Chief Scientist
Plant Microbe Interaction involving viral pathogens
01894-233339 Ext. 350/ 9816812300

My area of interest is plant- microbe- vector interaction, targeting identification of host factors which are manipulated by the viral pathogens for establishing infection in plant and for their spread (vector based). Viral pathogens encode a very small number of proteins, however, these proteins are of multifunctional nature to take care of the plant defense. The most important protein(s) encoded by them are suppressors of silencing or pathogenicity determinants. These proteins have been identified to directly or indirectly influence the host factors critical for taking care of plant defense (or Plant immunity which is the inherent or induced capacity of plants to withstand or ward off biological attack by pathogens: source Plant has a well-defined immunity, and is well studied in the case of bacterial and fungal pathogens. The various aspects and steps involve during this process have been reviewed nicely (Jones and Dangl, 2006; Dodds and Rathjen, 2010; Katagiri and Tsuda, 2010).


     Viral pathogens are extremely important in the world and Indian scenario causing huge losses. Keeping in view of their importance, plant virologists of the world got together and brought out “a list of ten most important viruses economically to pursue plant microbe interaction studies (Scholthoff et al., 2011 and Rybicki, EP (2014)”.  According to these lists Cucumber mosaic virus (CMV) (infects all kinds of crops such as tomato, potato, capsicum, chilli, Tomato etc) and geminiviruses occupy an important position (in the Indian context and world scenario large number of isolates have been described including Indian isolates of Tomato leaf curl viruses such as Tomato leaf curl Palampur virus TLCPMV). In the Indian scenario, in addition to above viruses, Pigeonpea sterility mosaic (SMD, states of UP, Punjab, Bihar, Madhya Pradesh, Karnataka, Tamilnadu and Kerala), and Urdbean leaf crinkle (ULCD, mid to northern states of the country) are extremely important diseases. Its We have obtained interesting information on siRNAs which are main players during disease development (leading to failure of flower and seed development). Therefore, keeping in view the importance of above viral pathogens, I propose to study plant microbe interaction to understand the immunity associated with these plants and specific pathogens. This will be totally dependent upon the mandate of NABI.

While working in this institute, my group has been able to generate highly relevant information in this context such as identification of host factors exploited by the viral proteins (direct association or indirectly effecting its expression) in relation to CMV (Kumari et al., 2016 and other publications in pipeline) and TLCPMV (Roshan et al., under revision in Nature Scientific Reports). Additionally, we are in the process of pin pointing the causal agent of SMD, meticulously characterizing the genome of isolates from various locations such as Coimbatore, Hyderabad and Bangalore. This manuscript is also in pipeline. Likewise, ULCD analysis by deep sequencing approaches is also under process and viruses belonging to Carlavirus group have been found predominately infecting this important legume of the country.


“Instead of targeting the crops, I feel it’s much more important to target a particular viral pathogen (as these can have a broad host range) and identify plant factors which (may or may not be components of the classical plant immunity list) could be targeted by transgenic and genome editing approaches such as CRISPER for resistance to these pathogens. This approach will be different from a fungal or bacterial pathogens which have a very specific association with a particular host”


Loss to nutritional quality of crop produce by Plant Viruses is well documented. Understanding association of viruses with the plants that they infect (and cause disease) will yield highly relevant information for developing cultivars resistant to virus infection. In this direction, my proposal on plant microbe interaction involving CMV, Pigeonpea sterility mosaic virus and tomato infecting Begomoviruses is highly relevant for the improving nutritional quality of crops.




