulation of expression of these transporters by the hormones, microRNAs and other non-coding RNAs can be utilized to manipulate the ion transport. Here, we reviewed paradigm of the ion transporters in salt stress signalling pathways from the recent and past studies aiding transformation of basic knowledge into biotechnological applications to generate engineered salt stress tolerant crops.
An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.)
(Nature Publishing Group, 2015) Parween, Sabiha; Nawaz, Kashif; Roy, Riti; Pole, Anil K.; Venkata Suresh, B.; Misra, Gopal; Jain, Mukesh; Yadav, Gitanjali; Parida, Swarup K.; Tyagi, Akhilesh K.; Bhatia, Sabhyata; Chattopadhyay, Debasis
Chickpea (Cicer arietinum L.) is an important pulse legume crop. We previously reported a draft genome assembly of the desi chickpea cultivar ICC 4958. Here we report an advanced version of the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and an improved genetic map. This resulted in 2.7-fold increase in the length of the pseudomolecules and substantial reduction of sequence gaps. The genome assembly covered more than 94% of the estimated gene space and predicted the presence of 30,257 protein-coding genes including 2230 and 133 genes encoding potential transcription factors (TF) and resistance gene homologs, respectively. Gene expression analysis identified several TF and chickpea-specific genes with tissue-specific expression and displayed functional diversification of the paralogous genes. Pairwise comparison of pseudomolecules in the desi (ICC 4958) and the earlier reported kabuli (CDC Frontier) chickpea assemblies showed an extensive local collinearity with incongruity in the placement of large sequence blocks along the linkage groups, apparently due to use of different genetic maps. Single nucleotide polymorphism (SNP)-based mining of intra-specific polymorphism identified more than four thousand SNPs differentiating a desi group and a kabuli group of chickpea genotypes.
Analysis of gene expression in response to water deficit of chickpea (Cicer arietinum L.) varieties differing in drought tolerance
(BioMed Central, 2010) Jain, Deepti; Chattopadhyay, Debasis
Chickpea (C. arietinum L.) ranks third in food legume crop production in the world. However, drought poses a serious threat to chickpea production, and development of drought-resistant varieties is a necessity. Unfortunately, cultivated chickpea has a high morphological but narrow genetic diversity, and understanding the genetic processes of this plant is hindered by the fact that the chickpea genome has not yet been sequenced and its EST resources are limited. In this study, two chickpea varieties having contrasting levels of drought-tolerance were analyzed for differences in transcript profiling during drought stress treatment by withdrawal of irrigation at different time points. Transcript profiles of ESTs derived from subtractive cDNA libraries constructed with RNA from whole seedlings of both varieties were analyzed at different stages of stress treatment.
Assessment of diversity in anti-nutrient profile, resistant starch, minerals and carbohydrate components in different ricebean (Vigna umbellata) accessions
(Elsevier B.V., 2023) Sharma, Paras; Goudar, Giridhar; Chandragiri, Anil Kumar; Ananthan, R; Subhash, K; Chauhan, Anitha; Longvah, T; Singh, Mohar; Bhardwaj, Rakesh; Parida, Swarup K.; Singh, Amit Kumar; Gayacharan; Chattopadhyay, Debasis
Ricebean accessions (n = 38) cultivated in India were evaluated for their comprehensive nutrient, anti-nutrients and mineral composition. Protein and total dietary fibre ranged between 23.23 and 27.33 and 12.27 to 16.69 g/100 g, respectively. Among the oligosaccharides, verbascose was not detected, however, raffinose and stachyose ranged between 47 and 186 and 117 to 5765 mg/100 g, respectively. Among the free sugars, sucrose was found dominating (up to 370 mg/100 g). Resistant starch (4.13 to 8.62 %), iron (3.49 to 7.46 mg/100 g), zinc (1.90 to 3.72 mg/100 g) and selenium (0.28 to 4.48 µg/100 g) varied significantly (p < 0.05) among ricebean samples. Phytic acid, saponin, trypsin inhibitor and oxalate analysed in ricebean accessions ranged between 303 and 760 mg/100 g, 19 to 46 mg/g, 309 to 1076 mg/100 g and 219 to 431 mg/100 g, respectively. Multivariate analysis using hierarchical clustering analysis (HCA), and principal component analysis (PCA) was employed to decipher the diversity of nutrients and anti-nutrients across the ricebean accessions. Based on HCA, dendrogram-1 (nutrients) and dendrogram-2 (minerals, anti-nutrients) were produced, having four clusters in each. In the dendrogram-1 and 2, the largest cluster had (n = 21) and (n = 15) accessions, respectively. The PCA analyse the uncorrelated set of variables (principal components) and it condenses a large set of data variables. Based on the eigenvalue >1, a total of eight PCs were formed contributing total variance of 78.8 %. The factor loading contribution in the PC1 and PC2 were from iron, fructose, glucose, raffinose and total dietary fibre, selenium (Se) and protein, respectively.
