Publications

Research Articles

  • Rajkumar MS, Banerjee AK, Bansal J, Jain M†, Garg R†. (2026) Pan-transcriptome analysis of diverse chickpea accessions reveals specific expression patterns and genetic variations associated with agronomic traits. Plant Molecular Biology 116, 41. doi: https://doi.org/10.1007/s11103-026-01707-9 †Joint corresponding authors
  • Singhal C, Upadhyaya G, Rajkumar MS, Modak A, Sethi V, Singh S, Das D, Jain M, Gangappa SN. (2026) CUL3LRB E3 ubiquitin ligases control thermosensory growth in Arabidopsis by differentially regulating HY5 and PIF4 protein stability. Science Advances, 12, eaec7817. doi: https://doi.org/10.1126/sciadv.aec7817
  • Sahil R, Pal V, Kharat AS, Jain M. (2025) A multi-omics meta-analysis of rhizosphere microbiome reveals growth-promoting marker bacteria at different stages of legume development. Plant, Cell & Environment, doi: https://doi.org/10.1111/pce.15429
  • Das S, Modak A, Rajkumar MS, Garhwal V, Sethi V, Jain M, Gangappa SN. (2025) The PHYTOCHROME INTERACTING FACTOR 3, a bHLH transcription factor, promotes thermosensory growth by directly activating PIF4 transcription and its protein accumulation. New Phytologist 247, 1742-1762. doi: 10.1111/nph.70278.
  • Gupta K, Rajkumar MS, Singh V, Rani P, Wani A, Pareek A, Garg R, Jain M. (2025) Temporal gene expression profiling suggests stage-specific regulation of apocarotenoid biosynthesis genes during stigma development in Crocus sativus L. Physiology and Molecular Biology of Plants 31, 863-876. doi: 10.1007/s12298-025-01621-2.
  • Rajkumar MS, Tembhare K, Garg R, Jain M. (2024) Genome-wide mapping of DNase I hypersensitive sites revealed differential chromatin accessibility and regulatory DNA elements under drought stress in rice cultivars. The Plant Journal 119, 2063-2079. doi: http://doi.org/10.1111/tpj.16864.
  • Bagri J, Singh VK, Gupta K, Dkhar J, Wani AA, Jain M, Singla-Pareek S, Pareek A. (2024) Integrated metabolomics and transcriptomic analysis reveals bioactive compound diversity in organs of saffron flower. Physiologia Plantarum 176:e14598. doi: 10.1111/ppl.14598
  • Tiwari S, Jain M, Singla-Pareek S, Bhalla PL, Singh M, Pareek A. (2023) Pokkali - a naturally evolved salt-tolerant rice shows a distinguished set of lncRNAs possibly contributing to the tolerant phenotype. International Journal of Molecular Sciences 24, 11677. doi: 10.3390/ijms241411677.
  • Garg T, Yadav M, Mushahary KKK, Kumar A, Pal V, Singh H, Jain M, Yadav SR. (2023) Spatially activated conserved auxin-transcription factor regulatory module controls de novo root organogenesis in rice. Planta 258, 52. doi: 10.1007/s00425-023-04210-3.
  • Singh V, Gupta K, Singh S, Jain M, Garg R. (2023) Unravelling the molecular mechanism underlying drought stress response in chickpea via integrated multi-omics analysis. Frontiers in Plant Science 14, 1156606. doi: 10.3389/fpls.2023.1156606.
  • Shankar R, Dwivedi A, Singh V, Jain M. (2023) Genome-wide discovery of genetic variations between rice cultivars with contrasting drought stress response and their potential functional relevance. Physiologia Plantarum 175, e13879. doi:10.1111/ppl.13879.
  • Dwivedi A, Singh V, Anwar K, Pareek A, Jain M. (2023) Integrated transcriptome, proteome and metabolome analyses revealed auxiliary carbohydrate metabolism augmenting drought tolerance in rice. Plant Physiology and Biochemistry 201, 107849. doi: 10.1016/j.plaphy.2023.107849.
  • Rajkumar MS, Garg R†, Jain M†. (2022) Genome-wide discovery of DNA polymorphisms via resequencing of chickpea cultivars with contrasting response to drought stress. Physiologia Plantarum 174, e13611. doi.org/10.1111/ppl.13611. †Joint corresponding author
  • Jain M, Bansal J, Rajkumar MS, Sharma N, Khurana JP, Khurana P. Draft genome sequence of Indian mulberry (Morus indica) provides a resource for functional and translational genomics. Genomics. 2022 Mar 22;114(3):110346. doi: 10.1016/j.ygeno.2022.110346. Epub ahead of print. PMID: 35331861.
