Scientist Profile

Dr Rupesh Deshmukh

Dr Rupesh Deshmukh

Ramalimgaswami Fellow

Date of Joining: 23 Apr 2018

+91 96507 92638

Molecular Breeding, Molecular Biology, Computational Genomics

Visiting Professor at  University Laval, Quebec (QC) Canada (Dec 2014 to Apr 2018)

Operated a project funded by a public-private partnership between Syngenta and University Laval. Responsibilities include coordination of research activities in-house, communication with collaborating centers, and to train graduate students.


Post-doctoral Fellow  at University of Missouri, Columbia, USA  (Feb 2014 to Nov 2014)

The project entitled “Drought, heat, and flood tolerant soybean varieties for the Midwest and South: building on success”.


Post-doctoral Fellow at University Laval, Quebec (QC) Canada (Jul 2011 to Feb 2014)

The project entitled “A novel approach to improve plant resistance to biotic and abiotic stresses”.

  • Demonstrated absolute requirement of NPA spacing for the solute specificity of Aquaporin 
  • Enhanced understanding of the role of aquaporins in plants
  • Developed tools and techniques for Aquaporin research
  • Identified Gn4-1 gene for high grain number in rice panicle
  • Developed highly variable SSR marker resource for rice
  • Enhanced understanding of the role of silicon in plants
  • Identified silicon transporter genes in several plant species including soybean, strawberry, Populous



Improvement in yield, fruit quality, and nutritive value of tomatoes using advanced approaches like genome-editing and molecular breeding

To achieve simultaneous improvement in yield, fruit quality, and nutritive value of tomatoes with minimum efforts, a multigene targeting with a single Cas9 based construct is being used. The target selected for the genome-editing include genes which have been previously shown to be involved in the trait of interest, in addition, some of the targeted are selected to verify the biological role of candidate genes.


Meta-analysis to understand the genetic regulation of important traits in tomato

MetaQTLs are being located in the precise chromosomal interval by using QTL information generated over the years and several different mapping populations. Integration of MetaQTL and RNAseq transcriptome profiling will be performed to select candidate genes.


Induced mutagenesis in Tomato

Physical, chemical and genetic approaches are being used to develop tomato mutant population. The mutant population will be used for the selection of improved trait as well as for gene identification

  1. Deshmukh R, Sonah H, Belanger R (2020) New evidence defining the evolutionary path of aquaporins regulating silicon uptake in land plants. Journal of Experimental Botany 71 (21) 6775–6788.

  2. Mandlik R, Thakral V, Raturi G, Shinde S, Nikoli M, Tripathi DK, Sonah H, Deshmukh R (2020) Significance of silicon uptake, transport, and deposition in plants. Journal of Experimental Botany. doi: 10.1093/jxb/eraa301

  3. Deshmukh R, Vivancos J, Balkrishnan G, et al. (2015) A precise spacing between NPA domains of aquaporins is essential for silicon permeability in plants. Plant Journal. 83(3):489-500.

  4. Deshmukh R, and Belanger R (2015) Molecular evolution of aquaporins and silicon influx in plants. Functional Ecology. DOI: 10.1111/1365-2435.12570

  5. Deshmukh R, Singh A, Jain N, et al. (2010) Identification of candidate genes for grain number in rice (Oryza sativa L.). Funct Integr Genomics 10:339–347 - nal1 (gn4) gene first report

  6. View All Publication
  7. Kumawat S, Khatri P, Ahmed A, Vats S, Kumar V, Jaiswal R, Wang Y, Xu P, Mandlik R, Shivaraj SM, Deokar A, Sharma TR, Deshmukh R. Understanding aquaporin transport system, silicon and other metalloids uptake and deposition in bottle gourd (Lagenaria siceraria). Journal of Hazardous Materials. 2020 Nov 18:124598.

