National Institute of Plant Genome Research
 
    Dr. Mukesh Jain
    Staff Scientist IV
    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.ac.in; mjainanid@gmail.com
 Research Area
Plant Genomics, Bioinformatics and Biotechnology
 Awards & Honors
Editor/Associate/Academic/Review Editor -  'PLoS ONE' (2014 onwards); 'Frontiers in Plant Science' (2014 onwards); 'Molecular Breeding' (2013 onwards); 'BMC Research Notes' (2010 onwards)
NASI-Scopus Young Scientist Award 2012 in 'Agriculture' from Elsevier.
Young Scientist Award from the National Academy of Agricultural Sciences, New Delhi for biennium (2011-2012).
Prof. B.K. Bachhawat Memorial Young Scientist Lecture Award (2012) from NASI.
Haryana Yuva Vigyan Ratna Award 2010-11 from the Haryana State Council for Science & Technology.
Associate Fellow of the National Academy of Agricultural Sciences, New Delhi (2011-2015).
Associate Fellow of the Indian Academy of Sciences, Bangalore (2007-2012).
Anil Kumar Bose Memorial Award (2011) from the Indian National Science Academy.
Young Scientist Platinum Jubilee Award (2009) from the National Academy of Sciences India (NASI).
Young Scientist Award from the Indian Science Congress Association (2007-08).
Indian National Science Academy (INSA) medal for Young Scientist (2007).
Professor LSS Kumar Memorial Award (2007) from INSA.
Innovative Young Biotechnologists Award (IYBA) from the Department of Biotechnology, Government of India (2006).
University Medal for First-Class-First position in M.Sc. Biotechnology from Kurukshetra University, Kurukshetra.
 Fellowships & Recognition
Annual Eminence Award 2014 in 'Agriculture' from Rawal Institutions, Faridabad
DBT-CREST Fellowship Award for 2010-2011 from the Department of Biotechnology, Government of India, New Delhi.
BOYCAST Fellowship for 2010-2011 from the Department of Science & Technology, Government of India, New Delhi (not availed).
Biography listed in the Marquis Who's Who in the World 2010 and 2012 editions.
Certificate of Recognition as Genomics Pioneer (2008) from the Ocimum Biosolutions in association with OBBeC.
Visiting Scientist at The Institute for Genomic Research, Rockville, MD for the Rice Genome Annotation workshop (2007).
Junior and Senior Research Fellowships from CSIR, New Delhi (February 2002-September 2006).
 Research Interests
1. Exploring transcriptional complexity and 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. 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. 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 complexity and regulatory network during water-deficit and high salinity stress. Next generation sequencing technologies are being used to identify novel genes/transcript isoforms involved in abiotic stress responses. 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. Exploring transcriptome  and  epigenome  diversity  during  seed  development  in chickpea
Seed development is one of the most important processes in the life cycle of a plant and is particularly important for its nutritive value in legumes. The understanding of molecular mechanisms governing seed development is very important to devise new strategies for improvement of agronomically important seed traits. We aim to catalog complex interactions between dynamic epigenome and transcriptome in chickpea by associating gene activity  with  DNA  methylation,  histone  modifications  and  small  RNA  population.  This study will generate global integrated epigenetic and transcriptional maps and their interactional relationships with the chickpea genome.
3. Genome and transcriptome sequencing/analysis of crop plants
Another area of interest is genome and transcriptome sequencing/analysis of important crop plants using next generation sequencing technologies and various bioinformatics tools. The work is aimed at generation of exhaustive and useful genomic resources (gene content and genetic variations) for the scientific community for further genetic enhancement of important crop plant by raising transgenic and/or implementing breeding programs. Presently, we are focusing on few medicinal plants important for Indian economy.
Our group is also a part of DBT funded “Next Generation Challenge Programme on Chickpea Genomics”. In this programme, we have generated a high-quality whole genome annotation, explored various features of the genome and performed high throughput transcriptome analysis in chickpea genotypes. Currently, we focus on the generation of functional and applied genomics resources for chickpea to facilitate its genetic enhancement via biotechnological and molecular breeding approaches.
