Publications of NIPGR Scientists

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Author: search.filters.author.Jain, MukeshSubject: search.filters.subject.Chickpea

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    Differential regulation of genes involved in root morphogenesis and cell wall modification is associated with salinity tolerance in chickpea
    (Nature Publishing Group, 2018) Kaashyap, Mayank; Ford, Rebecca; Kudapa, Himabindu; Jain, Mukesh; Edwards, Dave; Varshney, Rajeev; Mantri, Nitin
    Salinity is a major constraint for intrinsically salt sensitive grain legume chickpea. Chickpea exhibits large genetic variation amongst cultivars, which show better yields in saline conditions but still need to be improved further for sustainable crop production. Based on previous multi-location physiological screening, JG 11 (salt tolerant) and ICCV 2 (salt sensitive) were subjected to salt stress to evaluate their physiological and transcriptional responses. A total of ~480 million RNA-Seq reads were sequenced from root tissues which resulted in identification of 3,053 differentially expressed genes (DEGs) in response to salt stress. Reproductive stage shows high number of DEGs suggesting major transcriptional reorganization in response to salt to enable tolerance. Importantly, cationic peroxidase, Aspartic ase, NRT1/PTR, phosphatidylinositol phosphate kinase, DREB1E and ERF genes were significantly up-regulated in tolerant genotype. In addition, we identified a suite of important genes involved in cell wall modification and root morphogenesis such as dirigent proteins, expansin and casparian strip membrane proteins that could potentially confer salt tolerance. Further, phytohormonal cross-talk between ERF and PIN-FORMED genes which modulate the root growth was observed. The gene set enrichment analysis and functional annotation of these genes suggests they may be utilised as potential candidates for improving chickpea salt tolerance.
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    CTDB: an integrated chickpea transcriptome database for functional and applied genomics
    (PLOS, 2015) Verma, Mohit; Kumar, Vinay; Patel, Ravi K.; Garg, Rohini; Jain, Mukesh
    Chickpea is an important grain legume used as a rich source of protein in human diet. The narrow genetic diversity and limited availability of genomic resources are the major constraints in implementing breeding strategies and biotechnological interventions for genetic enhancement of chickpea. We developed an integrated Chickpea Transcriptome Database (CTDB), which provides the comprehensive web interface for visualization and easy retrieval of transcriptome data in chickpea. The database features many tools for similarity search, functional annotation (putative function, PFAM domain and gene ontology) search and comparative gene expression analysis. The current release of CTDB (v2.0) hosts transcriptome datasets with high quality functional annotation from cultivated (desi and kabuli types) and wild chickpea. A catalog of transcription factor families and their expression profiles in chickpea are available in the database. The gene expression data have been integrated to study the expression profiles of chickpea transcripts in major tissues/organs and various stages of flower development. The utilities, such as similarity search, ortholog identification and comparative gene expression have also been implemented in the database to facilitate comparative genomic studies among different legumes and Arabidopsis. Furthermore, the CTDB represents a resource for the discovery of functional molecular markers (microsatellites and single nucleotide polymorphisms) between different chickpea types. We anticipate that integrated information content of this database will accelerate the functional and applied genomic research for improvement of chickpea. The CTDB web service is freely available at http://nipgr.res.in/ctdb.html.
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    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.
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    Discovery of molecular markers for Fusarium wilt via transcriptome sequencing of chickpea cultivars
    (Springer, 2015) Jain, Mukesh; Pole, Anil K.; Singh, Vikash K.; Ravikumar, Ramapura L.; Garg, Rohini
    The wilt caused by Fusarium oxysporum f.sp. Ciceris is a major problem for chickpea. The large-scale discovery of DNA polymorphisms in different cultivars can provide insights into the genetic basis of phenotypic differences. In the present study, we sequenced the transcriptomes of four chickpea cultivars with contrasting response to Fusarium infection, including susceptible JG62 and resistant/tolerant ICCV2, K850 and WR315. Based on the analysis of their transcriptome sequences, we identified at least 303 polymorphic microsatellites, of which 64 % could be physically mapped on the chickpea genome. Further, we identified a total of 14,462 single nucleotide polymorphisms (SNPs) and 1864 insertions/deletions (InDels) among the chickpea cultivars analysed. More than 50 % of the SNPs and 19 % of the InDels were detected in the predicted coding regions, and about 46 % of these SNPs resulted in nonsynonymous changes. In addition, we identified at least 60 large-effect SNPs and 248 InDels that affected the integrity of the encoded protein. Several defence-related genes involved in different cellular processes were found to harbour nonsynonymous and/or large-effect SNPs and/or InDels. These data will provide functional markers and promising target genes for wilt resistance and present a valuable resource for molecular breeding for this important trait in chickpea.
