Research Groups

Nair

Plant Insect Interaction

Group Leader

Research Interests and Description

Suresh Nair

International Centre for Genetic Engineering and Biotechnology
Aruna Asaf Ali Marg
110 067 New Delhi, India

E-mail: sureshicgeb.res.in
Tel: +91-11-26741242
Fax: +91-11-26742316

Education

Department of Botany, University of Delhi, India, PhD, 1990
Department of Botany, University of Delhi, India, MSc, 1983
Hindu College, University of Delhi, India, BSc (Honours), 1981

Career History

Since 2016, Group Leader, Plant Insect Interaction, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
1989-2015, Staff Research Scientist, Plant Molecular Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
1987-1989, Research Scientist, Department of Botany, University of Delhi, India
2000-2001, Visiting Scientist, Department of Entomology, Purdue University, West Lafayette, Indiana, USA

Teaching Activity

Course co-ordinator for the module "Molecular Biology of Plant Stress" taught as part of the ICGEB, New Delhi, Ph.D. programme

Scientific Activity

Virulence of phytophagous insects is guided by their competence to evade or suppress host defense and reprogram host metabolic machinery to favour their sustenance. Our Group is interested in understanding the molecular basis of insect-plant interactions using the Asian rice gall midge (AGM) and rice as the insect and plant model, respectively. AGM (Orseolia oryzae; Order Diptera, Family Cecidomyiidae) is a major insect pest of rice and is proficient in extensively maneuvering rice defense and metabolic activities causing considerable yield and monetary loss to farmers in India, Africa, South-East Asia and neighbouring countries. The problem is further compounded by the occurrence of several gall midge biotypes (GMB) [currently, seven GMBs are known to occur in India] and these are able to overcome the deployed resistance genes (R) in rice. In most cases, a single, dominant R gene in rice governs resistance to AGM.

Our earlier initiatives lead to the tagging and mapping of gall midge resistance genes (Gm2, Gm4, Gm7 and Gm8) in rice. A PCR-based marker aided selection (MAS) system for these genes was first developed in our lab. Recently, we have initiated cloning and sequencing of identified R genes from different rice varieties.Currently, Gm4 is being functionally validated.

Additionally, multiple approaches are being followed to identify differentially expressed genes/metabolites and to reveal the remodeling events occurring in rice varieties harboring different R genes. Utilizing suppressive subtractive hybridization (SSH) cDNA libraries prepared from rice hosts in a compatible (rice variety TN1 [without R genes] with GMB4) and hypersensitive response-mediated incompatible (rice variety Suraksha [harbouring Gm11] with GMB4) interactions we showed that response in rice to AGM is similar to responses generated by plants against pathogens. Further, using microarray analyses, we showed the presence of a novel mechanism of resistance in one of the rice varieties, Kavya, that exhibited a non-hypersensitive response-mediated incompatible interaction with GMB1. Gas chromatography mass spectrometry (GC-MS) -based studies on the metabolome of several indica rice varieties identified biomarkers that could be grouped as resistance-, susceptibility-, infestation features-specific for compatible and incompatible interactions with GMB1.

Future investigations involve integrated omics (proteomics, transcriptomics, metabolomics) to discover mechanism/s involved in incompatible interactions in Kavya (Gm1), Aganni (Gm8) and RP2068 (gm3).

During the AGM infestation process, the initial interaction between the midge and the host determines whether the latter would succumb to the midge or resist it. Feeding larvae inject salivary secretions into the host and these we believe are determinants of the avirulence/virulence phenomenon. We developed a cDNA library from salivary gland-enriched tissue and from it successfully identified and cloned and subsequently, using a heterologous expression system, expressed secreted salivary gland proteins (SSGPs) of the AGM. Rice plants injected with recombinant SSGPs e.g. OoDAD1 and OoNDPK, showed necrosis and coleoptile cell elongation, respectively. These alterations in host physiology are akin to those seen in susceptible rice hosts after AGM infestation. Furthermore, transcriptome-based differential gene expression analyses, using next generation sequencing (NGS) technology, revealed differential response of large set of gall midge genes depending on whether it is in a compatible or incompatible interaction with its host.

