National Institute of Plant Genome Research
 
    Dr. Mukesh Jain
    Staff Scientist III
    Tel: 91-11-26741612, 14, 17 (Ext.) 182
    91-11-26735182 (Direct)
    Fax: 91-11-26741658
    Webpage: http://mjainanid.googlepages.com
    E-mail: mjain@nipgr.res.in; mjainanid@gmail.com
 Research Area
Plant Genomics, Bioinformatics and Biotechnology
 Awards & Honors
Anil Kumar Bose Memorial Award (2011) from the Indian National Science Academy, New Delhi.
Associate of the National Academy of Agricultural Sciences, New Delhi (2011-2015)
Associate Editor of 'BMC Research Notes' (2010 onwards).
Young Scientist Platinum Jubilee Award (2009) from the National Academy of Sciences India (NASI).
Associate of the Indian Academy of Sciences (2007-2012)
Certificate of Recognition as Genomics Pioneer (2008) from the Ocimum Biosolutions in association with OBBeC.
Young Scientist Award 2007-08 from the Indian Science Congress Association (ISCA).
Indian National Science Academy (INSA) medal for Young Scientist 2007.
Professor LSS Kumar Memorial Award 2007.
Innovative Young Biotechnologists Award (IYBA) 2006 from the Department of Biotechnology, Government of India.
Visiting Scientist at The Institute for Genomic Research, Rockville, MD for the Rice Genome Annotation workshop 2007.
Junior and Senior Research Fellowships from CSIR.
University Medal for First-Class-First position in M.Sc. Biotechnology from Kurukshetra University, Kurukshetra.
 Research Interests
1. Exploring transcriptional regulatory network during abiotic stress
Abiotic stresses water-deficit and high salinity are the most serious problems that limit growth and productivity of rice worldwide. Despite its importance, however, there are gaps in our knowledge regarding the molecular mechanisms responsible for the effect of these environmental stresses. Numerous studies have been performed to understand the mechanism of water-deficit and high salinity responses and a variety of genes exhibiting differential expression in response to these stresses have been identified. The differential gene expression is governed at the transcriptional and post-transcriptional levels. At transcriptional level, the regulatory transcription factors (TFs) regulate transcription by binding with cis-regulatory elements located in the promoters of target genes. Each TF likely regulate multiple target genes often in combination with other TFs, and may either activate or repress transcription. This combinatorial regulatory network results in exquisitely fine-tuned gene expression patterns and levels. The target genes or binding sites of only a few TFs involved in stress responses have been elucidated so far. A more throughput analysis is required to understand the transcriptional regulatory network underlying abiotic stress responses in crop plants. Earlier, we have identified several TFs involved in various abiotic stress responses. Currently the focus of my research group is to delineate the transcriptional regulatory network during water-deficit and high salinity stress. We sought to generate a system level understanding of transcriptional regulatory network during water-deficit and high salinity stress in crop plants utilizing various advanced molecular biology approaches, including yeast one-hybrid analysis, ChIP-chip, yeast two-hybrid analysis and generation of transgenic plants. This work is expected to provide new insight into molecular mechanisms underlying abiotic stress responses in plants, which will be very useful to engineer stress tolerance in crop plants.
2. Genome analysis of model plants
Another area of interest is genome analysis of model plants using various bioinformatics tools. The availability of complete genome sequences of various plants, extensive database resources, next generation sequencing platforms and gene expression profiling platforms such as microarrays, serial analysis of gene expression and massively parallel signature sequencing, provide an extraordinary opportunity to understand complex biological processes and serve as blueprints for crop improvement in future. The work involves genome-wide analysis of the genes/gene families involved in critical biological processes by utilizing various database resources. The aim of this study is to explore the molecular basis of several fundamental biological processes, plant responses and identify novel genes that regulate agronomically important traits
Our group is also a part of DBT funded "Next Generation Challenge Programme on Chickpea Genomics". In this programme, our goal is to generate a high-quality whole genome annotation, exploration of various features of the genome, high throughput transcriptome analysis and comparative genomics of chickpea.
 Group Members
Ms. Annapurna BhattacharjeePh.D. Student
Mr. Vikash SinghPh.D. Student
Ms. Swati SharmaPh.D. Student
Mr. Ravi PatelSenior Research Fellow
Ms. Shalu JhanwarJunior Research Fellow
Ms. Pushp PriyaJunior Research Fellow
 Web Resources Developed
1. Chickpea Transcriptome Database: (CTDB, http://www.nipgr.res.in/ctdb.html)
A web resource for mining/downloading sequence data, functional annotation (gene description, domain and gene ontology), and tissue-specific expression profiles of chickpea transcriptome.