  • Garg T, Singh Z, Chennakesavulu K, Mushahary KKK, Dwivedi AK, Varapparambathu V, Singh H, Singh RS, Sircar D, Chandran D, Prasad K, Jain M, Yadav SR. Species-specific function of conserved regulators in orchestrating rice root architecture. Development. 2022 May 1;149(9):dev200381. doi: 10.1242/dev.200381. Epub 2022 May 9. PMID: 35394032.
  • 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.
  • Khemka N, Rajkumar MS, Garg R, Jain M. (2022) Genome-wide analysis suggests role of lncRNAs during seed development and seed size/weight determination in chickpea. Planta 256, 79. doi: 10.1007/s00425-022-03986-0.
  • Bhattacharjee A, Srivastava P, Nath O, Jain M. (2021) Genome-wide discovery of OsHOX24-binding sites and regulation of desiccation stress response in rice. Plant Molecular Biology 105, 205-214. doi: 10.1007/s11103-020-01078-9.
  • Bhaskar A, Paul LK, Sharma E, Jha S, Jain M, Khurana JP. (2021) OsRR6, a type-A response regulator in rice, mediates cytokinin, light and stress responses when over-expressed in Arabidopsis. Plant Physiology and Biochemistry 161, 98-112. doi: 10.1016/j.plaphy.2021.01.047.
  • Khemka NK, Rajkumar MS, Garg R, Jain M. (2021) Genome-wide profiling of miRNAs during seed development reveals their functional relevance in seed size/weight determination in chickpea. Plant Direct 5:e00299. doi: 10.1002/pld3.299. (Article of the week)
  • Rajkumar MS, Garg R, Jain M. (2021) Genome resequencing reveals DNA polymorphisms associated with seed size/weight determination in chickpea. Genomics 113, 1458-1468. 10.1016/j.ygeno.2021.03.020.
  • Rajkumar, M. S., Jain, M., & Garg, R. (2021). Discovery of DNA polymorphisms via whole genome resequencing and their functional relevance in salinity stress response in chickpea. Physiologia plantarum, 10.1111/ppl.13507. Advance online publication. https://doi.org/10.1111/ppl.13507
  • Garg T, Singh Z, Dwivedi AK, Varapparambathu V, Singh RS, Yadav M, Chandran D, Prasad K, Jain M, Yadav SR. (2020) Genome-wide high resolution expression map and functions of key cell fate determinants reveal the dynamics of crown root development in rice. BioRxiv doi: 1101/2020.06.11.131565.
  • Bhaskarla V, Zinta G, Ford R, Jain M, Varshney R, Mantri N. (2020) Comparative root transcriptomics provide insights on drought adaptation strategies in chickpea (Cicer arietinum L.). International Journal of Molecular Sciences 21, 1781; https://doi.org/10.3390/ijms21051781.
  • Ghangal R†, Rajkumar MS†, Garg R, Jain M. (2020) Genome-wide analysis of glutathione S-transferase gene family in chickpea suggests its role during seed development and abiotic stress. Molecular Biology Reports 47, 2749-2761. doi: 10.1007/s11033-020-05377-8. †Equal contribution
  • Nawkarkar P, Chugh S, Sharma S, Jain M, Kajla S, Kumar S. (2020) Characterization of the chloroplast genome facilitated the transformation of Parachlorella Kessleri-I, a potential marine alga for biofuel production. Current Genomics doi: 10.2174/1389202921999201102164754.
  • Rajkumar MS, Shankar R, Garg R, Jain M. (2020) Bisulphite sequencing reveals dynamic DNA methylation under desiccation and salinity stresses in rice cultivars. Genomics 112, 3537-3548. doi: 10.1016/j.ygeno.2020.04.005. Preprint in 2019: BioRxiv doi: 10.1101/558064
  • 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.
  • Bansal J, Gupta K, Rajkumar MS, Garg R, Jain M. (2020) Draft genome and transcriptome analyses of wild halophyte rice Oryza coarctata provide resources for salinity and submergence stress response factors. Physiologia Plantarum doi: 10.1111/ppl.13284.
  • Subudhi P†, Shankar R, Jain M†. (2020) Whole genome sequence analysis of rice genotypes with contrasting response to salinity stress. Scientific Reports 10, 21259. doi: 10.1038/s41598-020-78256-8. †Joint corresponding author
  • Ghangal R, Singh VK, Khemka NK, Rajkumar MS, Garg R, Jain M. (2020) Updates on genomic resources in chickpea for crop improvement. Methods in Molecular Biology 2107: 19–33.