Biochemical analysis of anthocyanin and proanthocyanidin and their regulation in determining chickpea flower and seed coat colours
(Oxford University Press, 2023) Pal, Lalita; Dwivedi, Vikas; Gupta, Santosh Kumar; Saxena, Samiksha; Pandey, Ashutosh; Chattopadhyay, Debasis
Flower and seed coat colour are important agronomic traits in chickpea (Cicer arietinum L.). Cultivated chickpeas are of two types namely, desi (dark seeded, purple flower) and kabuli (light colour seeded, white flower). There has been limited information about the molecular mechanism underlying the colour variation of flower and seed coats in desi and kabuli chickpea. We profiled the anthocyanin and proanthocyanidin (PA) contents in chickpea flowers and seed coats. Tissue-specific silencing of two genes encoding a basic helix-loop-helix (CabHLH) protein and a tonoplast-localized multidrug and toxic compound extrusion (CaMATE1) transporter in a desi genotype resulted in the reduction in expressions of anthocyanin and PA biosynthetic genes and anthocyanin and PA contents in the flower and seed coat and produced flowers and seeds with kabuli characteristics. Transcriptional regulation of a subset of anthocyanin and PA biosynthetic genes by a natural CabHLH variant and transport assay of a natural CaMATE1 variant explained the association of these alleles with the kabuli phenotype. We carried out a detailed molecular characterization of these genes, and provided evidences that kabuli chickpea flower and seed colour phenotype can be derived by manipulation of single genes in a desi chickpea background.
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, Ashutosh
The 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.
CAP2 enhances germination of transgenic tobacco seeds at high temperature and promotes heat stress tolerance in yeast
(Wiley-Blackwell, 2009) Shukla, Rakesh Kumar; Tripathi, Vineeta; Jain, Deepti; Yadav, Rajiv Kumar; Chattopadhyay, Debasis
We reported earlier that ectopic expression of CAP2, a single AP2 domain containing transcription activator from chickpea (Cicer arietinum) in tobacco improves growth and development, and tolerance to dehydration and salt stress, of the transgenic plants. Here, we report that, in addition, the CAP2-transgenic tobacco seeds also exhibit higher germination efficiency at high temperature and show higher expression levels of genes for tobacco heat shock proteins and a heat shock factor. CAP2 was able to activate the 5¢-upstream activating sequence of tobacco heat shock factor. Surprisingly, expression of CAP2 cDNA in Saccharomyces cerevisiae also enhanced heat tolerance, with increased expression of the gene for yeast heat shock factor 1 (Hsf1) and its target, the gene for yeast heat shock protein 104 (Hsp104). Sequence analysis of the Hsf1 promoter revealed the presence of a dehydration-responsive element ⁄ C-repeat-like element (DRE/ CRE). Recombinant CAP2 protein bound to the DRE/CRE in the Hsf1 promoter in a gel shift assay and transactivated the Hsf1 promoter–His reporter construct. The full-length CAP2 protein was required to provide thermotolerance in yeast. If these findings are taken together, our results suggest that CAP2 is involved in the heat stress response and provides an example of functioning of a plant transcription factor in yeast, highlighting the strong evolutionary conservation of the stress response mechanism.
CaZF, a plant transcription factor functions through and parallel to HOG and calcineurin pathways in Saccharomyces cerevisiae to provide osmotolerance
(PLOS, 2009) Jain, Deepti; Roy, Nilanjan; Chattopadhyay, Debasis
Salt-sensitive yeast mutants were deployed to characterize a gene encoding a C2H2 zinc finger protein (CaZF) that is differentially expressed in a drought-tolerant variety of chickpea (Cicer arietinum) and provides salinity-tolerance in transgenic tobacco. In Saccharomyces cerevisiae most of the cellular responses to hyper-osmotic stress is regulated by two interconnected pathways involving high osmolarity glycerol mitogen-activated protein kinase (Hog1p) and Calcineurin (CAN), a Ca(2+)/calmodulin-regulated protein phosphatase 2B. In this study, we report that heterologous expression of CaZF provides osmotolerance in S. cerevisiae through Hog1p and Calcineurin dependent as well as independent pathways. CaZF partially suppresses salt-hypersensitive phenotypes of hog1, can and hog1can mutants and in conjunction, stimulates HOG and CAN pathway genes with subsequent accumulation of glycerol in absence of Hog1p and CAN. CaZF directly binds to stress response element (STRE) to activate STRE-containing promoter in yeast. Transactivation and salt tolerance assays of CaZF deletion mutants showed that other than the transactivation domain a C-terminal domain composed of acidic and basic amino acids is also required for its function. Altogether, results from this study suggests that CaZF is a potential plant salt-tolerance determinant and also provide evidence that in budding yeast expression of HOG and CAN pathway genes can be stimulated in absence of their regulatory enzymes to provide osmotolerance.
