Publications of NIPGR Scientists

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    Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds
    (Frontiers Media S.A., 2014) Pradhan, Seema; Bandhiwal, Nitesh; Shah, Niraj; Kant, Chandra; Gaur, Rashmi; Bhatia, Sabhyata
    Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L.) seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilized to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analyzed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs), about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.
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    Genome-wide discovery and differential regulation of conserved and novel microRNAs in chickpea via deep sequencing
    (Oxford University Press, 2014) Jain, Mukesh; Chevala, VVS Narayana; Garg, Rohini
    MicroRNAs (miRNAs) are essential components of complex gene regulatory networks that orchestrate plant development. Although several genomic resources have been developed for the legume crop chickpea, miRNAs have not been discovered until now. For genome-wide discovery of miRNAs in chickpea (Cicer arietinum), we sequenced the small RNA content from seven major tissues/organs employing Illumina technology. About 154 million reads were generated, which represented more than 20 million distinct small RNA sequences. We identified a total of 440 conserved miRNAs in chickpea based on sequence similarity with known miRNAs in other plants. In addition, 178 novel miRNAs were identified using a miRDeep pipeline with plant-specific scoring. Some of the conserved and novel miRNAs with significant sequence similarity were grouped into families. The chickpea miRNAs targeted a wide range of mRNAs involved in diverse cellular processes, including transcriptional regulation (transcription factors), protein modification and turnover, signal transduction, and metabolism. Our analysis revealed several miRNAs with differential spatial expression. Many of the chickpea miRNAs were expressed in a tissue-specific manner. The conserved and differential expression of members of the same miRNA family in different tissues was also observed. Some of the same family members were predicted to target different chickpea mRNAs, which suggested the specificity and complexity of miRNA-mediated developmental regulation. This study, for the first time, reveals a comprehensive set of conserved and novel miRNAs along with their expression patterns and putative targets in chickpea, and provides a framework for understanding regulation of developmental processes in legumes.
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    Two divergent genes encoding L-myo-inositol 1-phosphate synthase1 (CaMIPS1) and 2 (CaMIPS2) are differentially expressed in chickpea
    (Wiley-Blackwell, 2008) Kaur, Harmeet; Shukla, Rakesh Kumar; Yadav, Gitanjali; Chattopadhyay, Debasis; Majee, Manoj
    L-myo-inositol 1-phosphate synthase (MIPS; EC5.5.1.4) catalyses the rate-limiting step in inositol biosynthetic pathway, and is extremely widespread in living organisms including plants. Several plants possess multiple copies of MIPS gene(s) indicating a possibility of differential expression of each gene to perform distinct physiological functions. To explore this, two MIPS genes (CaMIPS1 and CaMIPS2) were isolated from a drought-tolerant plant chickpea. Both genes are extremely divergent in respect to their introns, at the same time retaining 85% identity to their exons and functionally complementing inositol auxotroph Schizosaccharomyces pombe. Expression analysis showed both genes were expressed in all organs except seed, where only CaMIPS2 transcript was detected. Under environmental stresses, only CaMIPS2 was induced whereas CaMIPS1 expression remained same, which could be explained by the divergence of their 5' upstream regulatory sequences. Remarkably, both gene products exhibited similar biochemical characteristics; however, CaMIPS2 retained higher activity than CaMIPS1 at a high temperature and salt concentration. Furthermore, functional expression of CaMIPS2 in S. pombe results better growth response than CaMIPS1 under stress environment. Taken together, our results suggest that CaMIPS1 and CaMIPS2 are differentially expressed in chickpea to play discrete though overlapping roles in plant; however CaMIPS2 is likely to be evolved through gene duplication to function under environmental stresses.