  • Sharma E, Jain M, Khurana JP. (2019) Differential quantitative regulation of specific gene groups and pathways under drought stress in rice. Genomics 111, 1699-1712.
  • Neogy A, Garg T, Kumar A, Dwivedi AK, Singh H, Singh U, Singh Z, Prasad K, Jain M, Yadav SR. (2019) Genome-wide transcript profiling reveals an auxin-responsive transcription factor, OsAP2/ERF-40, promoting rice adventitious root development. Plant Cell Physiology doi: 10.1093/pcp/pcz132.
  • Rajkumar MS, Garg R, Jain M. (2018) Genome-wide discovery of DNA polymorphisms among chickpea cultivars with contrasting seed size/weight and their functional relevance. Scientific Reports 8, 16795. DOI:10.1038/s41598-018-35140-w
  • Chai C, Shankar R, Jain M†, Subudhi P†. (2018) Genome-wide discovery of DNA polymorphisms by whole genome sequencing differentiates weedy and cultivated rice. Scientific Reports 8, 14218, DOI:10.1038/s41598-018-32513-z. †Joint corresponding author
  • Bhatia H, Khemka N, Jain M, Garg R. (2018) Genome-wide bisulphite-sequencing reveals organ-specific methylation patterns in chickpea. Scientific Reports 8, 9704. doi: 10.1038/s41598-018-27979-w.
  • Sharma C, Saripalli G, Kumar S, Gautam T, Kumar A, Rani S, Jain N, Prasad P, Raghuvanshi S, Jain M, Sharma JB, Prabhu KV, Sharma PK, Balyan HS, Gupta PK. (2018) A study of transciptome in leaf rust infected bread wheat involving seedling resistance gene Lr28. Functional Plant Biology. Doi: 10.1071/FP17326.
  • Kaashyap M, Ford R, Kudapa H, Jain M, Edwards D, Varshney RK, Mantri N. (2018) Differential regulation of genes involved in root morphogenesis and cell wall modification is associated with salinity tolerance in chickpea. Scientific Reports 8, 4855. Doi: 10.1038/s41598-018-23116-9.
  • Garg R, Singh VK, Rajkumar MS, Kumar V, Jain M. (2017) Global transcriptome and co-expression network analyses reveal cultivar-specific molecular signatures associated with seed development and seed size determination in chickpea. The Plant Journal 91, 1088-1107. doi: 10.1111/tpj.13621
  • Bhattacharjee A, Sharma R, Jain M. (2017) Over-expression of OsHOX24 confers enhanced susceptibility to abiotic stresses in transgenic rice via modulating stress-responsive gene expression. Frontiers in Plant Science 8, 628. doi: 10.3389/fpls.2017.00628.
  • Singh VK, Kumar MR, Garg R, Jain M. (2017) Genome-wide identification and co-expression network analysis provide insights into the roles of auxin response factor gene family in chickpea. Scientific Reports 7, 10895. Doi: 10.1038/s41598-017-11327-5.
  • Singh U, Khemka N, Rajkumar MS, Garg R, Jain M. (2017) PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea. Nucleic Acids Research 22, e183.
  • Shankar R, Bhattacharjee A, Jain M. (2016) Transcriptome analysis in different rice cultivars provides novel insights into drought and salinity stress responses. Scientific Reports 6, 23719
  • Bhattacharjee A, Khurana JP, Jain M. (2016) Characterization of rice homeobox genes, OsHOX22 and OsHOX24, and over-expression of OsHOX24 in transgenic Arabidopsis suggest their role in abiotic stress response. Frontiers in Plant Science 7, 627.
  • Khemka N, Singh VK, Garg R, Jain M. (2016) Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development. Scientific Reports 6, 33297
  • Jain M, Srivastava PL, Verma M, Ghangal R, Garg R. (2016) De novo transcriptome assembly and comprehensive expression profiling in Crocus sativus to gain insights into apocarotenoid biosynthesis. Scientific Reports 6, 22456
  • Garg R, Shankar R, Thakkar B, Kudapa H, Krishnamurthy L, Mantri N, Varshney RK, Bhatia S, Jain M. (2016) Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea. Scientific Reports 6, 19228.
  • Kotwal S, Kaul S, Sharma P, Shankar R, Jain M, Dhar M. (2016) De novo transcriptome analysis of medicinally important Plantago ovata using RNA-Seq. PLoS ONE 11, e0150273.
