Dr Rhitu Rai
Principal Scientist
Phone :
91-11-25841787 Ext 261
Education :
Ph D: Molecular Biology and Biotechnology, IARI

Research Interest

1. Plant pathogen interaction, Ongoing research efforts for past five years are focussed on studying interactions of rice with its bacterial pathogen, Xanthomonas oryzae pv oryzae to devise strategies for better management of bacterial blight disease.  With an aim to identify and characterize interacting partners from both- pathogen as well as the host, my lab is investigating:

  • Xoo pathogenesis: We are primarily studying Transcription Activator Like effectors (TALe), which are the key pathogenicity factors present in many plant pathogenic Xanthomonads. These effectors are injected via Type III secretion system into host cell, where they bind to effector binding elements (EBE) in host genes in a sequence specific manner and activate their expression.  The TALe targets include genes whose activation contributes to disease susceptibility. Effector-host DNA binding is specified by highly repetitive central domain of effector protein, composed of near identical repeats. Due to this repetitive character of TALe genes present in multiple copies in the genome, their cloning is complicated and difficult. They have determinative influence in Xoo-rice interaction, proven by the fact that, of all the resistance genes, those have been cloned and characterized for BLB, the functions of most relate to TAL effectors. Therefore, our current efforts are extensively channeled on an emerging Xoo pathotypes in India which overcome most of the resistance genes, in quest for TALe genes and their host targets responsible for facilitating disease in resistant lines.


  1. Rice defense: We are exploring rice for two classes of genes to develop durable resistance.

Susceptibility genes: We focus on Susceptibility genes targeted by TAL effectors. A mutation in the effector binding element (EBE) in the S gene impedes biding of effector and eliminates activation of the S gene conferring resistance through loss of susceptibility. In search of natural allelic variants of the known S genes, we are screening Indian rice germplasm, which include diverse land and wild races inhabiting remote locations in India. 


Novel resistance genes: We are also conducting phenotype based screening of Indian rice germplasm and Nagina22 EMS mutant population to identify a novel source of resistance to Xoo strains compatible on most of the resistance genes. 


  1. Genomics for trait improvement in crops:  Besides pathogenomics and functional genomics in rice, my research efforts have gone in a fibre crop, flax (Linum usitatissimum) in search of stress responsive genes. We are keenly interested in exploring aquaporin gene family, owing to its role in both biotic and abiotic stress responses.


Awards & Honors

  • Lal Bahadur Shashtri Young Scientist award for the biennium 2006-2007 awarded by Indian Council of Agricultural Research, Ministry of Agriculture, Govt. of India.
  • Jawahar Lal Nehru award for best PhD work awarded by Indian Council of Agricultural Research for the year 2003-04
  • Young scientist award by Indian Science Congress Association for the year 2003-04
  1. Carpenter S C, Mishra P, Ghoshal C, Dash P K, Wang Li, Midha S, Laha G S, Lore J S, Singh N K, Singh K, Patil P B, Oliva R, Bogdanove AJ and Rai R (2018) Frontiers in Microbiology doi:
  2. Dash P K, Rai R, Rai V and Pasupalak S N (2018) Drought induced signalling in rice: Delineating canonical and Non-canonical pathways. Frontiers in Chemistry
  3. Dash P K, Rai R, Mahato AK, Gaikwad K and Singh NK (2017) Transcriptome landscape at different developmental stages of a drought tolerant cultivar of flax (Linum usitatissimum). Frontiers in Chemistry doi: 10.3389/fchem.2017.00082. 
  4. Shivraj SM, Deshmukh RK, Rai R, Belanger R, Agrawal PK and Dash PK (2017) Genome-wide identification, characterization and expression profile of aquaporin gene family in flax (Linum usitatissimum). Nature Scientific Reports doi: 10.1038/srep46137. 
  5. Rai R, Srinivasmurthy, Dash P K and Gupta P (2017) Isolation, characterization and evaluation of biocontrol potential of Pseudomonas protegens RS9 against Ralstonia solanancearum in tomato. Ind J Exptl Biol 55(9): 595-603. 
  6. Prasanta K Dash and Rhitu Rai (2016) Translating the banana genome to delineate stress resistance, dwarfing, parthenocarpy and mechanisms of fruit ripening. Frontiers in Plant Sciences 7:1543 
  7. Dash PK, Cao Y, Jailani AK, Gupta P, Venglat P, Rai R, Sharma R, Thirunavukkarasu N, Abdin MZ, Yadav DK, Singh NK, Deyhlos M, Kumar PA & Datla R. (2014) Genome wide analysis of drought induced gene expression changes in flax (Linum usitatissimum). GM Crops & Food 5(2):106-119.
  8. Rhitu Rai, Prasanta Dash, Trilochan Mohapatra and Aqbal Singh (2012) Phenotypic and molecular characterization of indigenous rhizobia nodulating chickpea in India. Ind. J. Exptl. Biol. 50(5):340-350. 
  9. Srinivasmurthy R, A K Rai, R S Jaat, Aqbal Singh and Rhitu Rai (2012) Isolation and screening of phlD+ plant growth promoting rhizobacteria antagonistic to Ralstonia solanacearum. World J. Microbiol. And Biotechnol. 28 (4):1681-90. 
  10. Ferris P, Olson BJ…………Rai R, Grimwood J, Schmutz J, Nishii I, Hamaji T, Nozaki H, Pellegrini M and Umen JG (2010) Evolution of an expanded sex determining locus in Volvox. Science. 328(5976): 351-4). 
  11. Rhitu Rai, Prasanta Dash, B M Prasanna and Aqbal Singh (2007) Endophytic bacterial flora in the stem tissue of a tropical maize (Zea mays L.) genotype: isolation, identification and enumeration. World J Microbiol and Biotechnol, 23: 853-858.
  12. Rhitu Rai & Aqbal Singh (2001). Population dynamics studies on indigenous bacterial endophytes of maize. Annals of Agricultural Research, 22(3): 309 - 311.
  13. Rhitu Rai, S.P.S. Khanuja & Koundal, K.R. (1999). Isolation and molecular characterization of d-endotoxin gene from a native Bt. strain. J. Plant Biology 26(1): 69-75.