 Group Members
Ms. Annapurna BhattacharjeePh.D. Student
Mr. Vikash K. SinghPh.D. Student
Ms. Swati SharmaPh.D. Student
Mr. Rama ShankarPh.D. Student
Mr. Anil K. Pole Ph.D. Student
Dr. Vinay Kumar Research Associate
Mr. Mohit Verma Senior Research Fellow
Mr. VV SatyanarayanaJunior Research Fellow
 Lab Alumni
Research FellowsTrainees
Dr. Gaurav AgarwalMs. Annapurna Sahoo
Dr. Gunjan PandeyMs. Alka Shankar
Dr. Supriya Ms. Soma Behera
Dr. Rajesh Ghangal Ms. Pushp Priya
Mr. Challa Ghanashyam Mr. Shashank Agarwal
Ms. Shikha Gupta Ms. Paridhi Mehta
Mr. Mayank Chaudhary Ms. Neetu Tyagi
Mr. Bharat Yadav Ms. Jenifer Christy
Ms. Annapurna Sahoo 
Ms. Archana Kumari 
Ms. Khusbu Sharma 
Mr. Ragunathan D 
Mrs. Nitu Maity 
Ms. Shalu Jhanwar 
Mr. Shashank Agarwal 
Mr. Ravi K. Patel 
Ms. Pushp Priya 
Mr. Kanhu Charan Moharana 
Mr. Srinivas Nimmarajula 
Mr. Santosh Kumar Yadav  
Ms. Shweta Goyal  
Mr. Raghvendra Sharma 
 Web Resources/Products Developed
1. Chickpea Gene Expression Microarray: (Download Flyer)
2. Next Generation Sequencing Quality Control Toolkit: (NGS QC Toolkit, http://www.nipgr.res.in/ngsqctoolkit.html)
3. Rice Stress-Responsive Transcription Factor Database : ((RiceSRTFDB; http://www.nipgr.res.in/RiceSRTFDB.html))
4. Chickpea Transcriptome Database: (CTDB, http://www.nipgr.res.in/ctdb.html)
5. Plant Reference Gene Server: (PlantRGS, http://www.nipgr.res.in/PlantRGS)
6. Other Resources:
 Special Issue
Associate Editor, special issue of 'Frontiers in Plant Science' on Research Topic "Abiotic Stress: Molecular Genetics and Genomics"
 Selected Publications (View Complete List)
Jain M*, Moharana KC, Shankar R, Kumari R, Garg R* (2014) Genome-wide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance. Plant Biotechnol. J. 12: 253-264. *Joint corresponding authors.
Jain M, Chevala VVSN, Garg R. (2014) Genome-wide discovery and differential regulation of conserved and novel microRNAs in chickpea via deep sequencing. Journal of Experimental Botany (in press).
Garg R, Bhattacharjee A, Jain M (2014) Genome-scale transcriptomic insights into molecular aspects of abiotic stress responses in chickpea. Plant Molecular Biology Reporter DOI 10.1007/s11105-014-0753-x.
Garg R. Verma M, Agarwal S, Shankar R, Majee M, Jain M (2014) Deep transcriptome sequencing of wild halophyte rice, Porteresia coarctata, provides novel insights into the salinity and submergence tolerance factors. DNA Res. 21: 69-84.
Singh VK, Garg R, Jain M (2013) A global view of transcriptome dynamics during flower development in chickpea by deep sequencing. Plant Biotechnol. J. 11: 691-701.
Jain M , Misra G, Patel RK, Priya P, Jhanwar S, Khan AW, Shah N, Singh VK, Garg R, Jeena G, Sharma P, Kant C, Yadav M, Yadav G, Bhatia S, Tyagi AK, Chattopadhyay D. (2013) Draft genome sequence of the pulse crop chickpea( Cicer arietinum L.). Plant. J. 74: 715-729.
Sharma R, Priya P, Jain M (2013) Modified expression of an auxin-responsive rice CC-type glutaredoxin gene affects multiple abiotic stress responses. Planta 238: 871-884.
Priya P, Jain M. Jain M (2013) RiceSRTFDB: A database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis. Database 2013, bat027. DOI: 10.1093/database/bat027.
Agarwal G, Jhanwar S, Priya P, Singh VK, Saxena MS, Parida SK, Garg R, Tyagi AK, Jain M (2012) Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers. PLoS ONE 7: e52443. DOI: 10.1371/journal.pone.0052443
Jhanwar S, Priya P, Garg R, Parida SK, Tyagi AK, Jain M (2012) Transcriptome sequencing of wild chickpea as a rich resource for marker development. Plant Biotechnol. J. 10: 690-702.
Patel RK, Jain M (2012) NGS QC Toolkit: A toolkit for quality control of next generation sequencing data. PLoS ONE 7, e30619. DOI:10.1371/journal.pone.0030619.
Jain M (2012) Next generation sequencing technologies for gene expression profiling in plants. Brief Funct Genomics 2: 63-70.
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 Res 18: 463-470.
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 156: 1661-1678.
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.
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.
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).
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) (2nd most highly cited article among FEBS Journal articles in two years)
Jain M, Tyagi AK, Khurana JP (2008). Genome-wide identification, classification, evolutionary expansion, and expression analyses of homeobox genes in rice. FEBS J 275: 2845-2861.
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, 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 J 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. (Highly cited and second most downloaded article of BBRC in ScienceDirect)
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 Biol 6: 1. (Highly accessed article)
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.