  8. Manna M, Thakur  T, Chirom O, Mandlik  R, Deshmukh R, Salvi P (2020) Transcription factors as key molecular target to strengthen the drought stress tolerance in plants. Physiologia Plantarum

  9. Ram H, Singh A, Katoch M, Kaur R, Sardar S, Palia S, Satyam R, Sonah H, Deshmukh R, Pandey A, Sharma TR (2020) Dissecting the nutrient partitioning mechanism in rice grain using spatially resolved gene expression profiling. Journal of Experimental Botany, eraa536,

  10. Bansal R, Rana N, Singh A, Dhiman P, Mandlik R, Sonah H, Deshmukh R, Sharma TR (2020) Evolutionary Understanding of Metacaspase Genes in Cultivated and Wild Oryza Species and Its Role in Disease Resistance Mechanism in Rice. Genes 11:1412.

  11. Ratnaparkhe MB, Marmat N, Kumawat G, Shivakumar M, Kamble VG, Nataraj V, Ramesh SV, Deshmukh MP, Singh AK, Sonah H, Deshmukh R, Prasad M, Chand S, Gupta S (2020) Whole Genome Re-sequencing of Soybean Accession EC241780 Providing Genomic Landscape of Candidate Genes Involved in Rust Resistance. Current Genomics. 21(7):504-11

  12. Vats, Bansal R, Rana N, Kumawat S, Bhatt V, Jadhav P, Kale V, Sathe A, Sonah H, Jugdaohsingh R, Sharma TR, Deshmukh R (2020) Unexplored nutritive potential of tomato to combat global malnutrition. Critical Reviews in Food Science and Nutrition

  13. Kumar N, Kumawat S, Khatri P, Singla P, Tandon G, Bhatt V, Shinde S, Patil GB, Sonah H, Deshmukh R (2020) Understanding aquaporin transport system in highly stress-tolerant and medicinal plant species Jujube (Ziziphus jujuba Mill.). Journal of Biotechnology 324: 103-111

  14. Singh S, Bhatt V, Kumar V, Kumawat S, Khatri P, Singla P, Shivaraj SM, Nadaf A, Deshmukh R, Sharma TR, Sonah H (2020) Evolutionary Understanding of Aquaporin Transport System in the Basal Eudicot Model Species Aquilegia coerulea. Plants (6):799.

  15. Jaswal R, Kiran K, Rajarammohan S, Dubey H, Singh PK, Sharma Y, Deshmukh R, Sonah H, Gupta N, Sharma TR (2020) Effector Biology of Biotrophic Plant Fungal Pathogens: Current Advances and Future Prospective. Microbiological Research 23:126567.

  16. Ram H, Gandass N, Sharma A, Singh A, Sonah H, Deshmukh R, Pandey AK, Sharma TR (2020) Spatio-temporal distribution of micronutrients in rice grains and its regulation. Critical Reviews in Biotechnology 40(4):490-507.

  17. Singh RK, Deshmukh R, Muthamilarasan M, Rani R, Prasad M (2020) Versatile roles of aquaporin in physiological processes and stress tolerance in plants. Plant Physiology and Biochemistry 149:178-89.

  18. Shivaraj SM, Vats S, Bhat JA, Dhakte P, Goyal V, Khatri P, Kumawat S, Singh A, Prasad M, Sonah H, Sharma TR, Deshmukh R (2020) Nitric oxide and hydrogen sulfide crosstalk during heavy metal stress in plants. Physiologia Plantarum 168(2):437-55.

  19.  Ansari WA, Chandanshive SU, Bhatt V, Nadaf AB, Vats S, Katara JL, Sonah H, Deshmukh R (2020) Genome Editing in Cereals: Approaches, Applications and Challenges. International Journal of Molecular Sciences 21(11):4040.

  20. Mushtaq M, Mukhtar S, Sakina A, Dar AA, Bhat R, Deshmukh R, Molla K, Kundoo AA, Dar MS (2020) Tweaking genome-editing approaches for virus interference in crop plants. Plant Physiology and Biochemistry 147:242-50.

  21. Chaudhary J, Khatri P, Singla P, Kumawat S, Kumari A, Vikram A, Jindal SK, Kardile H, Kumar R, Sonah H, Deshmukh R (2019) Advances in Omics Approaches for Abiotic Stress Tolerance in Tomato. Biology 8(4):90.