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    Genome-scale transcriptomic insights into molecular aspects of abiotic stress responses in chickpea
    (Springer, 2015) Garg, Rohini; Bhattacharjee, Annapurna; Jain, Mukesh
    Chickpea is an important legume crop plant and various abiotic stresses are the major constraints affecting its overall productivity. For discovery of candidate genes involved in abiotic stress responses, we employed RNA sequencing for transcriptome profiling of roots and shoots of chickpea seedlings subjected to desiccation, salinity, and cold stresses. In total, we generated more than 250 million high-quality reads from non-stressed and stressed tissue samples. Data analyses provided a comprehensive view of the dynamic transcriptional response of chickpea tissues to different abiotic stresses. Differential expression analysis identified a total of 11,640 chickpea transcripts showing response to at least one of the stress conditions. The reference-based transcriptome assembly was generated and at least 3,536 previously unannotated gene loci differentially expressed under abiotic stress conditions were identified. We observed extensive transcriptional reprogramming of genes involved in transcription regulation, energy metabolism, photosynthesis, hormonal responses, secondary metabolite biosynthesis and osmoprotectant metabolism under stress conditions. In addition, genes involved in post-translational modifications, RNA metabolic processes, and epigenetic regulation were also significantly highlighted. The comprehensive transcriptome analyses presented in this study revealed several potential key regulators of plant response to abiotic stresses and open avenues to carry out functional and applied genomic studies for improving abiotic stress tolerance in chickpea.
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    Transcriptome analysis of Catharanthus roseus for gene discovery and expression profiling
    (PLOS, 2014) Verma, Mohit; Ghangal, Rajesh; Sharma, Raghvendra; Sinha, Alok Krishna; Jain, Mukesh
    The medicinal plant, Catharanthus roseus, accumulates wide range of terpenoid indole alkaloids, which are well documented therapeutic agents. In this study, deep transcriptome sequencing of C. roseus was carried out to identify the pathways and enzymes (genes) involved in biosynthesis of these compounds. About 343 million reads were generated from different tissues (leaf, flower and root) of C. roseus using Illumina platform. Optimization of de novo assembly involving a two-step process resulted in a total of 59,220 unique transcripts with an average length of 1284 bp. Comprehensive functional annotation and gene ontology (GO) analysis revealed the representation of many genes involved in different biological processes and molecular functions. In total, 65% of C. roseus transcripts showed homology with sequences available in various public repositories, while remaining 35% unigenes may be considered as C. roseus specific. In silico analysis revealed presence of 11,620 genic simple sequence repeats (excluding mono-nucleotide repeats) and 1820 transcription factor encoding genes in C. roseus transcriptome. Expression analysis showed roots and leaves to be actively participating in bisindole alkaloid production with clear indication that enzymes involved in pathway of vindoline and vinblastine biosynthesis are restricted to aerial tissues. Such large-scale transcriptome study provides a rich source for understanding plant-specialized metabolism, and is expected to promote research towards production of plant-derived pharmaceuticals.
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    Transcriptome profiling for discovery of genes involved in shoot apical meristem and flower development
    (Elsevier B.V., 2014) Singh, Vikash K.; Jain, Mukesh
    Flower development is one of the major developmental processes that governs seed setting in angiosperms. However, little is known about the molecular mechanisms underlying flower development in legumes. Employing RNA-seq for various stages of flower development and few vegetative tissues in chickpea, we identified differentially expressed genes in flower tissues/stages in comparison to vegetative tissues, which are related to various biological processes and molecular functions during flower development. Here, we provide details of experimental methods, RNA-seq data (available at Gene Expression Omnibus database under GSE42679) and analysis pipeline published by Singh and colleagues in the Plant Biotechnology Journal (Singh et al., 2013), along with additional analysis for discovery of genes involved in shoot apical meristem (SAM) development. Our data provide a resource for exploring the complex molecular mechanisms underlying SAM and flower development and identification of gene targets for functional and applied genomics in legumes.