We recently sequenced the complete mitochondrial genome of the AGM. Unique characters were identified that include rearrangement of gene order, truncation and unusual secondary structures of tRNAs as well as the presence of one pseudo-tRNA. Tandem repeats in one of the non-coding regions were also identified in the mitogenome. Further, the presence of unique repeats in this non-coding region of the AGM’s mitogenome allowed us to develop genetic markers capable of differentiating AGM biotypes and also different species of Orseolia.

We are currently trying to understand the role of miRNAs in this interaction using both compatible and incompatible interactions. Our group is also undertaking an NGS approach to study the microbiome of the AGM to see if it has any influence or role to play in the interaction.

Selected publications

Agarrwal, R., Padmakumari, A.P., Bentur, J.S., Nair, S. 2016. Metabolic and transcriptomic changes induced in host during hypersensitive response mediated resistance in rice against the Asian rice gall midge. Rice 9, 5

Divya D., Singh, Y.T., Nair, S., Bentur, J.S. 2016. Analysis of SSH library of rice variety Aganni reveals candidate gall midge resistance genes. Funct. Integr. Genomics 16, 153-169

Bentur, J.S., Rawat, N., Divya, D., Sinha, D.K., Agarrwal, R., Atray, I. Nair, S. 2016. Rice-gall midge interactions: Battle for survival. J. Insect Physiol. 84, 40-49 PubMed link

Sinha, D.K., Atray, I., Bentur, J.S., Nair, S. 2015. Feeding on resistant rice leads to enhanced expression of defender against apoptotic cell death (OoDAD1) in the Asian rice gall midge. BMC Plant Biol 15, 235 PubMed link

Atray, I., Bentur, J.S. and Nair, S. 2015. The Asian rice gall midge (Orseolia oryzae) mitogenome has evolved novel gene boundaries and tandem repeats that distinguish its biotypes. PLoS ONE 10 (7): e0134625. PubMed link

Divya D., Himabindu, K., Nair, S., Bentur, J.S. 2015. Cloning of a gene encoding LRR protein and its validation as candidate gall midge resistance gene, Gm4, in rice. Euphytica 203, 185–195

Agarrwal, R., Bentur, J.S., Nair, S. 2014. Gas chromatography mass spectrometry based metabolic profiling reveals biomarkers involved in rice-gall midge interactions. J Integr Plant Biol 56, 837–848 PubMed link

Rawat, N., Himabindu, K., Neeraja, C. N., Nair, S., Bentur, J. S. (2013) Suppressive subtraction hybridization reveals that rice gall midge attack elicits plant-pathogen-like responses in rice. Plant Physiol Biochem 63, 122-130 PubMed link

Bentur, J. S., Rawat, N., Sinha, D. K., Nagaraju, J., Nair, S. 2013. New genetic avenues for insect pest management in rice as revealed by studies on gall midge. In: Muralidharan, K. and Siddiq, E. A. (Eds). International Dialogue on Perception and Prospects of Designer Rice. Society for Advancement of Rice Research, Directorate of Rice Research, Hyderabad 500030, India. pp 185-187 

Nair, S. 2013. Strategies to understand insect resistance in plants through the rice-gall midge interaction. In: Saini, R. K. and Sharma, S. S. (Eds). Advances in Pest Management in Legume Crops. Department of Entomology, CCS Haryana Agricultural University, Hisar, India. pp 192-195

Nair, S., Bentur, J. S. Sama, V. S. A. K. 2011. Mapping gall midge resistance genes: towards durable resistance through gene pyramiding. In: Muralidharan, K. and Siddiq, E. A. (Eds). Genomics and crop improvement: Relevance and reservations. Institute of Biotechnology, Acharya N. G. Ranga Agricultural University, Rajendranagar, Hyderabad 500030, India. pp 256-264

Sinha, D.K., Bentur, J.S., Nair, S. 2011. Compatible interaction with its rice host leads to enhanced expression of the gamma subunit of oligosaccharyl transferase in the Asian rice gall midge, Orseolia oryzae. Insect Mol Biol 20, 567-575  PubMed link

Sinha, D.K., Lakshmi, M., Anuradha, G., Rahman, S.J., Siddiq, E.A., Bentur, J.S., Nair, S. 2011. Serine proteases-like genes in the Asian rice gall midge show differential expression in compatible and incompatible interactions with rice. Int J Mol Sci 12, 2842-2852  PubMed link

Bhattacharjee, B., Mohan, M., Nair, S. 2010. Transformation of chickpea: effect of genotype, explant, Agrobacterium-strain and composition of culture medium. Biol Plant 54, 21-32

Rawat, N., Sinha, D.K., Rajendrakumar, P., Shrivastava, P., Neeraja, C.N., Sundaram, R.M., Nair, S., Bentur, J.S. 2010. Role of pathogenesis-related genes in the rice-gall midge interactions. Curr Sci 99, 1361-1368.

