Genetic Transformation and Functional Genetics Lab

Tools of genetic and genome engineering are contributing to a better understanding of the genetic basis of plant growth and development in addition to generation of novel varieties with desirable traits like tolerance to salt and insect pests, and better wood pulping traits. Development of methods for regeneration and transformation of tree species are challenging, and significant advances have been made in Eucalyptus camaldulensis. Salt tolerant species like Casuarinas, Rhizophora and Artemia are being prospected for major genes conferring salt tolerance using the composite transgenic strategy developed for Eucalyptus. Functional analyses of genes are being carried out using tools of RNAi and CRISPR/Cas9 mediated gene regulation. Projects are underway using RNAi for incorporation of tolerance against the Eucalyptus pest, Leptocybe invasa. As these take shape, initiatives for engineering other traits like improved productivity under drought conditions, and improved pulping traits are envisaged through national and international collaboration. The lab has had collaborations with IRD, France, University of Wisconsin-Madison, University of Osnabrück, and has attracted CSIR scholars for Ph.D. studies and has hosted two Senegalese post-doctoral researchers through C.V.Raman fellowship. The laboratory houses facilities like the Gene gun, Electroporator, Sonicator, Stereo-fluorescent microscope, PCR and Real-time PCR. The Functional Genetics Experimental Facility enables conduct of transgenic research under contained conditions.

Vision

To reach out to farmers through genetically modified trees with enhanced productivity and quality traits for growing in areas affected by biotic and abiotic stresses.

Mission    

To evolve genetic modification approaches for understanding gene function and incorporating desired traits in forestry species.

Focus species:     Eucalyptus , Casuarina Rhizophora, Artemia

 

Achievements

  • Developed composite transgenic strategy, and using RNAi identified EcHKT1:1 as a key gene regulating salt stress tolerance in Eucalyptus.
  • Identified shoot to root ratio of sodium as a defining parameter for salt tolerance in Casuarina equisetifolia.
  • Developed an online database: In silico Gene bank for adaptation to abiotic stresses http://igbaas-ifgtb.icfre.gov.in.
  • Based on transcriptome sequences generated from Leptocybe invasa, developed an insect-specific, multigene targeting chimeric hpRNAi for use in transgenic incorporation of tolerance to L. invasa.
  • Identified key gene targets for RNAi based approaches for control of Hyblaea puera.   
  • Developed an accessory for gene delivery into live plants.

Ongoing Projects/ Studies

  • Development of a genome editing platform for functional characterization of genes. NFRP
  • Transcriptome analysis of the salt excluding roots of Rhizophora mucronata. NFRP
  • Evaluation of transgene-free genome engineering methods in Eucalyptus. NFRP
  • Evaluating genes of Artemia in Eucalyptus roots for enhancing salt tolerance. SERB-DST
  • To generate Eucalyptus transgenics/ transgrafts with enhanced salt and insect tolerance for confined field trials. AICRP - CAMPA

Completed Projects

  • Web enabled database and analysis of gene sequences implicated in abiotic stress tolerance for screening gene homologues in salt tolerant tree species. DBT
  • Incorporating resistance in Eucalyptus to Leptocybe invasa Fisher & La Salle (Hymenoptera: Eulophidae) through expression of insect specific dsRNA. NFRP
  • Development of methods for functional analysis of genes involved in salt tolerance in Eucalyptus. NFRP
  • Determination of the target genes in Leptocybe invasa for engineering resistance in Eucalyptus through gene-silencing approaches. NFRP
  • Genetic transformation of Eucalyptus and Casuarina to enhance salinity tolerance. NFRP

International Collaboration

  • Development of post-transcriptional gene silencing approaches as a tool for the functional analysis of symbiotic genes in the tropical actinorhizal tree Casuarina glauca" at Rhizogenesis Lab, IRD, France. DBT
  • Developing diagnostic methods and analyzing the incorporation of monolignol ferulates into FMT transgenic Poplars destined to improve pulping performance at Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison. USIEF.
  • A CSIR-PhD Fellow, Mrs Sowmiya Rani, availed DAAD PhD Sandwich Programme at University of Osnabrück, Germany (Dec 2014 to March 2016). DAAD.
  • Two  post-doctoral researchers, Dr. Nathalie Diagne, and Dr. Issa Diedhiou from UCAD, were hosted for a six months CV Raman Fellowship during 2012-13 and 2017-18.  MoST, MoEA & FICCI.

