Raja Ragupathy, Ph. D.

Image Raja Ragupathy
Research Scientist

Crop Breeding & Genomics. He has unique expertise in both field-based plant breeding and lab-based, state of the art genomics. His research is focused on developing perennial cereals (wheat and rye) towards sustainable agriculture and enhancing the genetic potential of Fall-rye and winter triticale adapted to western Canada.

Current research and/or projects

Plant breeding and genomic research, especially in winter cereals, with the objectives of improving crop yield, adaptation to both abiotic and biotic stresses and enhancing cropping system sustainability. Specifically, his research is focused on developing perennial cereals (in wheat and rye) towards sustainable agriculture and enhancing the genetic potential of fall-rye and winter triticale adapted to western Canada. He will be using modern genomics, epigenetic and bioinformatics tools for understanding the molecular basis of economically important traits and translating the knowledge to breed improved cereal cultivars, to retain Canada's pre eminent position in the world.

Research and/or project statements

  • Genomic prediction for cold tolerance and fusarium head blight (FHB) resistance in winter durum for western Canada. (2019-2023)
  • Identifying novel genes in perennial wheatgrass for stripe rust and FHB (Co-Lead)
  • Using agronomy to reduce ergot susceptibility in fall-rye (WGRF) (Co-Lead)
  • Developing winter durum wheat for Southern Alberta (WGRF/AWC) (Co-Lead)
  • Integration of agronomy and breeding to reduce disease susceptibility in fall-rye (SWCDC) (Co-Lead)
  • Organic cluster - Developing winter triticale and fall-rye cultivars for no-tillage cultivation (Co-Lead)

Professional activities / interests

  • Genomics and Breeding research in perennial cereals, and winter cereals
  • Mentoring students
  • Expert reviewer for funding organizations in Canada
  • Peer Reviewer for manuscripts submitted to Crop Science, Scientific Reports, BMC Genomics, Canadian Journal of Plant Science, Plant Molecular Biology, International Journal of Plant Genomics, Indian Journal of Genetics and Plant Breeding, Journal of Genetics, Genome and Plant Cell Reports


Education and awards

Ph.D.              University of Manitoba, Canada; 2004-2008  Major: Plant Science  

M.Sc. (Ag.)     Tamil Nadu Agricultural University, India; 1994-1996; Major: Plant Breeding and Genetics

B.Sc. (Ag.)             Tamil Nadu Agricultural University, India; 1989-1993; Major: Agriculture

Awards and Scholarships:


Visiting Fellowship from the Canadian Government Laboratory


University of Manitoba Graduate Fellowship


Manitoba Graduate Scholarship awarded by the Ministry of Advanced Education of the Government of Manitoba for outstanding international students in the province of Manitoba


Plant Science Graduate Student Travel Award

2004, 2007

William B. Malchy Graduate Fellowship


Clarence-Bougardus Sharp Memorial Scholarship


SRF from the Council of Scientific and Industrial Research, India


SRF from the Indian Council of Agricultural Research (ICAR)


Qualified in the National Eligibility Test (NET) for lectureship conducted by ICAR in the discipline of Plant Breeding


Qualified in the NET for lectureship in the discipline of Genetics


Junior Research Fellowship from ICAR


Awarded the gold medal for outstanding performance in the Bachelor of Agriculture programme

International experience and/or work

During the period from June 2000 to May 2009, Raja Ragupathy served as an Assistant Professor of Plant Breeding and Genetics at the Pandit Jawaharlal Nehru College of Agriculture and Research Institute (https://www.pajancoa.ac.in/, a government of Puducherry institution, with academic affiliation to Pondicherry University, http://www.pondiuni.edu.in/) in India.  He also co-ordinated multilocation field trials associated with the all India coordinated rice improvement project (AICRIP) trials in India.

During the period from December 2014 to May 2015, he served as a Senior Scientist (Genomics) at the Indian Rice Research Institute, Cuttack, India (http://www.icar-iirr.org) for the Federal government of India.

Key publications

  1. You, F.M., Li, P., Kumar, S., Ragupathy, R., Li, Z.N., Fu, Y.B., and Cloutier, S. (2014). "Genome-wide Identification and Characterization of the Gene Families Controlling Fatty Acid Biosynthesis in Flax (Linum usitatissimum L).", Journal of Proteomics & Bioinformatics, 7(10), pp. 310-326. doi : 10.4172/jpb.1000334

    2014 - View publication details

  2. Ragupathy, R., Madhi, S.R., Domaratzki, M., and Cloutier, S. (2014). "Micro RNAs and siRNAs underlying genetic and epigenetic mechanisms of adaptation to abiotic stresses in Triticum aestivum cutivar Glenlea.", 2nd Wheat Genetics Symposium, Saskatoon, SK, Canada, June 2014, pp. 8. (Poster)

    2014 - View publication details

  3. Ragupathy, R., You, F.M., and Cloutier, S. (2013). "Genome-wide comparative analysis of LTR retrotransposon dynamics In flax (Linum usitatissimum) and Its related genomes, cassava (Manihot esculenta) and poplar (Populus trichocarpa).", Plant & Animal Genome XXI Conference, Town & Country Convention Center, San Diego, CA, USA, January 12-16, 2013.

    2013 - View publication details

  4. You, F.M., Kumar, S., Banik, M., Ragupathy, R., Deyholos, M.K., Fu, Y.B., Sharpe, A.G., and Cloutier, S. (2013). "Ordering the draft genome sequence of flax (Linum usitatissimum).", Plant & Animal Genome XXI Conference, Town & Country Convention Center, San Diego, CA, USA, January 12-16, 2013.