  • Dixit AB, Banerjee J, Srivastava A, Tripathi M, Sarkar C, Kakkar A, Jain M, Chandra S. (2016) RNA-Seq analysis of hippocampal tissues reveals novel candidate genes for drug refractory epilepsy in patients with MTLE-HS. Genomics 107, 178-188.
  • Ram H, Jain M, Singh A, Chattopadhyay S. (2016) Functional relationship of GBF1 with HY5 and HYH in genome-wide gene expression in Arabidopsis. Plant Molecular Biology Reporter 34, 211-220.
  • Garg R†, Chevala VVSN, Shankar R, Jain M†. (2015) Divergent DNA methylation patterns associated with abiotic stress responses and regulation of gene expression in rice. Scientific Reports 5, 14922; †Joint corresponding authors.
  • Bhattacharjee A, Ghangal R, Garg R, Jain M. (2015) Genome-wide analysis of homeobox gene family in legumes: Identification, gene duplication and expression profiling. PLoS ONE 10, e0119198.
  • Singh VK, Jain M. (2015) Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean. Frontiers in Plant Science 6, 918.
  • Parida S, Verma M, Yadav SK, Ambawat S, Das S, Garg R, Jain M. (2015) Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource. Frontiers in Plant Science 6, 645.
  • Verma M, Kumar V, Patel RK, Garg R, Jain M. (2015) CTDB: An integrated chickpea transcriptome database for functional and applied genomics. PLoS ONE 10, 0136880.
  • Singh VK, Jain M, Garg R. (2015) Genome-wide analysis and expression profiling reveals diverse roles of GH3 gene family during development and abiotic stress responses in legumes. Frontiers in Plant Science 5, 789.
  • Garg R†, Bhattacharjee A, Jain M†. (2015) Genome-scale transcriptomic insights into molecular aspects of abiotic stress responses in chickpea. Plant Molecular Biology Reporter 33, 388-400. †Joint corresponding authors.
  • Jain M†, Pole AK, Singh VK, Ravikumar RL, Garg R. (2015) Discovery of molecular markers for Fusarium wilt via transcriptome sequencing of chickpea cultivars. Molecular Breeding 35, 198.
  • Parween S, Nawaz K, Roy, R, Pole AK, Suresh V, Misra G, Jain M, Yadav G, Parida SK, Tyagi AK, Bhatia S, Chattopadhyay D. (2015) An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.). Scientific Reports 5, 12806.
  • Gaur R, Jeena G, Shah N, Gupta S, Pradhan S, Tyagi AK, Jain M, Chattopadhyay D, Bhatia S. (2015) High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea. Scientific Reports 5, 13387.
  • Khujuria YP, Saxena MS, Gaur R, Chattopadhyay D, Jain M, Parida SK, Bhatia S. (2015) Genome-wide development and validation of polymorphic genic and genomic microsatellite markers for construction of a high-density chickpea genome map. PLoS ONE. 10,
  • Kumar V, Jain M. (2015) The CRISPR-Cas system for plant genome editing: advances and opportunities. Journal of Experimental Botany 66, 47-57.
  • Jain M. (2015) Function genomics of abiotic stress tolerance in plants: A CRISPR approach. Frontiers in Plant Science 6, 375
  • Kumar V, Jain M. (2015) The CRISPR-Cas system for plant genome editing: advances and opportunities. Journal of Experimental Botany 66, 47-57. doi: 10.1093/jxb/eru429.
  • Jain M. (2015) Function genomics of abiotic stress tolerance in plants: A CRISPR approach. Frontiers in Plant Science 6, 375. doi: 10.3389/fpls.2015.00375.
  • 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 Biotechnology Journal 12, 253-264.
  • Jain M†, Chevala VVSN, Garg R. (2014) Genome-wide discovery, analysis and implications of differential regulation of conserved and novel miRNAs in chickpea via deep sequencing. Journal of Experimental Botany 65, 5945-5958.
  • Verma M†, Ghangal R†, Sharma R, Sinha AK, Jain M. (2014) Transcriptome analysis of Catharanthus roseus for gene discovery and expression profiling. PLoS ONE 9,
  • 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 salinity and submergence tolerance factors. DNA Research 21, 69-84.
  • Sharma R, Sahoo A, Devendran R, Jain M. (2014) Over-expression of a rice tau class glutathione S-transferase gene improves tolerance to salinity and oxidative stresses in Arabidopsis. PLoS ONE 9, e92900.