CBL-interacting protein kinase 25 contributes to root meristem development
(Oxford University Press, 2019) Meena, Mukesh Kumar; Vishwakarma, Niraj Kumar; Tripathi, Vineeta; Chattopadhyay, Debasis
Coordination of auxin and cytokinin activities determines root meristem size during post-embryonic development. Calcineurin B-like proteins (CBLs) and their interacting protein kinases (CIPKs) constitute signaling modules that relay calcium signals. Here we report that CIPK25 is involved in regulating the root meristem size. Arabidopsis plants lacking CIPK25 expression displayed a short root phenotype and a slower root growth rate with less meristem cells. This phenotype was rescued by restoration of CIPK25 expression. CIPK25 interacted with CBL4 and -5, and displayed a strong gene expression in the flower and root except in the cell proliferation domain in the root apical meristem. Its expression in root was positively and negatively regulated by auxin and cytokinin, respectively. cipk25 T-DNA insertion line was compromised in auxin transport and auxin-responsive promoter activity. cipk25 mutant line showed altered expression of auxin efflux carriers and an Aux/IAA family gene SHY2. Decreased PIN1 and PIN2 expression in cipk25 mutant line was completely restored when combined with SHY2 loss-of-function mutation resulting in recovery of root growth. SHY2 and PIN1 expression was partially regulated by cytokinin even in absence of CIPK25, suggesting existence of CIPK25-independent cytokinin signaling pathway(s) as well. Our results suggested a role of CIPK25 in root meristem development.
CBL-interacting protein kinase 6 negatively regulates immune response to Pseudomonas syringae in Arabidopsis
(Oxford University Press, 2017) Sardar, Atish; Nandi, Ashis Kumar; Chattopadhyay, Debasis
Cytosolic calcium ion (Ca2+) is an essential mediator of the plant innate immune response. Here, we report that a calcium-regulated protein kinase Calcineurin B-like protein (CBL)-interacting protein kinase 6 (CIPK6) functions as a negative regulator of immunity against the bacterial pathogen Pseudomonas syringae in Arabidopsis thaliana. Arabidopsis lines with compromised expression of CIPK6 exhibited enhanced disease resistance to the bacterial pathogen and to P. syringae harboring certain but not all avirulent effectors, while restoration of CIPK6 expression resulted in abolition of resistance. Plants overexpressing CIPK6 were more susceptible to P. syringae. Enhanced resistance in the absence of CIPK6 was accompanied by increased accumulation of salicylic acid and elevated expression of defense marker genes. Salicylic acid accumulation was essential for improved immunity in the absence of CIPK6. CIPK6 negatively regulated the oxidative burst associated with perception of pathogen-associated microbial patterns (PAMPs) and bacterial effectors. Accelerated and enhanced activation of the mitogen-activated protein kinase cascade in response to bacterial and fungal elicitors was observed in the absence of CIPK6. The results of this study suggested that CIPK6 negatively regulates effector-triggered and PAMP-triggered immunity in Arabidopsis.
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, Debasis
Plant 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.