  22. Singh A, Sharma AK, Singh NK, Sonah H, Deshmukh R, Sharma TR (2019) Understanding the Effect of Structural Diversity in WRKY Transcription Factors on DNA Binding Efficiency through Molecular Dynamics Simulation. Biology 8(4):83.

  23. Shivaraj SM, Deshmukh R, Sonah H, Bélanger RR (2019) Identification and characterization of aquaporin genes in Arachis duranensis and Arachis ipaensis genomes, the diploid progenitors of peanut. BMC Genomics 20(1):222.

  24. Chattopadhyay A, Purohit J, Tiwari KK, Deshmukh R (2019) Targeting transcription factors for plant disease resistance: Shifting paradigm. Curr. Sci. 117:1598-607.

  25. Rana N, Rahim MS, Kaur G, Bansal R, Kumawat S, Roy J, Deshmukh R, Sonah H, Sharma TR (2019) Applications and challenges for efficient exploration of omics interventions for the enhancement of nutritional quality in rice (Oryza sativa L.). Critical Reviews in Food Science and Nutrition 8:1-7.

  26. de Ronne M, Labbé C, Lebreton A, Sonah H, Deshmukh R, Jean M, Belzile F, O’Donoughue L, Bélanger R (2019) Integrated QTL mapping, gene expression and nucleotide variation analyses to investigate complex quantitative traits: a case study with the soybean–Phytophthora sojae interaction. Plant Biotechnology Journal 18(7):1492-4.

  27. Vats S, Kumawat S, Kumar V, Patil GB, Joshi T, Sonah H, Sharma TR, Deshmukh R (2019) Genome editing in plants: Exploration of technological advancements and challenges. Cells. 8(11):1386.

  28. Guerriero G, Deshmukh R, Sonah H, Sergeant K, Hausman JF, Lentzen E, Valle N, Siddiqui KS, Exley C (2019) Identification of the aquaporin gene family in Cannabis sativa and evidence for the accumulation of silicon in its tissues. Plant Science 287:110167.

  29. Coskun D, Deshmukh R, Sonah H, Shivaraj SM, Frenette?Cotton R, Tremblay L, Isenring P, Bélanger RR. Si permeability of a deficient Lsi1 aquaporin in tobacco can be enhanced through a conserved residue substitution. Plant Direct 3(8):e00163.

  30. Vishwakarma K, Mishra M, Patil G, Mulkey S, Ramawat N, Pratap Singh V, Deshmukh R, Kumar Tripathi D, Nguyen HT, Sharma S. Avenues of the membrane transport system in adaptation of plants to abiotic stresses. Critical Reviews in Biotechnology 39(7):861-83.

  31. Singh A, Singh PK, Sharma AK, Singh NK, Sonah H, Deshmukh R, Sharma TR (2019) Understanding the role of the WRKY gene family under stress conditions in pigeonpea (Cajanus cajan L.). Plants 8(7):214.

  32. Coskun D, Deshmukh R, Sonah H, Menzies JG, Reynolds O, Ma JF, Kronzucker HJ, Bélanger RR. In defence of the selective transport and role of silicon in plants. New Phytologist. doi/full/10.1111/nph.15764

  33. Kumawat S, Rana N, Bansal R, Vishwakarma G, Mehetre ST, Das BK, Kumar M, Yadav SK, Sonah H, Sharma TR, Deshmukh R (2019) Expanding Avenue of Fast Neutron Mediated Mutagenesis for Crop Improvement. Plants 8(6):164.

  34. Ram H, Kaur A, Gandass N, Singh S, Deshmukh R, Sonah H, Sharma TR (2019) Molecular characterization and expression dynamics of MTP genes under various spatio-temporal stages and metal stress conditions in rice. PloS One 14(5):e0217360.

  35. Ram H, Singh BP, Katara J, Chopra R, Kumar P, Jaiswal R, Geetika, Deshmukh R, Sonah H (2019) A genome-wide resource of intron spanning primers compatible for quantitative PCR and intron length polymorphism in rice. Indian J. Genet. 79(2):499-502.