  • Singh VK, Jain M. (2014) Transcriptome profiling for discovery of genes involved in shoot apical meristem and flower development. Genomics Data 2, 135-138.
  • Ram H, Priya P, Jain M, Chattopadhyay S. (2014) Genome-wide DNA binding of GBF1 is modulated by its heterodimerizing partners, HY5 and HYH. Molecular Plant 7, 448-451.
  • Misra G, Priya P, Bandhiwal N, Bareja N, Jain M, Bhatia S, Chattopadhyay D, Tyagi AK, Yadav G. (2014) The Chickpea Genomic Web Resource: Visualization and analysis of the desi-type Cicer arietinum nuclear genome for comparative exploration of legumes. BMC Plant Biology 14, 315.
  • Kujur A, Bajaj D, Saxena MS, Tripathi S, Upadhyaya HD, Gowda CLL, Singh S, Tyagi AK, Jain M, Parida SK. (2014) An efficient and cost-effective approach for genic microsatellite marker-based large-scale trait association mapping: identification of candidate genes for seed weight in chickpea. Molecular Breeding 34, 241-265.
  • Garg R, Varshney R, Jain M (2014). Molecular genetics and genomics of abiotic stress responses. Frontiers in Plant Science 5, 398.
  • Garg R, Varshney R, Jain M. (2014). Molecular genetics and genomics of abiotic stress responses. Frontiers in Plant Science 5, 398. doi: 10.3389/fpls.2014.00398.
  • Singh VK, Garg R, Jain M. (2013) A global view of transcriptome dynamics during flower development in chickpea by deep sequencing. Plant Biotechnology Journal 11, 691-701.
  • Jain M, Mishra 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.). The Plant Journal 74, 715-729. (Featured and cover photo article)
  • 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. (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.
  • Ghangal R, Chaudhary S, Jain M, Purty RS, Sharma PC. (2013) Optimization of de novo short read assembly of seabuckthorn (Hippophae rhamnoides L.) transcriptome. PLoS ONE 8
  • Kujur A, Bajaj D, Saxena MS, Tripathi S, Upadhyaya HD, Gowda CLL, Singh S, Jain M, Tyagi AK, Parida SK. (2013) Functionally relevant microsatellite markers from chickpea transcription factor genes for efficient genotyping applications and trait association mapping. DNA Research 20, 355-374.
  • Garg R, Jain M. (2013) Transcriptome analyses in legumes: A resource for functional genomics. The Plant Genome 6,
  • Garg R, Jain M (2013). RNA-seq for transcriptome analysis in non-model plants. Methods in Molecular Biology 1069, 43-58.
  • Jain M (2013). Emerging role of metabolic pathways in abiotic stress tolerance. J Plant Biochem Physiol
  • Garg R, Jain M. (2013) Transcriptome analyses in legumes: A resource for functional genomics. The Plant Genome 6, doi: 10.3835/plantgenome2013.04.0011.
  • Garg R, Jain M. (2013). RNA-seq for transcriptome analysis in non-model plants. Methods in Molecular Biology 1069, 43-58.
  • Jain M. (2013). Emerging role of metabolic pathways in abiotic stress tolerance. J Plant Biochem Physiol 1, 108.
  • 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.
  • 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 Biotechnology Journal 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.
  • Gaur R, Azam S, Jeena G, Khan AW, Chaudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D, Bhatia S (2012). High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Research 19, 357-373.
  • Garg R, Tyagi AK, Jain M (2012). Microarray analysis reveals overlapping and specific transcriptional responses to different plant hormones in rice. Plant Signaling & Behavior 7, 951-956.
  • Sharma R, Agarwal P, Ray S, Deveshwar P, Sharma P, Sharma N, Nijhawan A, Jain M, Singh AK, Singh VP, Khurana JP, Tyagi AK, Kapoor S (2012). Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice. Functional and Integrative Genomics 12, 229-248.
  • Jain M (2012). Next generation sequencing technologies for gene expression profiling in plants. Briefings in Functional 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 Research 18, 463-470.
  • Garg R, Jain M (2011). Pyrosequencing data reveals tissue-specific expression of lineage-specific transcripts in chickpea. Plant Signaling & Behavior 6, 1868-1870.
  • 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 Physiology 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 Research 18, 53-63.
  • Jain M (2011). A next generation approach to the characterization of a non-model plant transcriptome. Current Science 101, 1435-1439.
  • 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 Research 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.). Biochemical and Biophysical Research Communications 396, 283-288.