A chickpea genetic variation map based on the sequencing of 3,366 genomes
(Springer Nature Publishing AG, 2021) Varshney, Rajeev K; Roorkiwal, Manish; Sun, Shuai; Bajaj, Prasad; Chitikineni, Annapurna; Thudi, Mahendar; Singh, Narendra P; Du, Xiao; Upadhyaya, Hari D; Khan, Aamir W; Wang, Yue; Garg, Vanika; Fan, Guangyi; Cowling, Wallace A; Crossa, José; Gentzbittel, Laurent; Voss-Fels, Kai Peter; Valluri, Vinod Kumar; Sinha, Pallavi; Singh, Vikas K; Ben, Cécile; Rathore, Abhishek; Punna, Ramu; Singh, Muneendra K; Tar'an, Bunyamin; Bharadwaj, Chellapilla; Yasin, Mohammad; Pithia, Motisagar S; Singh, Servejeet; Soren, Khela Ram; Kudapa, Himabindu; Jarquín, Diego; Cubry, Philippe; Hickey, Lee T; Dixit, Girish Prasad; Thuillet, Anne-Céline; Hamwieh, Aladdin; Kumar, Shiv; Deokar, Amit A; Chaturvedi, Sushil K; Francis, Aleena; Howard, Réka; Chattopadhyay, Debasis; Edwards, David; Lyons, Eric; Vigouroux, Yves; Hayes, Ben J; Wettberg, Eric von; Datta, Swapan K; Yang, Huanming; Nguyen, Henry T; Wang, Jian; Siddique, Kadambot H M; Mohapatra, Trilochan; Bennetzen, Jeffrey L; Xu, Xun; Liu, Xin
Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.
The chickpea genomic web resource: visualization and analysis of the desi-type Cicer arietinum nuclear genome for comparative exploration of legumes
(BioMed Central Ltd, 2014) Misra, Gopal; Priya, Piyush; Bandhiwal, Nitesh; Bareja, Neha; Jain, Mukesh; Bhatia, Sabhyata; Chattopadhyay, Debasis; Tyagi, Akhilesh K.; Yadav, Gitanjali
Background: Availability of the draft nuclear genome sequences of small-seeded desi-type legume crop Cicer arietinum has provided an opportunity for investigating unique chickpea genomic features and evaluation of their biological significance. The increasing number of legume genome sequences also presents a challenge for developing reliable and information-driven bioinformatics applications suitable for comparative exploration of this important class of crop plants. Results: The Chickpea Genomic Web Resource (CGWR) is an implementation of a suite of web-based applications dedicated to chickpea genome visualization and comparative analysis, based on next generation sequencing and assembly of Cicer arietinum desi-type genotype ICC4958. CGWR has been designed and configured for mapping, scanning and browsing the significant chickpea genomic features in view of the important existing and potential roles played by the various legume genome projects in mutant mapping and cloning. It also enables comparative informatics of ICC4958 DNA sequence analysis with other wild and cultivated genotypes of chickpea, various other leguminous species as well as several non-leguminous model plants, to enable investigations into evolutionary processes that shape legume genomes. Conclusions: CGWR is an online database offering a comprehensive visual and functional genomic analysis of the chickpea genome, along with customized maps and gene-clustering options. It is also the only plant based web resource supporting display and analysis of nucleosome positioning patterns in the genome. The usefulness of CGWR has been demonstrated with discoveries of biological significance made using this server. The CGWR is compatible with all available operating systems and browsers, and is available freely under the open source license at http://www.nipgr.res.in/CGWR/home.php.
The chickpea WIP2 gene underlying a major QTL contributes to lateral root development
(Oxford University Press, 2024) Dwivedi, Vikas; Pal, Lalita; Singh, Shilpi; Singh, Nagendra Pratap; Parida, Swarup K.; Chattopadhyay, Debasis
Lateral root is a major component of root system architecture and lateral root count (LRC) positively contributes to yield under drought in chickpea. To understand the genetic regulation of LRC, a biparental mapping population derived from two chickpea accessions having contrasting LRC was genotyped by sequencing and phenotyped to map four major quantitative trait loci (QTLs) contributing to 13 to 32% of the LRC trait variation. A SNP tightly linked to the locus contributing to highest trait variation was located on the coding region of a gene (CaWIP2) orthologous to WIP2 gene of Arabidopsis thaliana. A polymorphic simple sequence repeat (SSR) in the CaWIP2 promoter showed differentiation between low vs. high LRC parents and mapping individuals suggesting its utility for marker-assisted selection. CaWIP2 promoter showed strong activities in chickpea apical root meristem and lateral root primordia. Expression of CaWIP2 under its native promoter in Arabidopsis wip2wip4wip5 mutant rescued its root-less phenotype to produce more lateral root than the wild type plants and led to formation of amyloplasts in the columella. CaWIP2 expression also induced expression of genes that regulate lateral root emergence. Our study identified a gene-based marker for LRC which will be useful to develop drought tolerant high-yielding chickpea.