  36. Chaudhary J, Alisha A, Bhatt V, Chandanshive S, Kumar N, Mir Z, Kumar A, Yadav SK, Shivaraj SM, Sonah H, Deshmukh R (2019) Mutation breeding in tomato: advances, applicability and challenges. Plants 8(5):128.

  37. Bhat JA, Shivaraj SM, Singh P, Navadagi DB, Tripathi DK, Dash PK, Solanke AU, Sonah H, Deshmukh R (2019) Role of silicon in mitigation of heavy metal stresses in crop plants. Plants. 8(3):71.

  38. Zargar SM, Mahajan R, Bhat JA, Nazir M, Deshmukh R (2019) Role of silicon in plant stress tolerance: opportunities to achieve a sustainable cropping system. 3 Biotech., 1;9(3):73.

  39. Yadav MK, Aravindan S, Raghu S, Prabhukarthikeyan SR, Keerthana U, Ngangkham U, Pramesh D, Banerjee A, Adak T, Kar MK, Parameswaran C, Deshmukh R, Tiwari JK, Mohanty MR, Rath PC (2019) Assessment of genetic diversity and population structure of Magnaporthe oryzae causing rice blast disease using SSR markers. Physiological and Molecular Plant Pathology, 106:157-165

  40. Yadav MK, Aravindan S, Ngangkham U, Raghu S, Prabhukarthikeyan SR, Keerthana U, Marndi BC, Adak T, Munda S, Deshmukh R, Pramesh D (2019) Blast resistance in Indian rice landraces: Genetic dissection by gene specific markers. PloS one, 23;14(1):e0211061.

  41. Coskun D, Deshmukh R, Sonah H, Menzies J, Reynolds O, Ma J, Kronzucker H, Bélanger R (2018) The controversies of silicon’s role in plant biology. New Phytologist. (Highly prestigious Tansley review)

  42. Sevanthi AMV, Kandwal P, Kale BS, …, Deshmukh R, et al. (2018) Whole Genome Characterization of a few EMS Induced Mutants of Upland Rice Variety Nagina 22 reveals staggeringly high frequency of SNPs with high phenotype plasticity. Front. Plant Sci., In Press.

  43. Rasoolizadeh A, Labbé C, Sonah H, Deshmukh R, Belzile F, Menzies J, Bélanger R (2018) Silicon protects soybean plants against Phytophthora sojae by interfering with effector-receptor expression. BMC Plant Biology. 18:97

  44. Agarwal G, Clevenger J, Pandey MK, Wang H, Shasidhar Y, Chu Y, Fountain JC, Choudhary D, Culbreath AK, Liu X, Huang G, Wang X, Deshmukh R, et al. (2018) High?density genetic map using whole?genome re?sequencing for fine mapping and candidate gene discovery for disease resistance in peanut. Plant Biotechnology Journal.

  45. Patil G, Vuong TD, Kale S, Valliyodan B, Deshmukh R, et al. (2018) Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high?density linkage mapping. Plant Biotechnology Journal.

  46. Tayade R, Nguyen T, Oh SA, Hwang YS, Yoon IS, Deshmuk R, et al. (2018) Effective Strategies for Enhancing Tolerance to High-Temperature Stress in Rice during the Reproductive and Ripening Stages. Plant Breeding and Biotechnology. 1;6(1):1-8.

  47. Ouellette S, Goyette MH, Labbé C, Laur J, Gaudreau L, Gosselin A, Dorais M, Deshmukh RK, Bélanger RR (2017) Silicon transporters and effects of silicon amendments in strawberry under high tunnel and field conditions. Frontiers in Plant Science. 8;8:949.

  48. Ratcliffe S, Jugdaohsingh R, Vivancos J, Marron A, Deshmukh R, Ma JF, Mitani-Ueno N, Robertson J, Wills J, Boekschoten MV, Müller M (2017) Identification of a mammalian silicon transporter. American Journal of Physiology-Cell Physiology. 1;312(5):C550-61

  49. Shivaraj SM, Deshmukh RK, Rai R, Bélanger R, Agrawal PK, Dash PK (2017) Genome-wide identification, characterization, and expression profile of aquaporin gene family in flax (Linum usitatissimum). Scientific Reports;7. 10.1038/srep46137

  50. Zargar SM, Nagar P, Deshmukh R, Nazir M, Wani AA, Masoodi KZ, Agrawal GK, Rakwal R (2017) Aquaporins as potential drought tolerance inducing proteins: Towards instigating stress tolerance. Journal of Proteomics.

