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. Sangha et al. (2022). Spectral reflectance indices reveal wheat variety response to heat and drought stress. CSA-CWSS joint meeting, November 14-18, 2022, Halifax, NS

    2022 - View publication details

  2. Natarajan, M., Singh, K.D., George, J., and Ragupathy, R., “Developing a Low-cost Digital Imaging System for Plant Phenotyping using Raspberry Pi Computers”, ISCB-ISMB Digital Agriculture Conference, Jul. 2022, Madison, Wisconsin, USA, Abstract # 921. (Virtual Online)

    2022 - View publication details

  3. Ragupathy R, Larsen JR, Frick M, Cattani DJ, Miller J, Elwood J, Zezula A, OrtegaPolo R, Soto-Cerda BJ, Laroche A. 2020. Genomic prediction of heading date in intermediate wheatgrass (Thinopyrum intermedium). PAG XXVIII Conference PE0510

    2020 - View publication details

  4. Zhang, W., Ruan, Y., Knox, R.E., Berraies, S., Campbell, H.L., Ragupathy, R., Boyle, K., Polley, B., Henriquez, M.A., Burt, A., Kumar, S., Cuthbert, R.D., Fobert, P.R., Buerstmayr, H., and DePauw, R. 2019. Genome wide association analysis to characterize Fusarium head blight resistance in durum wheat. 1st International Wheat Congress, Saskatoon, SK, Canada, July 21-26, 2019.

    2019 - View publication details

  5. Ravichandran, S., Ragupathy, R., Edwards, T., Domaratzki, M., Cloutier, S. (2019). Microrna-guided regulation of heat stress response in wheat. BMC Genomics, [online] 20(1), http://dx.doi.org/10.1186/s12864-019-5799-6

    2019 - View publication details

  6. Ragupathy, R., Ruan, Y., Berraies, S., Campbell, H., Meyer, B., Henriquez, M.A., Kumar, S., Burt, A., Zhang, W., Cuthbert, R.D., Fobert, P., and Knox, R.E. 2019. Genomic Selection for Fusarium Head Blight Resistance in Durum Wheat. XXVII International Plant and Animal Genome Conference, San Diego, CA, USA, January 12-16, 2019.

    2019 - View publication details

  7. Ruan, Y., Barraies, S., Sari, E., Knox, R.E., Cuthbert, R., Piché, I., Henriquez, M.A., Kumar, S., Burt, A., Konkin, D., Campbell, H.L., Li, L., Ragupathy, R., Zhang, W., and Fobert, P.R. 2018. Marker validation for FHB resistance in durum wheat. National Fusarium Head Blight Forum, St. Louis, MO, USA. December 2-4, 2018.

    2018 - View publication details

  8. Ragupathy, R., Ruan, Y., Berraies, S., Campbell, H., Meyer, B., Cuthbert, R.D., Henriquez, M.A., Kumar, S., Burt, A., Zhang, W., Fobert, P., and Knox, R.E. 2018. Genomic selection in durum wheat: prediction accuracies of FHB resistance in a diversity panel and its application in biparental breeding populations. 9th Canadian Workshop on Fusarium Head Blight/4th Canadian Wheat Symposium, Winnipeg, Canada, November 19-22, 2018.

    2018 - View publication details

  9. Ravichandran S, Ragupathy R, Edwards T, Robinson S, Domaratzki M, Cloutier S (2017) MicroRNA guided post-transcriptional gene regulation in response to heat stress in wheat. Joint Meeting Canadian Society of Plant Biologists and Canadian Society for Horticultural Science, Vancouver, July 4-7 (oral)

    2017 - View publication details

  10. House M, Ragupathy R, Vasudevan A, You FM, Jia G, Robinson S, Booker H (2017) Genome-wide approaches to identifying the basis of early flowering in epimutagenized royal Flax. Proc 25th Plant and Animal Genome Conference, San Diego, CA, January 14-18, W327 (workshop oral talk).

    2017 - View publication details

  11. You, F.M., Li, P., Ragupathy, R., Kumar, S., Zhu, T., Luo, M.-C., Duguid, S.D., Rashid, K.Y., Booker, H.M., Deyholos, M.K., Fu, Y.B., Sharpe, A.G., and Cloutier, S. (2016). "The Draft Flax Genome Pseudomolecules.", 66th Flax Institute of the United States, Holiday Inn, Fargo, North Dakota, USA, March 31-April 1, 2016, pp. 17-24.

    2016 - View publication details

  12. You FM, Li P, Ragupathy R, Kumar S, Zhu T, Luo M-C, Duguid SD, Rashid K, Booker H, Deyholos M, Fu Y-B, Sharpe A, Cloutier S (2016) The draft flax genome pseudomolecules. 66th Flax Institute of the United States, Fargo, North Dakota, March 31-April 1, 2016.

    2016 - View publication details

  13. Cloutier, S., Deyholos, M.K., Ragupathy, R., Zhu, T., Li, P., Luo, M.-C., and You, F.M. (2016). "BioNano optical map improves the flax reference genome.", XXIV Plant and Animal Genome Conference, San Diego, USA, January 9-13, 2016.

    2016 - View publication details

  14. Ragupathy, R., Ravichandran, S., Mahdi, M.S.R., Huang, D., Reimer, E., Domaratzki, M., Cloutier, S. (2016). Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV. Scientific Reports, [online] 6 http://dx.doi.org/10.1038/srep39373

    2016 - View publication details

  15. Xiao J, Sekhwal MK, Li P, Ragupathy R, Cloutier S, Wang X, You FM (2016) Pseudogenes and Their Genome-Wide Prediction in Plants. Int J Mol Sci. 17(12). pii: E1991.

    2016 - View publication details

  16. Ravichandran S, Ragupathy R, Edwards T, Mahdi MSR, Lévesque-Lemay M, Domaratzki M, Cloutier S (2016) Heat stress-responsive miRNA are transiently expressed to impart stress tolerance in wheat plants. Proc 3rd Can Wheat Symposium, Ottawa, Nov22-25, S29

    2016 - View publication details

  17. Ravichandran S, Ragupathy R, Mahdi MSR, Huang D, Reimer E, Domaratzki M, Cloutier S (2016) Sequencing of small RNA transcriptome demonstrates distinct temporal expression pattern of stress regulated miRNA in wheat. Canadian Society of Agronomy Annual Meeting, Montreal, 24-26 July, P22

    2016 - View publication details

  18. Thambugala D, Ragupathy R, Cloutier S (2016) Structural organization of fatty acid desaturase loci in linseed lines with contrasting linolenic acid contents. Funct Integr Genomics 16:429-439

    2016 - View publication details

  19. You, F.M., Cloutier, S., Shan, Y.F., and Ragupathy, R. (2015). "LTR Annotator: Automated Identification and Annotation of LTR Retrotransposons in Plant Genomes.", International Journal of Bioscience, Biochemistry and Bioinformatics, 5(3), pp. 165-174. doi : 10.17706/ijbbb.2015.5.3.165-174

    2015 - View publication details

  20. You, F.M., Li, P., Kumar, S., Ragupathy, R., Banik, M., Duguid, S.D., Booker, H.M., Deyholos, M.K., Fu, Y.B., Sharpe, A.G., and Cloutier, S. (2015). "The refined flax genome, its evolution and application.", XXIII Plant and Animal Genome Conference, San Diego, CA, USA, January 10-14, 2015, P1039. (Poster)

    2015 - 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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