2. Plant Reference Gene Server: (PlantRGS, http://www.nipgr.res.in/PlantRGS)
A web server for the identification of most suitable candidate reference gene(s) with minimum expression variance for quantitative gene expression studies in plants.
 Selected Publications (View Complete List)
Patel RK, Jain M (2011). PlantRGS: A web server for the identification of most suitable candidate reference genes for quantitative gene expression studies in plants. DNA Research doi: 10.1093/dnares/dsr032.
Jain M (2011). Next generation sequencing technologies for gene expression profiling in plants. Briefings in Functional Genomics. Doi:10.1093/bfgp/elr038.
Garg R, Patel RK, Jhanwar S, Priya P, Bhattacharjee A, Yadav G, Bhatia S, Chattopadhyay D, Tyagi AK, Jain M (2011). Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol DOI:10.1104/pp.111.178616.
Garg R, Patel RK, Tyagi AK, Jain M (2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 18: 53-63.
Garg R, Jhanwar S, Tyagi AK, Jain M (2010) Genome-wide survey and expression analysis suggest diverse roles of glutaredoxin gene family members during development and response to various stimuli in rice. DNA Res 17: 353-367.
Jain M*, Ghanashyam C, Bhattacharjee A (2010). Comprehensive expression analysis suggests overlapping and specific roles of glutathione S-transferases during development and stress responses in rice. BMC Genomics 11: 73. (*corresponding author).
Garg R, Sahoo A, Tyagi AK, Jain M (2010). Validation of internal control genes for quantitative gene expression studies in chickpea (Cicer arietinum L.). Biochem Biophys Res Commun 396: 283-288.
Ghanashyam C, Jain M (2009). Role of auxin-responsive genes in biotic stress responses. Plant Signal Behav 4: 846-848.
Jain M*, Khurana JP (2009). Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS J 276: 3148-3162. (*corresponding author).
Jain M, Tyagi AK, Khurana JP (2008). Genome-wide identification, classification, evolutionary expansion, and expression analyses of homeobox genes in rice. FEBS Journal 275: 2845-2861.
Jain M, Tyagi AK, Khurana JP (2008). Differential gene expression of rice two-component signaling elements during reproductive development and regulation by abiotic stress. Funct Integr Genomics 8: 175-180.
Nijhawan A, Jain M, Tyagi AK, Khurana JP (2008). A genomic survey and gene expression analysis of basic leucine zipper (bZIP) transcription factor family in rice. Plant Physiol 146: 333-350.
Jain M, Khurana P, Tyagi AK, Khurana JP (2008). Genome-wide analysis of intronless genes in rice and Arabidopsis. Funct Integr Genomics 8: 69-78.
Jain M, Tyagi AK, Khurana JP (2008). Constitutive expression of a meiotic recombination protein gene homolog, OsTOP6A1, from rice confers abiotic stress tolerance in transgenic Arabidopsis plants. Plant Cell Rep 27: 767-778.
Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AK, Khurana JP (2007). F-box proteins in rice: genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143: 1467-1483.
Jain M, Tyagi AK, Khurana JP (2006). Overexpression of putative topoisomerase 6 genes from rice confers stress tolerance in transgenic Arabidopsis plants. FEBS Journal 273: 5245-5260. (cover photo article)
Jain M, Tyagi AK, Khurana JP (2006). Genome-wide analysis, evolutionary expansion, and expression of early auxin-responsive SAUR gene family in rice (Oryza sativa). Genomics 88: 360-371.
Jain M, Nijhawan A, Tyagi AK, Khurana JP (2006). Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochem Biophys Res Commun 345: 646-651.
Jain M, Tyagi AK, Khurana JP (2006). Molecular characterization and differential expression of cytokinin-responsive type A response regulators in rice (Oryza sativa). BMC Plant Biology 6: 1.
Jain M, Kaur N, Garg R, Thakur JK, Tyagi AK, Khurana JP (2006). Structure and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa). Funct Integr Genomics 6: 47-59.
Jain M, Kaur N, Tyagi AK, Khurana JP (2006). The auxin-responsive GH3 gene family in rice (Oryza sativa). Funct Integr Genomics 6: 36-46.