  51. Shivaraj SM, Deshmukh R, Bhat JA, Sonah H, Bélanger RR (2017) Understanding Aquaporin Transport System in Eelgrass (Zostera marina L.), an Aquatic Plant Species. Frontiers in Plant Science.  3;8:1334.

  52. Sonah H, Deshmukh R, Labbe C, Belanger RR (2017) Analysis of aquaporins in Brassicaceae species reveals high-level of conservation and dynamic role against biotic and abiotic stress in canola. 

  53. Deshmukh R, Sonah H, Belanger R (2016) Plant Aquaporins: genome-wide identification, transcriptomics, proteomics, and advanced analytical tools. Front Plant Sci, 7, 1896. having equal contribution

  54. Song L, Nguyen LN, Deshmukh R, Patil GB, Prince SJ, et al. (2016) Soybean TIP gene family analysis and characterization of GmTIP1; 5 and GmTIP2; 5 in water transport. Frontiers in Plant Science, 7:1564.

  55. Sonah H, Zhang X, Deshmukh R, Borhan M, Fernando W, Bélanger R (2016) Comparative transcriptomic analysis of virulence factors in Leptosphaeria maculans during compatible and incompatible interactions with canola. Front Plant Sci, 7.

  56. Vivancos J, Deshmukh R, Grégoire C, Rémus-Borel W, Belzile F, Bélanger R (2016) Identification and characterization of silicon efflux transporters in horsetail (Equisetum arvense). J Plant Physiol. doi:10.1016/j.jplph.2016.06.011

  57. Tomar R, Tiwari S, Naik B, Chand S, Deshmukh R, et al. (2016) Molecular and Morpho-Agronomical Characterization of Root Architecture at Seedling and Reproductive Stages for Drought Tolerance in Wheat. PloS One 11(6): p.e0156528.

  58. Deshmukh R, Sonah H, Bélanger R (2016) Computational Prediction of Effector Proteins in Fungi: Opportunities and Challenges. Front Plant Sci 7: 126. doi:10.3389/fpls.2016.00126. having equal contribution

  59. Kadam S, Vuong T, Qiu D, Meinhardt C, Song L, Deshmukh R, et al. (2016). Genomic-assisted phylogenetic analysis and marker development for next generation soybean cyst nematode resistance breeding. Plant Science. doi:10.1016/j.plantsci.2015.08.015

  60. Deshmukh R, Sonah H, Singh N (2016). Intron gain, a dominant evolutionary process supporting high levels of gene expression in rice. J Plant Biochem Biotech. 25(2):142-146.

  61. Deshmukh R, Vivancos J, Balkrishnan G, et al. (2015) A precise spacing between NPA domains of aquaporins is essential for silicon permeability in plants. Plant Journal. 83(3):489-500.

  62. Deshmukh R, and Belanger R (2015) Molecular evolution of aquaporins and silicon influx in plants. Functional Ecology. DOI: 10.1111/1365-2435.12570

  63. Sonah H, Vuong T, Meinhardt C, Deshmukh R, et al. (2015) Genetic architecture of cyst nematode resistance revealed by genome-wide association study in soybean. BMC Genomics 16:593. having equal contribution

  64. Manavalan L, Prince S, Musket T, Chaky J, Deshmukh R, et al. (2015) Identification of novel QTL governing root architectural traits in an interspecific soybean population. PloS One, 10(3), e0120490. having equal contribution

  65. Chaudhary J, Patil G, Sonah H, Deshmukh R, et al. (2015) Expanding omics resources for improvement of soybean seed composition traits.  Front Plant Sci. doi: 10.3389/fpls.2015.0102

  66. Deshmukh R, Tomar R, Naik K, et al (2014) Development of chloroplast?specific microsatellite markers for molecular characterization of alloplasmic lines and phylogenetic analysis in wheat. Plant Breeding 133 (1), 12-18. having equal contribution

