Institutional Publications

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Author: search.filters.author.Bhatia, SabhyataSubject: search.filters.subject.Cicer arietinum

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    Dissecting the root nodule transcriptome of chickpea (Cicer arietinum L.)
    (PLOS, 2016) Kant, Chandra; Pradhan, Seema; Bhatia, Sabhyata
    A hallmark trait of chickpea (Cicer arietinum L.), like other legumes, is the capability to convert atmospheric nitrogen (N2) into ammonia (NH3) in symbiotic association with Mesorhizobium ciceri. However, the complexity of molecular networks associated with the dynamics of nodule development in chickpea need to be analyzed in depth. Hence, in order to gain insights into the chickpea nodule development, the transcriptomes of nodules at early, middle and late stages of development were sequenced using the Roche 454 platform. This generated 490.84 Mb sequence data comprising 1,360,251 reads which were assembled into 83,405 unigenes. Transcripts were annotated using Gene Ontology (GO), Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways analysis. Differential expression analysis revealed that a total of 3760 transcripts were differentially expressed in at least one of three stages, whereas 935, 117 and 2707 transcripts were found to be differentially expressed in the early, middle and late stages of nodule development respectively. MapMan analysis revealed enrichment of metabolic pathways such as transport, protein synthesis, signaling and carbohydrate metabolism during root nodulation. Transcription factors were predicted and analyzed for their differential expression during nodule development. Putative nodule specific transcripts were identified and enriched for GO categories using BiNGO which revealed many categories to be enriched during nodule development, including transcription regulators and transporters. Further, the assembled transcriptome was also used to mine for genic SSR markers. In conclusion, this study will help in enriching the transcriptomic resources implicated in understanding of root nodulation events in chickpea.
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    Development of gene-based markers for use in construction of the chickpea (Cicer arietinum L.) genetic linkage map and identification of QTLs associated with seed weight and plant height
    (Springer, 2015) Gupta, Shefali; Kumar, Tapan; Verma, Subodh; Bharadwaj, Chellapilla; Bhatia, Sabhyata
    Seed weight and plant height are important agronomic traits and contribute to seed yield. The objective of this study was to identify QTLs underlying these traits using an intra-specific mapping population of chickpea. A F11 population of 177 recombinant inbred lines derived from a cross between SBD377 (100-seed weight- 48 g and plant height- 53 cm) and BGD112 (100-seed weight- 15 g and plant height- 65 cm) was used. A total of 367 novel EST-derived functional markers were developed which included 187 EST-SSRs, 130 potential intron polymorphisms (PIPs) and 50 expressed sequence tag polymorphisms (ESTPs). Along with these, 590 previously published markers including 385 EST-based markers and 205 genomic SSRs were utilized. Of the 957 markers tested for analysis of parental polymorphism between the two parents of the mapping population, 135 (14.64 %) were found to be polymorphic. Of these, 131 polymorphic markers could be mapped to the 8 linkage groups. The linkage map had a total length of 1140.54 cM with an average marker density of 8.7 cM. The map was further used for QTL identification using composite interval mapping method (CIM). Two QTLs each for seed weight, qSW-1 and qSW-2 (explaining 11.54 and 19.24 % of phenotypic variance, respectively) and plant height, qPH-1 and qPH-2 (explaining 13.98 and 12.17 % of phenotypic variance, respectively) were detected. The novel set of genic markers, the intra-specific linkage map and the QTLs identified in the present study will serve as valuable genomic resources in improving the chickpea seed yield using marker-assisted selection (MAS) strategies.
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    A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.)
    (John Wiley & Sons, 2013) Jain, Mukesh; Misra, Gopal; Patel, Ravi K.; Priya, Pushp; Jhanwar, Shalu; Khan, Aamir W.; Shah, Niraj; Singh, Vikas K.; Garg, Rohini; Jeena, Ganga; Yadav, Manju; Kant, Chandra; Sharma, Priyanka; Yadav, Gitanjali; Bhatia, Sabhyata; Tyagi, Akhilesh K.; Chattopadhyay, Debasis
    Cicer arietinum L. (chickpea) is the third most important food legume crop. We have generated the draft sequence of a desi-type chickpea genome using next-generation sequencing platforms, bacterial artificial chromosome end sequences and a genetic map. The 520-Mb assembly covers 70% of the predicted 740-Mb genome length, and more than 80% of the gene space. Genome analysis predicts the presence of 27,571 genes and 210 Mb as repeat elements. The gene expression analysis performed using 274 million RNA-Seq reads identified several tissue-specific and stress-responsive genes. Although segmental duplicated blocks are observed, the chickpea genome does not exhibit any indication of recent whole-genome duplication. Nucleotide diversity analysis provides an assessment of a narrow genetic base within the chickpea cultivars. We have developed a resource for genetic markers by comparing the genome sequences of one wild and three cultivated chickpea genotypes. The draft genome sequence is expected to facilitate genetic enhancement and breeding to develop improved chickpea varieties.
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    Isolation and characterization of sequence-tagged microsatellite sites markers in chickpea (Cicer arietinum L.)
    (Wiley-Blackwell, 2003) Sethy, Niroj K.; Shokeen, Bhumika; Bhatia, Sabhyata
    In this study we report the isolation of microsatellite sequences and their conversion to sequence-tagged microsatellite sites (STMS) markers in chickpea (Cicer arietinum L.). Thirteen putative recombinants isolated from a chickpea genomic library were sequenced, and used to design 10 STMS primer pairs. These were utilized to analyse the genetic polymorphism in 15 C. arietinum varieties and two wild varieties, C. echinospermum and C. reticulatum. All the primer pairs amplified polymorphic loci ranging from four to seven alleles per locus. The observed heterozygosity ranged from 0 to 0.6667. Most of the STMS markers also amplified corresponding loci in the wild relatives suggesting conservation of these markers in the genus. Hence, these polymorphic markers will be useful for the evaluation of genetic diversity and molecular mapping in chickpea.