  • Jain M†, Ghanashyam C, Bhattacharjee A (2010). Comprehensive expression analysis suggests overlapping and specific roles of rice glutathione S-transferase genes during development and stress responses. BMC Genomics 11, 73. (†corresponding author). (Highly accessed article)
  • Jain M†, Khurana JP (2009). Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS Journal 276, 3148-3162. (†corresponding author) (2nd most highly cited article among FEBS Journal articles in last two years)
  • Ghanashyam C, Jain M (2009). Role of auxin-responsive genes in biotic stress responses. Plant Signaling & Behavior 4, 846-848.
  • Jain M (2009). Genome-wide identification of novel internal control genes for normalization of gene expression during various stages of development in rice. Plant Science 176, 702-706.
  • Jain M*, Khurana JP (2008). Small RNA regulation of rice homeobox genes. Plant Signaling & Behavior 3, 1024-1025. (*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). Constitutive expression of a meiotic recombination protein gene homolog, OsTOP6A1, from rice confers abiotic stress tolerance in transgenic Arabidopsis plants. Plant Cell Reports 27, 767-778.
  • Jain M, Tyagi AK, Khurana JP (2008). Differential gene expression of rice two-component signaling elements during reproductive development and regulation by abiotic stress. Functional and Integrative 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 Physiology 146, 333-350.
  • Jain M, Khurana P, Tyagi AK, Khurana JP (2008). Genome-wide analysis of intronless genes in rice and Arabidopsis. Functional and Integrative Genomics 8, 69-78.
  • 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 Physiology 143, 1467-1483.
  • Singh G, Jain M, Kulshreshtha R, Khurana JP, Kumar S, Singh P (2007). Expression analysis of genes encoding translation initiation factor 3 subunit g (TaeIF3g) and vesicle-associated membrane protein-associated protein (TaVAP) in drought tolerant and susceptible cultivars of wheat. Plant Science 173, 660-669.
  • Sehgal A, Khurana JP, Sethi M, Ara H, Jain M (2007). Organ identity of the thalloid plant body of Griffithella hookeriana and Polypleurum stylosum–Podostemoideae (Podostemaceae). Plant Systematics and Evolution 267, 93-104.
  • Jain M, Sharma P, Tyagi SB, Tyagi AK, Khurana JP (2007). Light regulation and differential tissue-specific expression of phototropin homologues from rice (Oryza sativa ssp. indica). Plant Science 172, 164-171.
  • 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.
  • 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. Biochemical and Biophysical Research Communications 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 Biology 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). Functional and Integrative Genomics 6, 47-59.
  • Jain M, Kaur N, Tyagi AK, Khurana JP (2006). The auxin-responsive GH3 gene family in rice (Oryza sativa). Functional and Integrative Genomics 6, 36-46.
  • Thakur JK, Jain M, Tyagi AK, Khurana JP (2005). Exogenous auxin enhances the degradation of a light down-regulated and nuclear-localized OsiIAA1, an Aux/IAA protein from rice, via proteasome. Biochimica et Biophysica Acta 1730, 196-205.
  • Dasgupta U, Jain M, Tyagi AK, Khurana JP (2005). Regulatory elements for light-dependent and organ-specific expression of Arabidopsis thaliana PSBO1 gene encoding 33 kDa polypeptide of the oxygen-evolving complex. Plant Science 168, 1633-1642.
  • Agarwal SM†, Jain M†, Grover A† (2005). Genomic distribution of genes encoding 68 cytoplasmic ribosomal protein families in rice. Acta Physiologiae Plantarum 27, 439-446. (†equal contribution)
  • Jain M, Tyagi SB, Thakur JK, Tyagi AK, Khurana JP (2004). Molecular characterization of a light-responsive gene, breast basic conserved protein 1 (OsiBBC1), encoding nuclear-localized protein homologous to ribosomal protein L13 from Oryza sativa indica. Biochimica et Biophysica Acta 1676, 182-192.
Review articles

  • Garg R, Jain M (2026). Single-cell multi-omics atlases unlock cellular mysteries. Trends in Plant Science doi: https://doi.org/10.1016/j.tplants.2025.12.011
  • Sen MK†, Roy A, Mondal SK, Hamouzova, Jain M† (2026) RNA-directed DNA methylation: epigenome-guided herbicide-tolerant crop management. Journal of Experimental Botany https://doi.org/10.1093/jxb/erag094 †Joint corresponding author
  • Anand R, Sahil R, Jain M, Maurya GK, Khrat AS (2025). Plant-based diet as a precursor to human gut diversity. The Journal of Nutrition 156, 101251. doi: 10.1016/j.tjnut.2025.11.020
  • Sahil R, Jain M (2026). A multi-omics approach for microbiome data analysis in legumes. Methods in Molecular Biology 2977, 181-196.