PhD students guided (10):



  1. Dr Lakhmir Singh: Currently at DAV university, Jalandhar (2007), India;
  2. Dr Yogesh Kumar: Currently at DAV university, Jalandhar (2010), India;
  3. Dr Salik Khan, Currently at Jamia Millia Islamia, New Delhi (2013), India,
  4. Dr Yashika Walia (2016); young investigator at Regional center of Biotechnology, Faridabad, HR, India
  5. Dr Reenu Kumari (2016)
  6. Dr Prachi Awasthi (2016)
  7. Dr Sunny Dhir (2016), Currently at LPU, Jalandhar, India
  8. Dr Pooja Bhardwaj (2016); currently working as project coordinator, IARI regional center, Shimla, HP, India
  9. Dr Surender Kumar (2017)
  10. Dr Rahul Mohan Singh (October 23 2017)


Total publications: 163

 Publications in last 10 years: 62

1.     Singh B, Sharma S, Rani G, Zaidi AA, Hallan V and Nagpal, A (2006) In vitro production of Indian Citrus Ringspot virus free plants of Kinnow mandarin Citrus nobilis Lour.C. deliciosa Tenora by Nucellar embryo cultures. Plant Pathology Journal 5: 274-282

2.    Singh B, Sharma S, Rani G, Zaidi AA, Hallan V, Nagpal A and Virk GS (2006) In vitro production of Indian citrus ringspot virus free plants of Kinnow Mandarin (Citrus nobilis x C. deliciosa Teriora) by ovule culture. J. Plant Biotechnology 7(4): 254-265

3.     Sherpa AR, Hallan V, Pathak P and Zaidi AA (2006) Coat protein gene of Cymbidium mosaic virus: Characterization of geographical isolates from India. Journal of Phytopathology 154:275-280

4.   Kulshrestha S, Hallan V, Raikhy G, Ram R, Garg ID and Zaidi AA (2006) Incidence of Bean yellow mosaic virus on Iris.Acta Horticulture 722, 235-240

5.   Verma N, Hallan V, Ram R, Kumar K, Garg ID and Zaidi AA (2006) Detection and molecular characterization of a Tomato aspermy virus isolate infecting chrysanthemums in India.  Acta Horticulture 722, 41-53

6.    Raikhy G, Hallan V, Kulshrestha S, Ram R and Zaidi AA (2006) Detection of Carnation ringspot and Carnation vein mottle virus (es) in Carnation cultivars in India. Acta Horticulture 722, 247-258

7.     Verma N, Mehra A, Singh L, Hallan V, Singh AK, Jabeen N, Singh MK, Ram R and Zaidi AA (2007) Screening of viruses infecting chrysanthemum cultivars in India. Scientia Horticulturae 111(3): 260-265

8.    Singh L, Hallan V, Jabeen N, Singh A K, Ram R, Martin DP and Zaidi AA (2007) Coat protein gene diversity among Chrysanthemum virus B isolates from India. Archives of Virology 152(2): 405-413 

9.     Singh MK, Sherpa AR, Hallan V and Zaidi AA (2007) A potyvirus in Cymbidium northern India. Autralasian Plant pathology 2: 11-13

10.  Kumar Y, Hallan V and Zaidi AA (2008)Molecular characterization of a distinct bipartite begomovirus species infecting tomato in India. Virus Genes 37: 425–431

11.  ChandelV, Rana T, Hallan V and Zaidi AA. (2008) Occurrence of Prunus necrotic ringspot virus on nectarine (Prunus persica) in India. European plant protection organization (EPPO), 38: 223-225

12.  Chandel V, Rana T, Handa A, Thakur PD, Hallan V and ZaidiAA (2008) Incidence of Prunus necrotic ring spot virus on Malus domestica in India. Journal of Phyotopathology, 156:382-384

13.  Singh AK, Mahinghara BK, Hallan V, Ram R and Zaidi AA (2008) Recombination and phylogeographical analysis of lily symptomless virus. Virus Genes 36: 421-427.