    2013 - View publication details

  5. You, F.M., Kumar, S., Ragupathy, R., Deyholos, M.K., Fu, Y.B., Sharpe, A.G., and Cloutier, S. (2013). "Organization and evolution of the flax genome.", 2013 CSPB/SCBV Annual General Meeting, Laval University, Quebec City, Canada, June 25-28, 2013, Poster no. F6, page no. 89 of the abstract book. (Poster)

    2013 - View publication details

  6. Ragupathy, R., You, F.M., and Cloutier, S. (2013). "Arguments for standardizing transposable element annotation in plant genomes.", Trends in Plant Science. doi : 10.1016/j.tplants.2013.03.005

    2013 - View publication details

  7. Soto-Cerda, B.J., Diederichsen, A., Ragupathy, R., Cloutier, S. (2013). Genetic characterization of a core collection of flax (Linum usitatissimum L.) suitable for association mapping studies and evidence of divergent selection between fiber and linseed types, 13(1), http://dx.doi.org/10.1186/1471-2229-13-78

    2013 - View publication details

  8. Cloutier, S., Ragupathy, R., Miranda, E., Radovanovic, N., Reimer, E., Walichnowski, A., Ward, K., Rowland, G., Duguid, S., Banik, M. (2012). Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.), 125(8), 1783-1795. http://dx.doi.org/10.1007/s00122-012-1953-0

    2012 - View publication details

  9. Cloutier, S., Miranda, E., Ward, K., Radovanovic, N., Reimer, E., Walichnowski, A., Datla, R., Rowland, G., Duguid, S., Ragupathy, R. (2012). Simple sequence repeat marker development from bacterial artificial chromosome end sequences and expressed sequence tags of flax (Linum usitatissimum L.), 125(4), 685-694. http://dx.doi.org/10.1007/s00122-012-1860-4

    2012 - View publication details

  10. Cloutier, S., Ragupathy, R., Niu, Z., Duguid, S. (2011). SSR-based linkage map of flax (Linum usitatissimum L.) and mapping of QTLs underlying fatty acid composition traits, 28(4), 437-451. http://dx.doi.org/10.1007/s11032-010-9494-1

    2011 - View publication details

  11. Ragupathy, R., Rathinavelu, R., Cloutier, S. (2011). Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome, 12 http://dx.doi.org/10.1186/1471-2164-12-217

    2011 - View publication details

  12. Ragupathy, R., Cloutier, S., Rowland, G.G., Duguid, S.D., Datla, R.S.S., Selvaraj, G., Deyholos, M.K., Wang, E., Fofana, B., Zou, J., Reaney, M.J.T., Weselake, R.J., Philips, P., Smyth, S., and Barker, C. (2010 Internal). "Total utilization of flax genomics (TUFGEN).", Internal Review Meeting, Department of Biotechnology (DBT-Government of India) supported flaxproject, National Chemical Laboratory (NCL), Pune, India, June 16, 2010. (Presentation)

    2010 - View publication details

  13. Fofana, B., Ragupathy, R., and Cloutier, S. (2010). "Flax Lipids: Classes, biosynthesis, genetics and the promise of applied genomics for understanding and altering of fatty acids.", in Gilmore, P.L. (ed.) - Lipids: Categories, Biological Functions and Metabolism, Nutrition, and Health, Nova Science Publishers Inc, Chapter 3, pp. 71-98.

    2010 - View publication details

  14. Ragupathy, R., Banks, T., Cloutier, S. (2010). Molecular characterization of the Sasanda LTR copia retrotransposon family uncovers their recent amplification in Triticum aestivum (L.) genome, 283(3), 255-271. http://dx.doi.org/10.1007/s00438-009-0509-8

    2010 - View publication details

  15. Ragupathy, R. and Cloutier, S. (2008). "Molecular phylogeny of Sasanda LTR Copia retrotransposon family in Triticum aestivum (L.) reveals recent transposition activity.", 11th International Wheat Genetics Symposium (IWGS), Brisbane Convention & Exhibition Centre, Brisbane, Queensland, Australia, August 24-29, 2008.

    2008 - View publication details

  16. Ragupathy, R., Cloutier, S. (2008). Genome organisation and retrotransposon driven molecular evolution of the endosperm Hardness (Ha) locus in Triticum aestivum cv Glenlea, 280(6), 467-481. http://dx.doi.org/10.1007/s00438-008-0380-z

    2008 - View publication details

  17. Ragupathy, R., Naeem, H.A., Reimer, E., Lukow, O.M., Sapirstein, H.D., Cloutier, S. (2008). Evolutionary origin of the segmental duplication encompassing the wheat GLU-B1 locus encoding the overexpressed Bx7 (Bx7OE) high molecular weight glutenin subunit, 116(2), 283-296. http://dx.doi.org/10.1007/s00122-007-0666-2

    2008 - View publication details

Research facility

5403 1st Avenue South
Lethbridge, AB T1J 4B1


• Member, Canadian Society of Plant Biologists (2013 - present)

• Member, American Association for the Advancement of Science (2008 - present)

• Member, Crop Science Society of America

• Life Member, Indian Society of Genetics and Plant Breeding

• Member, Prairie Recommending Committee for Wheat, Rye & Triticale

• Member, Alberta Regional Variety Advisory Committee (fall-rye)

• Member, Saskatchewan Variety Performance Group (fall-rye)



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