  67. Deshmukh R, Sonah H, Patil G, et al (2014) Integrating omic approaches for abiotic stress tolerance in soybean. Front Plant Sci. doi: 10.3389/fpls.2014.00244

  68. Deshmukh R, Vivancos J, Guérin V, et al (2013) Identification and functional characterization of silicon transporters in soybean using comparative genomics of major intrinsic proteins in Arabidopsis and rice. Plant Mol Bio, 83(4-5):303-15

  69. Katara J, Deshmukh R, Singh NK, Kaur S (2012). Molecular typing of native Bacillus thuringiensis isolates from diverse habitats in India using REP-PCR and ERIC-PCR analysis. J General Appl Microb, 58(2): 83-94.

  70. Deshmukh R, Sonah H, Sharma A, et al.  (2011) Genome-wide Distribution and Organization of Microsatellites in Plants: An Insight of Marker Development in Brachypodium. PlosOne: 6 (6):e21298 having equal contribution

  71. Sonah H, Deshmukh R, Singh VP, et al. (2011) Genomic resources in horticultural crops: Status, Utility and Challenges. Biotechnological Advances. Biotech. Adv. 29:199–209

  72. Deshmukh R, Singh A, Jain N, et al. (2010) Identification of candidate genes for grain number in rice (Oryza sativa L.). Funct Integr Genomics 10:339–347

  73. Deshmukh R, Singh H, Singh A, et al. (2010) Highly variable SSR markers suitable for rice genotyping using agarose gels. Mol Breeding 25:359–364 having equal contribution

NASI Scopus Young Scientist Awards – Elsevier. The Award is from NASI and Elsevier to recognize India’s most promising researchers who are working in the field of AGRICULTURE and are committed to developing sustainable models that help in increasing food security and improving the quality of life of people living in rural areas (November 2019)

Fellow of Indian Society of Genetics and Plant Breeding (FISGPB) (December 2018)

Ramalingaswami Fellowship a highly prestigious award by Ministry of Science & Technology Department of Biotechnology Government of India (November 2017)

Awarded Research Excellence fellowship for postdoctoral research by FSAA Laval University, Quebec (QC) Canada (July 2011)

Best Reviewer of the year award by Plants (ISSN: 2223-7747)      (November 2019)

Best Reviewer award by Indian Journal of Genetics and Plant Breeding (ISSN: 0975-6906) (December 2019)

Global Peer Review Award (Web of Science) in category - Top reviewers in Plant and Animal Science (September 2019)

Global Peer Review Award (Web of Science)- Top reviewers for Multidisciplinary (September 2018)

Global Peer Review Award (Web of Science)- Top reviewers for General (September 2017)

Global Peer Review Award (Web of Science) - Sentinels of Science: Agricultural and Biological Sciences (September 2016)

Link for Publons records:

Qualified National Eligibility Test (NET) for Lectureship conducted by Agricultural Scientist Recruitment Board, Government of India (December 2010)

Qualified National Eligibility Test (NET) for Lectureship conducted by Agricultural Scientist Recruitment Board, Government of India (December 2009)

Qualified National Eligibility Test (NET) for Lectureship conducted by University Grant Commission and CSIR, Government of India (June 2008)

Associate Editor for The Plant Genome (IF 3.5) from November, 2020

Associate Editor for Journal of Plant Biochemistry and Biotechnology (IF 0.8) from 2018

Associate Editor for Bulletin of the National Research Centre from 2017

Topic Editor for Biomolecules (IF 4.0) from 2020

Guest Associate Editor of Environmental and Experimental Botany (Impact Factor (IF)4.3)

Guest Associate Editor of Frontiers in Plant Science (IF 4.3)

Guest Associate Editor of Frontiers in Physiology (IF 4.1)

Guest Associate Editor of International Journal of Genomics (IF 2.4)

Guest Associate Editor of Plant Physiology and Biochemistry (IF 3.7)

Lead Guest Associate Editor of International Journal of Genomics (IF 2.4)

Editorial board member of the Indian Journal of Genetics and Plant Breeding (IF 0.4)

Editorial board member of the American Association for Science and Technology