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Item CLAVATA signaling pathway genes modulating flowering time and flower number in chickpea(Springer Nature, 2019) Basu, Udita; Narnoliya, Laxmi; Srivastava, Rishi; Sharma, Akash; Bajaj, Deepak; Daware, Anurag; Thakro, Virevol; Malik, Naveen; Upadhyaya, Hari D.; Tripathi, Shailesh; Hegde, V. S.; Tyagi, Akhilesh K.; Parida, Swarup K.Unraveling the genetic components involved in CLAVATA (CLV) signaling is crucial for modulating important shoot apical meristem (SAM) characteristics and ultimately regulating diverse SAM-regulated agromorphological traits in crop plants. A genome-wide scan identifed 142 CLV1-, 28 CLV2- and 6 CLV3-like genes, and their comprehensive genomic constitution and phylogenetic relationships were deciphered in chickpea. The QTL/fne mapping and map-based cloning integrated with high-resolution association analysis identifed SNP loci from CaCLV3_01 gene within a major CaqDTF1.1/ CaqFN1.1 QTL associated with DTF (days to 50% fowering) and FN (fower number) traits in chickpea, which was further ascertained by quantitative expression profling. Molecular haplotyping of CaCLV3_01 gene, expressed specifcally in SAM, constituted two major haplotypes that diferentiated the early-DTF and high-FN chickpea accessions from late-DTF and low-FN. Enhanced accumulation of transcripts of superior CaCLV3_01 gene haplotype and known fowering promoting genes was observed in the corresponding haplotype-introgressed early-DTF and high-FN near-isogenic lines (NILs) with narrow SAM width. The superior haplotype-introgressed NILs exhibited early-fowering, high-FN and enhanced seed yield/ productivity without compromising agronomic performance. These delineated molecular signatures can regulate DTF and FN traits through SAM proliferation and diferentiation and thereby will be useful for translational genomic study to develop early-fowering cultivars with enhanced yield/productivity.Item Impact of drought stress on simultaneously occurring pathogen infection in field-grown chickpea(Springer Nature, 2019) Sinha, Ranjita; Irulappan, Vadivelmurugan; Mohan-Raju, Basavaiah; Suganthi, Angappan; Senthil-Kumar, MuthappaDrought stress and pathogen infection simultaneously occur in the field. In this study, the interaction of these two stresses with chickpea, their individual and combined effect and the net impact on plant growth and yield traits were systematically assessed under field and confined pot experiments. The field experiments were conducted for four consecutive years from 2014–15 to 2017–18 at different locations of India. Different irrigation regimes were maintained to impose mild to severe drought stress, and natural incidence of the pathogen was considered as pathogen stress. We observed an increased incidence of fungal diseases namely, dry root rot (DRR) caused by Rhizoctonia bataticola, black root rot (BRR) caused by Fusarium solani under severe drought stress compared to well-irrigated field condition. Similar to field experiments, pot experiments also showed severe disease symptoms of DRR and BRR in the presence of drought compared to pathogen only stress. Overall, the results from this study not only showed the importance of combined drought and DRR stress but also provided systematic data, first of its kind, for the use of researchers.Item Transcriptional signatures modulating shoot apical meristem morphometric and plant architectural traits enhance yield and productivity in chickpea(John Wiley & Sons, 2019) Narnoliya, Laxmi; Basu, Udita; Bajaj, Deepak; Malik, Naveen; Thakro, Virevol; Daware, Anurag; Sharma, Akash; Tripathi, Shailesh; Hegde, V.S.; Upadhyaya, Hari D.; Singh, Ashok K.; Tyagi, Akhilesh K.; Parida, Swarup K.Plant height (PH) and plant width (PW), two of the major plant architectural traits determining the yield and productivity of a crop, are defined by diverse morphometric characteristics of the shoot apical meristem (SAM). The identification of potential molecular tags from a single gene that simultaneously modulates these plant/SAM architectural traits is thus prerequisite to achieve enhanced yield and productivity in crop plants, including chickpea. Large‐scale multi‐environment phenotyping of the association panel and mapping population have ascertained the efficacy of three vital SAM morphometric trait parameters, SAM width, SAM height and SAM area, as key indicators to unravel the genetic basis of the wide PW and PH trait variations observed in desi chickpea. The present study integrated a genome‐wide association study (GWAS); QTL/fine‐mapping and map‐based cloning with molecular