  • Sahil R, Jain M (2026). A computational pipeline for the identification of RNA virome in legumes. Methods in Molecular Biology 2977, 197-204.
  • Banerjee AK, Jain M, Garg R (2026). Large-scale identification of transposon insertion polymorphisms in leguminous plants from paired-end WGS data. Methods in Molecular Biology 2977, 15-28.
  • Sahil R, Jain M (2025). Selenobacteria: The unsung friends of plants. Trends in Plant Science 30, 915-917. doi: 10.1016/j.tplants.2025.03.017
  • Garg R, Sahu SK, Jain M (2025). Single same-cell multiome for dissecting key plant traits. Trends in Plant Science 30, 128-130. doi: 10.1016/j.tplants.2024.10.008
  • Jain M (2024). Gene regulatory networks in abiotic stress responses via single-cell sequencing and spatial technologies: Advances and opportunities. Current Opinion in Plant Biology 82, 102662. doi: 10.1016/j.pbi.2024.102662.
  • Garg R, Subudhi PK, Varshney R, Jain M (2023). Abiotic Stress: Molecular genetics and genomics. Frontiers in Plant Science 13, 1101139. doi: 10.3389/fpls.2022.1101139.
  • Singh V, Jain M. (2022) Recent advancements in CRISPR-Cas toolbox for imaging applications. Critical Reviews in Biotechnology 42, 508-531. doi: 10.1080/07388551.2021.1950608.
  • Kandhol N, Jain M†, Tripathi DK†. (2022) Nanoparticles as potential hallmark of drought stress tolerance in plants: A systematic overview. Physiologia Plantarum 174, e13665. Doi: 10.1111/ppl.13665 †Joint corresponding author
  • Jain M, Garg R. (2021) Enhancers as potential targets for engineering abiotic stress tolerance in crop plants. Physiologia Plantarum 173, 1382-1391. doi: 10.1111/ppl.13421.
  • Chennakesavulu K, Singh H, Trivedi P, Jain M, Yadav SR. (2021) State-of-the-art in CRISPR technology and engineering drought, salinity, and thermo-tolerant crop plants. Plant Cell Reports doi: 10.1007/s00299-021-02681-w.
  • Ghangal R, Singh VK, Khemka N, Rajkumar MS, Garg R, Jain M (2020). Updates on genomic resources in chickpea for crop improvement. Methods in Molecular Biology 2107, 19-33.
  • Khemka N, Singh U, Dwivedi A, Jain M (2020). Machine-learning based annotation of long non-coding RNAs using PLncPRO. Methods in Molecular Biology 2107, 253-260.
  • Kumar V, Jain M. (2015) The CRISPR-Cas system for plant genome editing: advances and opportunities. Journal of Experimental Botany 66, 47-57. doi: 1093/jxb/eru429.
  • Jain M. (2015) Function genomics of abiotic stress tolerance in plants: A CRISPR approach. Frontiers in Plant Science 6, 375. doi: 10.3389/fpls.2015.00375.
  • Garg R, Varshney R, Jain M (2014). Molecular genetics and genomics of abiotic stress responses. Frontiers in Plant Science 5, 398. doi: 10.3389/fpls.2014.00398.
  • Garg R, Jain M. (2013) Transcriptome analyses in legumes: A resource for functional genomics. The Plant Genome 6, doi: 10.3835/plantgenome2013.04.0011.
  • Garg R, Jain M (2013). RNA-seq for transcriptome analysis in non-model plants. Methods in Molecular Biology 1069, 43-58.
  • Jain M (2013). Emerging role of metabolic pathways in abiotic stress tolerance. Journal of Plant Biochemistry & Physiology
  • Jain M (2012). Next generation sequencing technologies for gene expression profiling in plants. Briefings in Functional Genomics 2, 63-70.
  • Jain M (2011). A next generation approach to the characterization of a non-model plant transcriptome. Current Science 101, 1435-1439.

Book Chapters/Proceedings/Reports
  • Khandelwal R, Jain M (2018). Genome engineering tools for functional genomics and crop improvement in legumes. In: Wani SH, Jain M (eds.), Pulse Improvement - Physiological, Molecular and Genetic Perspectives, Springer Nature Switzerland AG pp 219-234. ISBN 978-3-030-01742-2.
