Exploring intricacies of 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. The focus of my research group is to delineate the 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-seq, 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.

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.

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.

My group was 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, my group focus on the generation of functional and applied genomics resources for chickpea to facilitate its genetic enhancement via biotechnological and molecular breeding approaches.


  • M. Jain selected for Tata Innovation Fellowship, Department of Biotechnology, Government of India, New Delhi (2018-19)
  • M. Jain selected for National Bioscience Award for Career Development 2016 from the Department of Biotechnology
  • M. Jain was conferred India Research Excellence - Citation Young Achiever Award 2017 across all disciplines from Clarivate

Highly motivated researchers are welcome to contact via e-mail for the Post-doctoral Fellow/Research Associate/Research Fellow position that may be available immediately. 

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Recent Publications

  • Jain M, Bansal J, Rajkumar MS, Garg R. (2022) An integrated transcriptome mapping the regulatory network of coding and long non-coding RNAs provides a genomics resource in chickpea. Communications Biology 5, 1106. doi: 10.1038/s42003-022-04083-4.
  • Rajkumar MS, Gupta K, Khemka N, Garg R, Jain M. (2020) DNA methylation reprogramming during seed development and its functional relevance in seed size/weight determination in chickpea. Communications Biology 3, 340. doi: 10.1038/s42003-020-1059-1.

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Professor Mukesh Jain

Room No. 21
School of Computational and Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067. INDIA
Off. Phone : 91 11 26704686