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• Extracted root protein from resistant and susceptible tobacco genotype at 60 DAI of nematode infection. • 2DE and in-solution digested proteins analyzed by RPLC-MS/MS to identify the unknown proteins. • Comparative proteomics revealed RFK1 and RPP 13 like candidate genes exclusively present in resistant genotype. • Out of 306 proteins, 79 proteins were up-regulated and 51 proteins were down-regulated. • These candidate genes can be exploited for the development to resistant crop against nematode disease. Root knot nematode (RKN) is an obligate endoparasitic pest of many vegetable, fruits, non-food cash crops etc. It causes more economic losses in terms of production and productivity worldwide. A range of management strategies including synthetic nematicides are available which can be harmful to human health, environment, wildlife, beneficial organisms and may induce resistance in plant populations. Therefore, identification of resistant gene is an alternative strategy to improve the crop either through breeding or by transgenic technology. In present investigation, an attempt was made to identify the candidate genes resistant to root knot nematode through proteomics approach. Comparative proteome was executed using RKN resistant ABT-10 and susceptible A-119 genotype. Proteomics was performed on nematode-challenged root tissue using 2D gel electrophoresis, in-solution trypsin digestion, and reverse phase liquid chromatography mass spectrometry. A total of 306 proteins were identified of which 79 proteins were up-regulated, 51 were down-regulated and 176 proteins showed no significant expression in resistant genotype. Out of 51 up-regulated proteins, two genes namely LRR Receptor-Like Serine/Threonine-Protein Kinase RFK1 and Putative Disease Resistance RPP13-Like Protein were identified in RKN resistant genotype. In addition to these two genes, RT-PCR analysis showed that three additional genes—Putative Wall-Associated Receptor Kinase-Like 11, Alpha-mannosidase, and TMV Resistance Protein N-Like gene—had significantly higher gene expression levels in the resistant root sample, exhibiting 14.89, 9.95, and 6.81 fold expression, respectively. The identified candidate genes can be exploited further for development of nematode resistant genotype in vegetables as well as other field crops through transgenic approaches. [ABSTRACT FROM AUTHOR]