CIPK6, a CBL-interacting protein kinase is required for development and salt tolerance in plant
(Wiley-Blackwell, 2009) Tripathi, Vineeta; Parasuraman, Boominathan; Laxmi, Ashverya; Chattopadhyay, Debasis
Calcineurin B-like proteins (CBL) and CBL-interacting protein kinases (CIPK) mediate plant responses to a variety of external stresses. Here we report that Arabidopsis CIPK6 is also required for the growth and development of plants. Phenotype of tobacco plants ectopically expressing a homologous gene (CaCIPK6) from the leguminous plant chickpea (Cicer arietinum) indicated its functional conservation. A lesion in AtCIPK6 significantly reduced shoot-to-root and root basipetal auxin transport, and the plants exhibited developmental defects such as fused cotyledons, swollen hypocotyls and compromised lateral root formation, in conjunction with reduced expression of a number of genes involved in auxin transport and abiotic stress response. The Arabidopsis mutant was more sensitive to salt stress compared to wild-type, while overexpression of a constitutively active mutant of CaCIPK6 promoted salt tolerance in transgenic tobacco. Furthermore, tobacco seedlings expressing the constitutively active mutant of CaCIPK6 showed a developed root system, increased basipetal auxin transport and hypersensitivity to auxin. Our results provide evidence for involvement of a CIPK in auxin transport and consequently in root development, as well as in the salt-stress response, by regulating the expression of genes.
A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea
(Nature Publishing Group, 2015) Bajaj, Deepak; Upadhyaya, Hari D.; Khan, Yusuf; Das, Shouvik; Badoni, Saurabh; Shree, Tanima; Kumar, Vinod; Tripathi, Shailesh; Gowda, C. L. L.; Singh, Sube; Sharma, Shivali; Tyagi, Akhilesh K.; Chattopadhyay, Debasis; Parida, Swarup K.
High experimental validation/genotyping success rate (94-96%) and intra-specific polymorphic potential (82-96%) of 1536 SNP and 472 SSR markers showing in silico polymorphism between desi ICC 4958 and kabuli ICC 12968 chickpea was obtained in a 190 mapping population (ICC 4958 × ICC 12968) and 92 diverse desi and kabuli genotypes. A high-density 2001 marker-based intra-specific genetic linkage map comprising of eight LGs constructed is comparatively much saturated (mean map-density: 0.94 cM) in contrast to existing intra-specific genetic maps in chickpea. Fifteen robust QTLs (PVE: 8.8-25.8% with LOD: 7.0-13.8) associated with pod and seed number/plant (PN and SN) and 100 seed weight (SW) were identified and mapped on 10 major genomic regions of eight LGs. One of 126.8 kb major genomic region harbouring a strong SW-associated robust QTL (Caq'SW1.1: 169.1-171.3 cM) has been delineated by integrating high-resolution QTL mapping with comprehensive marker-based comparative genome mapping and differential expression profiling. This identified one potential regulatory SNP (G/A) in the cis-acting element of candidate ERF (ethylene responsive factor) TF (transcription factor) gene governing seed weight in chickpea. The functionally relevant molecular tags identified have potential to be utilized for marker-assisted genetic improvement of chickpea.
Criteria for the choice of plant species for genome sequencing, to advance plant biology and agriculture
(Indian Academy of Sciences, 2006) Kumar, Sushil; Chattopadhyay, Debasis; Prasad, Manoj
Information from genome sequences is essential to understand the organization of genomes, chromosomes, genes, regulatory and repetitive elements present in plant genomes and also to understand the evolutionary significance of variations observed in genome compositions. Understandably, the plant genome sequencing effort has been growing in recent years, since the plant genome organization is not fully understood. The genome sequences of Arabidopsis thaliana and rice have been completed and a draft sequence of the poplar genome (http://genome.jgi- psf.org/Poptr1/Poptr1.home.html) has also been completed.
Decoding and relay of calcium signals by CBL-CIPK module in plants
(Indian National Science Academy, 2019) Meena, Mukesh Kumar; Sardar, Atish; Chattopadhyay, Debasis
Calcium is an essential macronutrient and a second messenger for signal transduction in plants. Apart from acting as a second messenger, calcium is also required for cytoskeleton, cell division, pollen tube growth and as a co-factor. Cytoplasmic calcium ion ([Ca2+](cyt)) is maintained at a low level, however, is rapidly elevated using storages in organelles on perception of a stimulus. Ca2+-binding proteins that sense the kinetics and magnitude of elevated [Ca2+](cyt) convert the chemical signals to biological signals and define specificity of responses. These proteins are broadly classified into sensor relays and sensor responders. Sensor relay proteins require another interacting protein to transmit the signal; whereas, the sensor responders combine within one protein the relay, amplification and response functions. A significant achievement has been made in the last three decades that identified and characterized various proteins instrumental in decoding Ca2+-signals in plant cells. The latest addition in Ca2+-signaling is Calcineurin B-like proteins (CBLs) and their interacting kinases (CIPKs). It is believed that flexibility of interactions between different CBL and CIPK proteins and their sub-cellular localizations are crucial in sensing and responding to specific signals. In this review, we have laid emphasis on the recent and emerging advancements in understanding of the CBL-CIPK module.