  • Gupta V, Jain M, Reddy CRK (2017). Macroalgal functional genomics: A missing area. In: Kumar M, Ralph P (eds.), Systems Biology of Marine Ecosystems, Springer pp 3-12. ISBN 978-3-319-62092-3.
  • Sharma E, Sharma R, Borah P, Jain M., Khurana JP (2015). Emerging roles of auxin in abiotic stress responses. In: Pandey GK (eds.), Elucidation of Abiotic Stress Signaling in Plants: A Functional Genomic Perspective, Springer ISBN 978-1-4939-2210-9.
  • Bhattacharjee A, Jain M. (2013). Transcription factor mediated abiotic stress signaling in rice. In: Pandey GK (eds.), Plant Stress - Stress-Mediated Signaling in Plants, Global Science Books, Academic Press, Japan. 7, 16-25.
  • Patel R, Jain M. (2013). NGS QC Toolkit: A Platform for quality control of next generation sequencing data. In: Nelson K (ed.), Encyclopedia of Metagenomics: SpringerReference, Springer-Verlag Berlin Heidelberg, DOI: 10.1007/SpringerReference_304214.
  • Bhattacharjee A, Jain M. (2013). Homeobox genes as potential candidates for crop improvement under abiotic stress. In: Tuteja N, Gill SS (eds.), Plant Acclimation to Environmental Stress, Springer Science+Business Media, New York, USA, pp 163-176.
  • Tyagi AK, Khurana JP, Khurana P, Vij S, Jain M., Vaidhyanathan R (2007). Evolution and phylogenetic relationship of the rice genome. In: Sharma AK, Sharma A (eds.), Plant Genome: Biodiversity and Evolution (Volume IE-Phanerogam-Angiosperm), Science Publishers, New Hampshire, USA, pp 15-41.
  • Khurana JP, Jain M., Tyagi AK (2007). Auxin and cytokinin signaling component genes and their potential for crop improvement. In: Varshney RK, Tuberosa R (eds.), Genomics-Assisted Crop Improvement (Volume I-Genomics Approaches and Platforms), Springer Verlag, Germany, pp 289-314.
  • Chandra A, Jain M., Bhatt V, Vora J, Ghawna S, Ahuja PS (2007). Frontiers of plant biology research (Meeting report on ISPMB 2006). Current Science 92, 1331-1335.
  • Khurana JP, Jain M. (2007). Understanding plant reproductive pathways-molecular genetic analysis of floral induction and flower development. In: Chopra VL, Sharma RP, Bhat SR, Prasanna BM (eds.) Search for New Genes, Academic Foundation & National Academy of Agricultural Sciences, New Delhi. pp 173-195.
  • Tyagi AK, Khurana JP, Khurana P, Kapoor S, Singh VP, Singh AK, Thakur JK, Gupta V, Anand S, Vij S, Jain M., Ray S, Agarwal P, Arora R, Sharma P, Mukherjee S, Nijhawan A, Giri J, Khurana R (2007). Expression and functional analysis of rice genes involved in reproductive development and stress response. In: Brar DS, Mackill DJ, Hardy B (eds.), Rice Genetics V, International Rice Research Institute, Philippines, pp 313-330
Edited Books

Book on “Legume Genomics: Methods and Protocols - Second Edition”, Methods in Molecular Biology (Eds.) Jain M, Garg R, (2026) Springer Science+Business Media LLC, New York, USA. Vol 2977, pp 1-303 (ISBN 978-1-0716-4819-3; ISBN 978-1-0716-4820-9 for eBook) https://link.springer.com/book/10.1007/978-1-0716-4820-9


E-book/Special Issue on “Abiotic Stress: Molecular Genetics and Genomics, Volume II”, Frontiers in Plant Science (2022) Eds. Jain M, Garg R, Varshney RK, Subudhi PK. Frontiers Media SA https://www.frontiersin.org/research-topics/27165/abiotic-stress-molecular-genetics-and-genomics-volume-ii pp 1-464 (ISBN 978-2-83251-541-9).



Abiotic Stress: Molecular Genetics and Genomics
(ISBN 978-2-88919-359-2)


Pulse Improvement: Physiological, Molecular and Genetic Perspectives
(ISBN 978-3-030-01742-2)


Legume Genomics: Methods and Protocol
(ISBN 978-1-0716-0235-5)













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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
Email: mjain@jnu.ac.in | mjainanid@gmail.com

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