haplotyping; transcript profiling; and protein‐DNA interaction assays for the dissection of plant architectural traits in chickpea. These exertions delineated natural alleles and superior haplotypes from a CabHLH121 transcription factor (TF) gene within the major QTLs governing PW, PH and SAM morphometric traits. A genome‐wide protein‐DNA interaction assay assured the direct binding of a known stem cell master regulator, CaWUS, to the WOX‐homeodomain TF binding sites of a CabHLH121 gene and its constituted haplotypes. The differential expression of CaWUS and transcriptional regulation of its target CabHLH121 gene/haplotypes were apparent, suggesting their collective role in altering SAM morphometric characteristics and plant architectural traits in the contrasting near isogenic lines (NILs). The NILs introgressed with a superior haplotype of a CabHLH121 exhibited optimal PW and desirable PH as well as enhanced yield and productivity without compromising any component of agronomic performance. These molecular signatures of the CabHLH121 TF gene have the potential to regulate both PW and PH traits through the modulation of proliferation, differentiation and maintenance of the meristematic stem cell population in the SAM; therefore, these signatures will be useful in the translational genomic study of chickpea genetic enhancement. The restructured cultivars with desirable PH (semi‐dwarf) and PW will ensure maximal planting density in a specified cultivable field area, thereby enhancing the overall yield and productivity of chickpea. This can essentially facilitate the achievement of better remunerative outputs by farmers with rational land use, thus ensuring global food security in the present scenario of an increasing population density and shrinking per capita land area.Item ABC transporter-mediated transport of glutathione conjugates enhances seed yield and quality in chickpea(American Society of Plant Biologists, 2019) Basu, Udita; Upadhyaya, Hari D.; Srivastava, Rishi; Daware, Anurag; Malik, Naveen; Sharma, Akash; Bajaj, Deepak; Narnoliya, Laxmi; Thakro, Virevol; Kujur, Alice; Tripathi, Shailesh; Bharadwaj, Chellapilla; Hegde, V. S.; Pandey, Ajay K.; Singh, Ashok K.; Tyagi, Akhilesh K.; Parida, Swarup K.The identification of functionally relevant molecular tags is vital for genomics-assisted crop improvement and enhancing the seed yield, quality and productivity in chickpea. The simultaneous improvement of yield/productivity as well as quality traits often requires pyramiding of multiple genes, which remains a major hurdle given various associated epistatic and pleotropic effects. Unfortunately, no single gene that can improve yield/productivity along with quality and other desirable agromorphological traits is known, hampering the genetic enhancement of chickpea. Using a combinatorial genomics-assisted breeding and functional genomics strategy, this study identified natural alleles and haplotypes of an ABCC3-type transporter gene that regulates seed weight, an important domestication trait, by transcriptional regulation and modulating the transport of glutathione conjugates in seeds of desi and kabuli chickpea. The superior allele/haplotype of this gene introgressed in desi and kabuli near-isogenic lines enhances the seed weight, yield, productivity and multiple desirable plant architecture and seed-quality traits without compromising the agronomic performance. These salient findings can expedite crop improvement endeavors and the development of nutritionally enriched high-yielding cultivars in chickpea.Item A toolbox for nodule development studies in chickpea: a hairy-root transformation protocol and an efficient laboratory strain of Mesorhizobium sp.(American Phytopathological Society, 2019) Mandal, Drishti; Sinharoy, SenjutiMesorhizobium sp. produces root nodules in chickpea. Chickpea and model legume Medicago truncatula are members of inverted repeat lacking clade (IRLC). The rhizobia after internalization into the plant cell are called 'bacteroid'. Nodule Specific Cysteine-rich (NCR) peptides in IRLC legumes guide bacteroids to a 'terminally differentiated swollen (TDS)' form. Bacteroids in chickpea are less TDS than those in Medicago. Nodule development in chickpea indicates recent evolutionary diversification and merits further study. A hairy root transformation protocol and an efficient laboratory strain are prerequisites for performing any genetic study on nodulation. We have standardized a protocol for composite plant generation in chickpea with a transformation frequency above 50 %, as shown by fluorescent markers. This protocol also works well