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    A global view of transcriptome dynamics during flower development in chickpea by deep sequencing
    (John Wiley & Sons Ltd, 2013) Singh, Vikash K.; Garg, Rohini; Jain, Mukesh
    Measurement of gene expression can provide important clues about gene function and molecular basis of developmental processes. Here, we have analysed the chickpea transcriptome in vegetative and flower tissues by exploiting the potential of high-throughput sequencing to measure gene expression. We mapped more than 295 million reads to quantify the transcript abundance during flower development. We detected the expression of more than 90% genes in at least one tissue analysed. We found quite a large number of genes were differentially expressed during flower development as compared to vegetative tissues. Further, we identified several genes expressed in a stage-specific manner. Various transcription factor families and metabolic pathways involved in flower development were elucidated. The members of MADS-box family were most represented among the transcription factor genes up-regulated during various stages of flower development. The abundant expression of several well-known genes implicated in flower development in chickpea flower development stages confirmed our results. In addition, we detected the expression specificities of lineage-specific genes during flower development. The expression data presented in this study is the most comprehensive dataset available for chickpea as of now and will serve as resource for unraveling the functions of many specific genes involved in flower development in chickpea and other legumes.
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    High-Throughput SNP discovery and genotyping for constructing a saturated linkage map of Chickpea (Cicer arietinum L.)
    (Oxford University Press, 2012) Gaur, Rashmi; Azam, Sarwar; Jeena, Ganga; Khan, Aamir Waseem; Choudhary, Shalu; Jain, Mukesh; Yadav, Gitanjali; Tyagi, Akhilesh K.; Chattopadhyay, Debasis; Bhatia, Sabhyata
    The present study reports the large-scale discovery of genome-wide single-nucleotide polymorphisms (SNPs) in chickpea, identified mainly through the next generation sequencing of two genotypes, i.e. Cicer arietinum ICC4958 and its wild progenitor C. reticulatum PI489777, parents of an inter-specific reference mapping population of chickpea. Development and validation of a high-throughput SNP geno- typing assay based on Illumina’s GoldenGate Genotyping Technology and its application in building a high-resolution genetic linkage map of chickpea is described for the first time. In this study, 1022 SNPs were identified, of which 768 high-confidence SNPs were selected for designing the custom Oligo Pool All (CpOPA-I) for genotyping. Of these, 697 SNPs could be successfully used for genotyping, demonstrating a high success rate of 90.75%. Genotyping data of the 697 SNPs were compiled along with those of 368 co-dominant markers mapped in an earlier study, and a saturated genetic linkage map of chickpea was constructed. One thousand and sixty-three markers were mapped onto eight linkage groups spanning 1808.7 cM (centiMorgans) with an average inter-marker distance of 1.70 cM, thereby representing one of the most advanced maps of chickpea. The map was used for the synteny analysis of chickpea, which revealed a higher degree of synteny with the phylogenetically close Medicago than with soybean. The first set of validated SNPs and map resources developed in this study will not only facilitate QTL mapping, genome-wide association analysis and comparative mapping in legumes but also help anchor scaffolds arising out of the whole-genome sequencing of chickpea.
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    Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers
    (Public Library of Science, 2012) Agarwal, Gaurav; Jhanwar, Shalu; Priya, Pushp; Singh, Vikash K.; Saxena, Maneesha S.; Parida, Swarup K.; Garg, Rohini; Tyagi, Akhilesh K.; Jain, Mukesh
    Chickpea (Cicer arietinum L.) is an important crop legume plant with high nutritional value. The transcriptomes of desi and wild chickpea have already been sequenced. In this study, we sequenced the transcriptome of kabuli chickpea, C. arietinum (genotype ICCV2), having higher commercial value, using GS-FLX Roche 454 and Illumina technologies. The assemblies of both Roche 454 and Illumina datasets were optimized using various assembly programs and parameters. The final optimized hybrid assembly generated 43,389 transcripts with an average length of 1065 bp and N50 length of 1653 bp representing 46.2 Mb of kabuli chickpea transcriptome. We identified a total of 5409 simple sequence repeats (SSRs) in these transcript sequences. Among these, at least 130 and 493 SSRs were polymorphic with desi (ICC4958) and wild (PI489777) chickpea, respectively. In addition, a total of 1986 and 37,954 single nucleotide polymorphisms (SNPs) were predicted in kabuli/desi and kabuli/wild genotypes, respectively. The SNP frequency was 0.043 SNP per kb for kabuli/desi and 0.821 SNP per kb for kabuli/wild, reflecting very low genetic diversity in chickpea. Further, SSRs and SNPs present in tissue-specific and transcription factor encoding transcripts have been identified. The experimental validation of a selected set of polymorphic SSRs and SNPs exhibited high intra-specific polymorphism potential between desi and kabuli chickpea, suggesting their utility in large-scale genotyping applications. The kabuli chickpea gene index assembled, and SSRs and SNPs identified in this study will serve as useful genomic resource for genetic improvement of chickpea.