Reddy, R.A., Kumar, B., Reddy, P.S., Mishra, R.N., Mahanty, S., Kaul, T., Nair, S., Sopory, S.K., Reddy, M.K. 2009. Molecular cloning and characterization of genes encoding Pennisetum glaucum ascorbate peroxidase and heat-shock factor: Interlinking oxidative and heat-stress responses. J Plant Physiol 166, 1646-1659 PubMed link

Reddy, P.S., Mahanty, S., Kaul, T., Nair, S., Sopory, S.K., Reddy, M.K. 2008. A high-throughput genome-walking method and its use for cloning unknown flanking sequences. Anal Biochem 381, 248-253  PubMed link

Reddy, P.S., Nair, S., Mallikarjuna, G., Kaul, T., Markandeya, G., Sopory, S.K., Reddy, M.K. 2008. A high-throughput, low-cost method for the preparation of ‘sequencing-ready’ phage DNA template. Anal. Biochem. 376, 258-261 PubMed link

Mishra, R.N., Reddy, P.S., Nair, S., Markandeya, G., Reddy, A.R., Sopory, S.K., Reddy, M.K. 2007. Isolation and characterization of expressed sequence tags (ESTs) from subtracted cDNA libraries of Pennisetum glaucum seedlings. Plant Mol. Biol. 64, 713-732 PubMed link

Agarwal, P., Agarwal, P.K., Nair, S., Sopory, S.K., Reddy, M.K. 2007. Stress-inducible DREB2A transcription factor from Pennisetum glaucum is a phosphoprotein and its phosphorylation negatively regulates its DNA-binding activity. Mol. Genet. Genomics 277, 189-198 PubMed link

Mishra, R.N., Ramesha, A., Kaul, T., Nair, S., Sopory, S.K., Reddy, M.K. 2005. A modified cDNA subtraction to identify differentially expressed genes from plants with universal application to other eukaryotes. Anal. Biochem. 345, 149-157 PubMed link

Jain, A., Ariyadasa, R., Kumar, A., Srivastava, M.N., Mohan, M., Nair, S. 2004. Tagging and mapping of a rice gall midge resistance gene, Gm8, and development of SCARs for use in marker-aided selection and gene pyramiding. Theor. Appl. Genet. 109, 1377-1384 PubMed link

Harris, M.O., Stuart, J.J., Mohan, M., Nair, S., Lamb, R.J., Rohfritsch, O. 2003. Grasses and gall midges: Plant defense and insect adaptation. Annu. Rev. Entomol. 48, 549-577 PubMed link

Mishra, R.N., Singla-Pareek, S.L., Nair, S., Sopory, S.K., Reddy, M.K. 2002. Directional genome walking using PCR. BioTechniques 33, 830-834 PubMed link

Sardesai, N, Kumar, A., Rajyashri, K.R., Nair, S., Mohan, M. 2002. Identification and mapping of an AFLP marker linked to Gm7, a gall midge resistance gene and its conversion to a SCAR marker for its utility in marker aided selection in rice. Theor. Appl. Genet. 105, 691-698 PubMed link

Behura, S.K., Nair, S., Mohan M. 2001. Polymorphisms flanking the mariner integration sites in the rice gall midge (Orseolia oryzae Wood-Mason) genome are biotype-specific. Genome 44, 947-954 PubMed link

Behura, S.K., Nair, S., Sahu S.C., Mohan, M. 2000. An AFLP marker that differentiates biotypes of the Asian rice gall midge (Orseolia oryzae, Wood-Mason) is sex-linked and also linked to avirulence. Mol. Gen. Genet. 263, 328-334 PubMed link

ICGEB New Delhi

ICGEB Campus
Aruna Asaf Ali Marg
110 067 New Delhi
INDIA
Tel: +91-11-26741358/1007
Fax: +91-11-26742316
icgebicgeb.res.in

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