14.  Singh B, Sharma S, Rani G, Hallan V, Zaidi AA, Virk GS and Nagpal A (2008) In vitro micrografting for production of Indian citrus ringspot virus (ICRSV)-free plants of kinnow mandarin (Citrus nobilis Lour X C. deliciosa Tenora). Plant Biotechnology Reports 2(2): 137-143

15.  Verma N, Kumar K, Kulshrestha S, Raikhy G, Hallan V, Ram R, Zaidi AAand Garg ID (2008) Molecular studies on Tomata aspermy virus isolates infecting chrysanthemums. Archives of Phytopathology and Plant Protection 42(2): 99-111

16.  Rana T, Chandel V, Hallan V and Zaidi AA (2008) Characterisation of apple chlorotic leaf spot virus infecting almonds in India. Australasian Plant Disease 3(1): 65-67

17.  Kumar Y, Hallan V and ZaidiAA (2009)First finding of Freesia mosaic virus infecting freesia in India. Plant Pathology 58: 404

18.  Rana T, Chandel V, Hallan V, Zaidi AA. 2009. Molecular evidence for the presence of Apple chlorotic leaf spot virus in infected peach trees in India. Scientia Horticulturae 120 (2) :296-299.

19.  Singh MK, Chandel, V., Hallan, V., Verma, R.R. and Zaidi, A.A. 2009. Occurrence of Peanut stripe virus on Patchouli and Raising of Virus Free Patchouli Plants by Meristem Tip Culture. Journal of Phytopathology and Plant protection 116(1):2-6

20.  Zaidi AA, Hallan V, Rana T, Raikhy G and Raja Ram (2009) Viruses in ornamental crops and their management: an Indian scenario. Journal of Ornamental Horticulture 12(3): 147-166.

21.  Kumar Y, Hallan V and Zaidi AA (2010) Emerging begomovirus problems in India. In: Emerging Geminiviral Diseases and their Management, Eds. P Sharma, RK Gaur and M Ikegami, Nova Science Publishers, Inc, pp 105-128.

22.  Ayman OF, Kumar Y, Hallan V and Zaidi AA (2010) Molecular characterization of the phytoplasmas associated with toon trees and periwinkle in India. Journal of General Plant Pathology 76: 351-354.

23.  Hossain MM, Khan SN, Sharma M, Pathak P, Hallan V and Zaidi AA (2009) Cymbidium mosaic potexvirus and Odontoglossum ringspot tobamovirus: Major threat to orchid industry. Journal of the Orchid Society of India 23 (1&2): 20-24.

24.  Kumar Y, Bhardwaj P, Hallan V and Zaidi AA (2010) Detection and characterization of Ageratum enation virus and a nanovirus-like satellite DNA1 from zinnia causing leaf curl symptoms in India. Journal of General Plant Pathology 76: 395-398.

25.  Mahinghara BK, Singh AK, Hallan V, Raja Ram and Zaidi AA (2010) Analysis of coat protein gene & untranslated region of Cucumber mosaic virus isolate infecting various Lilium species and hybrids : association of the isolate infecting Asiatic hybrid lily with subgroup II. Archives of Phytopathology and Plant Protection 43: 826-848.

26.  Negi A, Rana T, Kumar Y, Raja Ram, Hallan V and Zaidi AA (2010) Analysis of the coat protein gene of Indian strain of Apple stem grooving virus. Journal of Plant Biochemistry and Biotechnology 19(1): 91-94.


Shri VP Gokhale Award for significant contribution in teh area of Phytopathology, instituted by Prof. DV Gokhale, University of California, Riverside, USA and administered by Maharahstra Association for the cultivation of Science (MACS), Agharkar Research Institute, Pune (November 2016)




PhD Scholars:

From (year)- Jan 2017

Usha K Rattan


I am Usha K Rattan, DST Woman Scientist A, Ph. D student, Virology Lab, Department of Biotechnology, CSIR -Institute of Himalayan Bioresource Technology, Palampur, HP. I am an Alumni of Shoolini University, Solan. I am working on host pathogen interaction and aim to elucidate the role of host transcription factor(s) in disease development by Cucumber mosaic virus. The overall goal is to identify the potential host transcription factor to develop resistance in crop plants against viral pathogens. The insights gained through this study can be used to formulate a strategy to develop CMV resistance in various host plants and move towards an era of broad viral resistance.


 Surender Kumar

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