Facilities

Gene gun, Real-time PCR, Electroporator, Stereo fluorescent microscope, Transgenic green house (Functional Genetics Experimental Facility)

 

Selected Publications

  • Sowmiya R Kottaipalayam-Somasundaram, John P Jacob, Balasubramanian Aiyar, Hans Merzendorfer, Mathish Nambiar-Veetil. 2022. Chitin metabolism as a potential target for RNAi-based control of the forestry pest Hyblaea puera Cramer (Lepidoptera: Hyblaeidae).   78: 296-303. https://doi.org/10.1002/ps.6634 Impact factor: 4.85
  • Nambiar-Veetil M, Balasubramanian A, Bogusz D and Franche C. 2018. Composite transgenic plants: an advantageous transgenic tool for elucidating gene function in difficult to transform trees. South Asia Biosafety Program Newsletter, 15(5): 2-3.
  • Chonglu Zhong, Nambiar-Veetil M, Bogusz, D and Franche, C. 2018. Hairy roots as a tool for the functional analysis of plant genes, 275-294. In Hairy roots: an effective tool of plant Biotechnology, Srivastava V, Mehrotra S, Mishra S (eds.) Springer Nature Singapore Pvt.  Ltd, Singapore.
  • Selvakesavan, R. K., Dhanya, N. N., Thushara, P., Abraham, S. M., Jayaraj, R.S.C., Balasubramanian, A., Deeparaj, B., Sudha, S., Sowmiya Rani, K.S., Bachpai, V. K. W., Ganesh, C. D., Diagne, N., Laplaze, L., Gherbi, H., Svistoonoff, S., Hocher, V., Franche, C., Bogusz, D., Nambiar-Veetil, M. 2016. Intraspecies variation in sodium partitioning, potassium and proline accumulation under salt stress in Casuarina equisetifolia Forst. Symbiosis. doi:10.​1007/​s13199-016-0424-9 Impact factor 1.438
  • Svistoonoff, S., Benabdoun, F.M., Nambiar-Veetil, M., Imanishi, L., Vaissayre, V., et al. 2013. The independent acquisition of plant root nitrogen-fixing symbiosis in Fabids recruited the same genetic pathway for nodule organogenesis. PLoS ONE, 8: e64515. doi:10.1371/journal.pone.0064515. Impact factor: 3.234
  • Zhong, C., Mansour, S., Nambiar-Veetil, M., Bogusz, D., and Franche, C. 2013. Casuarina glauca: A model tree for basic research in actinorhizal symbiosis. J Biosci, 38: 815-23. Impact factor: 1.8
  • Diagne, N., Arumugam, K., Ngom, M., Nambiar-Veetil, M., Franche, C., Narayanan, K.K., and Laplaze, L. 2013.  Use of Frankia and actinorhizal plants for degraded lands reclamation. Biomed Res Int, 2013:948258. Epub  Nov 11. Impact factor: 2.880
  • Balasubramanian, A., Venkatachalam, R., Selvakesavan R. K., Abraham, S. M., Gherbi, H., Svistoonoff, S., Franche, C., Bogusz, D., Krishna Kumar, N. and Nambiar-Veetil, M., 2011. Optimisation of methods for Agrobacterium rhizogenes mediated generation of composite plants in Eucalyptus camaldulensis. BMC Proc, 5 (Suppl 7):O45.
  • Nambiar-Veetil, M., Sangeetha, M., Sowmiya Rani, K. S., Aravinthakumar, V., Selvakesavan, R. K., Balasubramanian, A., Venkatachalam, R.,  Abraham, S. M., Jacob, J. P. and  Krishna Kumar,  N. 2011. Identification of insect-specific target genes for development of RNAi based control of the Eucalyptus gall pest Leptocybe invasa Fisher & La Salle (Hymenoptera: Eulophidae). BMC Proc, 5 (Suppl 7): P98
  • Benabdoun, F.M., Nambiar-Veetil, M., Imanishi, L. Svistoonoff, S., Ykhlef, N., Gherbi, H. and Franche, C. 2011. Composite actinorhizal plants with transgenic roots for the study of symbiotic associations with Frankia. J Bot, Article ID 702947, 8 pages
  • Perrine-Walker, F., Gherbi, H., Imanishi, L., Hocher, V., Ghodhbane-Gtari, F., Lavenus, J, Benabdoun, M, Nambiar-Veetil, M., Svistoonoff, S., and Laplaze, L. 2011. Symbiotic signaling in actinorhizal symbioses. Curr Protein Pept Sci, 12: 156-164.  Impact Factor: 2.328
  • Svistoonoff, S., Gherbi, H., Nambiar-Veetil, M., Zhong, C., Michalak, Z., Laplaze, L., Vayssaire, V., Auguy, F., Hocher, V., Doumas, P., Bonneau, J., Bogusz, D., and Franche, C. 2009. Contribution of transgenic Casuarinaceae to knowledge of the actinorhizal symbiosis. Symbiosis, 50: 3-11. Impact Factor : 1.438
  • Gherbi, H.,  Nambiar-Veetil, M., Zhong,C., Félix, J., Autran, D., Girardin, R., Vaissayre, V., Auguy, F., Bogusz, D and Franche, C. 2008.  Post- transcriptional gene silencing in the root system of the actinorhizal tree Allocasuarina verticillata. Mol Plant Microbe In, 21: 518–524. Impact Factor: 3.944
  • Tripathi, S.B., Nambiar-Veetil, M., and Gurumurthi, K. 2006. Use of genetic markers in the management of micropropagated Eucalyptus germplasm. New Forest, 31:361-372. Impact Factor: 1.829, Citation 8
  • Nambiar-Veetil, M., Tripathi S.B., and Gurumurthi K. 2001. DNA- Fingerprint database management using Microsoft Access- a simple strategy to corroborate fingerprints of clones. PCBMB, 2: 119-124.