Development and integration of genome-wide polymorphic microsatellite markers onto a reference linkage map for constructing a high-density genetic map of chickpea
(PLOS, 2015) Khajuria, Yash Paul; Saxena, Maneesha S.; Gaur, Rashmi; Chattopadhyay, Debasis; Jain, Mukesh; Parida, Swarup K.; Bhatia, Sabhyata
The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777) of an inter-specific reference mapping population. High amplification efficiency (87%), experimental validation success rate (81%) and polymorphic potential (55%) of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48%) detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic potential (59%). An advanced, high-density, integrated and inter-specific chickpea genetic map (ICC4958 x PI489777) having 1697 map positions spanning 1061.16 cM with an average inter-marker distance of 0.625 cM was constructed by assigning 634 novel informative transcript-derived and genomic microsatellite markers on eight linkage groups (LGs) of our prior documented, 1063 marker-based genetic map. The constructed genome map identified 88, including four major (7-23 cM) longest high-resolution genomic regions on LGs 3, 5 and 8, where the maximum number of novel genomic and genic microsatellite markers were specifically clustered within 1 cM genetic distance. It was for the first time in chickpea that in silico FLP analysis at genome-wide level was carried out and such a large number of microsatellite markers were identified, experimentally validated and further used in genetic mapping. To best of our knowledge, in the presently constructed genetic map, we mapped highest number of new sequence-based robust microsatellite markers (634) which is an advancement over the previously documented (~300 markers) inter-specific genetic maps. This advanced high-density map will serve as a foundation for large-scale marker validation and genotyping applications, including identification and targeted mapping of trait-specific genes/QTLs (quantitative trait loci) with sub-optimal use of resources and labour in chickpea.
Development of an Agrobacterium-delivered codon-optimized CRISPR/Cas9 system for chickpea genome editing
(Springer Nature Publishing AG, 2023) Gupta, Santosh Kumar; Vishwakarma, Niraj Kumar; Malakar, Paheli; Vanspati, Poonam; Sharma, Nilesh Kumar; Chattopadhyay, Debasis
Chickpea is considered recalcitrant to in vitro tissue culture amongst all edible legumes. The clustered, regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)–based genome editing in chickpea can remove the bottleneck of limited genetic variation in this cash crop, which is rich in nutrients and protein. However, generating stable mutant lines using CRISPR/Cas9 requires efficient and highly reproducible transformation protocols. As an attempt to solve this problem, we developed a modified and optimized protocol for chickpea transformation. This study transformed the single cotyledon half-embryo explants using CaMV35S promoter to drive two marker genes (β-glucuronidase gene; GUS and green fluorescent protein; GFP) through binary vectors pBI101.2 and modified pGWB2, respectively. These vectors were delivered in the explants through three different strains of Agrobacterium tumefaciens, viz., GV3101, EHA105, and LBA4404. We found better efficiency with the strain GV3101 (17.56%) compared with two other strains, i.e., 8.54 and 5.43%, respectively. We recorded better regeneration frequencies in plant tissue culture for the constructs GUS and GFP, i.e., 20.54% and 18.09%, respectively. The GV3101 was further used for the transformation of the genome editing construct. For the development of genome-edited plants, we used this modified protocol. We also used a modified binary vector pPZP200 by introducing a CaMV35S-driven chickpea codon-optimized SpCas9 gene. The promoter of the Medicago truncatula U6.1 snRNA gene was used to drive the guide RNA cassettes. This cassette targeted and edited the chickpea phytoene desaturase (CaPDS) gene. A single gRNA was found sufficient to achieve high efficiency (42%) editing with the generation of PDS mutants with albino phenotypes. A simple, rapid, highly reproducible, stable transformation and CRISPR/Cas9-based genome editing system for chickpea was established. This study aimed to demonstrate this system’s applicability by performing a gene knockout of the chickpea PDS gene using an improved chickpea transformation protocol for the first time.