in different ecotypes of chickpea. Localization of subcellular markers in these transformed roots is similar to the localization observed in transformed Medicago roots. When checked inside transformed nodules, peroxisomes were concentrated along the periphery of the nodules, while ER and Golgi bodies surrounded the symbiosomes. Different Mesorhizobium strains were evaluated for their ability to initiate nodule development and efficiency of nitrogen fixation. Inoculation with different strains resulted in different shapes of TDS bacteroids with variable nitrogen fixation. Our study provides a toolbox to study nodule development in the crop legume chickpea.Item Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea(Springer Nature Limited, 2018) Basu, Udita; Srivastava, Rishi; Bajaj, Deepak; Thakro, Virevol; Daware, Anurag; Malik, Naveen; Upadhyaya, Hari D.; Parida, Swarup K.We discovered 2150 desi and 2199 kabuli accessions-derived SNPs by cultivar-wise individual assembling of sequence-reads generated through genotyping-by-sequencing of 92 chickpea accessions. Subsequent large-scale validation and genotyping of these SNPs discovered 619 desi accessions-derived (DAD) SNPs, 531 kabuli accessions-derived (KAD) SNPs, 884 multiple accessions-derived (MAD) SNPs and 1083 two accessions (desi ICC 4958 and kabuli CDC Frontier)-derived (TAD) SNPs that were mapped on eight chromosomes. These informative SNPs were annotated in coding/non-coding regulatory sequence components of genes. The MAD-SNPs were efcient to detect high intra-specifc polymorphic potential and wide natural allelic diversity level including high-resolution admixed-population genetic structure and precise phylogenetic relationship among 291 desi and kabuli accessions. This signifes their efectiveness in introgression breeding and varietal improvement studies targeting useful agronomic traits of chickpea. Six trait-associated genes with SNPs including quantitative trait nucleotides (QTNs) in combination explained 27.5% phenotypic variation for seed yield per plant (SYP). A pentatricopeptide repeat (PPR) gene with a synonymous-coding SNP/QTN signifcantly associated with SYP trait was found most-promising in chickpea. The essential information delineated can be of immense utility in genomics-assisted breeding applications to develop high-yielding chickpea cultivars.Item Genome-wide bisulphite-sequencing reveals organ-specific methylation patterns in chickpea(Springer Nature, 2018) Bhatia, Himanshi; Khemka, Niraj; Jain, Mukesh; Garg, RohiniDNA methylation is widely known to regulate gene expression in eukaryotes. Here, we unraveled DNA methylation patterns in cultivated chickpea to understand the regulation of gene expression in different organs. We analyzed the methylation pattern in leaf tissue of wild chickpea too, and compared it with cultivated chickpea. Our analysis indicated abundant CG methylation within gene-body and CHH methylation in intergenic regions of the chickpea genome in all the organs examined. Analysis of differentially methylated regions (DMRs) demonstrated a higher number of CG context DMRs in wild chickpea and CHH context DMRs in cultivated chickpea. We observed increased preponderance of hypermethylated DMRs in the promoter regions and hypomethylated DMRs in the genic regions in cultivated chickpea. Genomic location and context of the DMRs correlated well with expression of proximal genes. Our results put forth a positive correlation of promoter hypermethylation with increased transcript abundance via identification of DMR-associated genes involved in flower development in cultivated chickpea. The atypical correlation observed between promoter hypermethylation and increased transcript abundance might be dependent on 24-nt small RNAs and transcription factors binding to the promoter region. This study provides novel insights into DNA methylation patterns in chickpea and their role in regulation of gene expression.Item Integrative network analyses of wilt transcriptome in chickpea reveal genotype dependent regulatory hubs in immunity and susceptibility(Springer Nature, 2018) Ashraf, Nasheeman; Basu, Swaraj; Narula, Kanika; Ghosh, Sudip; Tayal, Rajul; Gangisetty, Nagaraju; Biswas, Sushmita; Aggarwal, Pooja R.; Chakraborty, Niranjan; Chakraborty, SubhraHost specific resistance and non-host resistance are two plant immune responses to counter pathogen invasion. Gene network organizing principles leading to quantitative differences in resistant and susceptible host during host specific resistance are poorly understood. Vascular wilt caused by root pathogen Fusarium species is complex and governed by host specific resistance in crop plants, including chickpea. Here, we temporally profiled two contrasting chickpea genotypes in disease and immune state to better understand gene expression switches in host specific resistance. Integrative gene-regulatory network elucidated tangible insight into interaction coordinators leading to pathway determination governing distinct (disease or immune) phenotypes. Global network analysis identified five major hubs with 389 co-regulated genes. Functional enrichment revealed immunome containing three subnetworks involving CTI, PTI and ETI and wilt diseasome encompassing four subnetworks highlighting pathogen perception, penetration, colonization and disease establishment. These subnetworks likely represent key components that coordinate various biological processes favouring defence or disease. Furthermore, we identified core 76 disease/immunity related genes through subcellular analysis. Our regularized network with robust statistical assessment captured known and unexpected gene interaction, candidate novel regulators as future biomarkers and first time showed system-wide quantitative architecture corresponding to genotypic characteristics in wilt landscape.Item Genetic dissection of photosynthetic efficiency traits for enhancing seed yield in chickpea(John Wiley & Sons, 2019) Basu, Udita; Bajaj, Deepak; Sharma, Akash; Malik, Naveen; Daware, Anurag; Narnoliya, Laxmi; Thakro, Virevol; Upadhyaya, Hari D.; Kumar, Rajendra; Tripathi, Shailesh; Bharadwaj, Chellapilla; Tyagi, Akhilesh K.; Parida, Swarup K.Understanding the genetic basis of photosynthetic efficiency (PE) contributing to enhanced seed yield per plant (SYP) is vital for genomics-assisted crop improvement of chickpea. The current study employed an integrated genomic strategy involving photosynthesis pathway gene-based association mapping, genome-wide association study, QTL mapping and expression profiling. This identified 16 potential SNP loci linked to major QTLs underlying 16 candidate genes significantly associated with PE and SYP traits in chickpea. The allelic variants were tightly linked to positively interacting QTLs regulating both enhanced PE and SYP traits as exemplified by a chlorophyll A-B binding protein-coding gene. The leaf tissue-specific pronounced up-regulated expression of 16 associated genes in germplasm accessions and homozygous individuals of mapping population was evident. Such combinatorial genomic strategy coupled with gene haplotype-specific association as well as in silico protein-protein interaction study delineated natural alleles and superior haplotypes from a chlorophyll A-B binding protein-coding gene and its interacting gene, Timing of CAB Expression 1, which appear to be most-promising candidates in modulating chickpea PE and SYP traits. These functionally pertinent molecular signatures identified have efficacy to drive marker-assisted selection for developing PE-enriched cultivars with high seed yield in chickpea.Item Possible strategies for the establishment of VIGS protocol in chickpea(Caister Academic Press, 2018) Sinha, Ranjita; Senthil-Kumar, MuthappaChickpea is the second largest legume in the world. The worldwide production of chickpea is far below its potential because of the factors like nitrogen deficiency, low nutrient absorption, flower or seed abortion and its vulnerability to the abiotic and biotic stresses. Consequently, it is important to understand the key molecular factors involved in stress tolerance, growth, flowering and seed development for the genetic improvement of the existing varieties. Currently the whole genome sequencing data and transcriptome information are widely facilitating functional genomic studies in chickpea. Further, marker based trait association mapping information is available for assistance in breeding program. However, information about exact function of genes is still lacking because of the absence of genetic mutants and difficult genetic transformation in this crop. Hence, the current scenario demands the establishment of virus-induced gene silencing (VIGS) technique in chickpea. VIGS would serve as an important tool for the functional characterization of large number of genes. Despite attempts by several research teams, the VIGS protocol is not yet available till date, though VIGS has been successfully applied for the gene characterization in other legumes. In this chapter we propose some strategies that can be attempted for development of successful VIGS protocol. We also describe our experience from present and past research projects aimed to study VIGS in chickpea.