Sylvie Cloutier, Ph.D.

Image Sylvie Cloutier
Principal Research Scientist

Lead and/or principal investigator of Genome Canada, industry-led and government-funded projects;

Conduct research in Genomics, Genetics, Epigenetics and Bioinformatics of wheat and flax;

Focus on genetic diversity, wild relatives, resistance to biotic (disease) and abiotic (drought, heavy metals) stresses.

Current research and/or projects

  • 4DWheat: Diversity, Domestication, Discovery and Delivery
    • Leads: Curtis Pozniak and Sylvie Cloutier
    • Collaborators: Frank M. You, Sean Walkowiak, Steve Robinson, Sateesh Kagale, Curt McCartney, Colin Hiebert, Andrew Sharpe, Richard Cuthbert, Steve Shirtliffe, Maria Antonia Henriquez, Richard Gray, Jill Hobbs, Tristan Skolrud, Peter Slade and Alfons Weersink
    • Funding: $11,401,111
    • Funding source: Genome Canada, AAFC Partnership, Canadian Wheat Research Coalition, Western Grains Research Foundation, Illumina, Saskatchewan Wheat Development Commission, Alberta Wheat Development Commission, Manitoba Wheat and Barley Development Commission, Viterra, Province of Saskatchewan, Ontario Ministry of Economic Development, Job Creation and Trade
    • Time: 2019-2024
  • A pre-breeding platform for Canadian wheat improvement
    • Leads: Sylvie Cloutier and Curt McCartney
    • Collaborators: Frank You, Brent McCallum, Reem Aboukhaddour, Adam Foster, George Fedak, Maria Antonia Henriquez, Barbara Blackwell, Dan MacEachern
    • Funding: $1,034,574
    • Funding Source: Canadian Agricultural partnership – AAFC/Canadian Wheat Cluster (managed by Saskatchewan Wheat Development Commission)
    • Time: 2018-2023
  • Assessing genotypic diversity and environmental impact on cadmium concentration in flax seed in support of enhanced plant breeding
    • Leads: Axel Diederichsen and Sylvie Cloutier
    • Collaborators: Scott Duguid, Dallas Kessler and Richard Gugel
    • Funding: $284,476
    • Funding source: Canadian Agricultural partnership – AAFC/Diversified Field Crop Cluster (managed by AgWest Bio)
    • Time: 2018-2023
  • Genomics and molecular markers to identify disease resistance genes in flax
    • Leads: Frank You and Sylvie Cloutier
    • Collaborators: Khalid Rashid, Helen Booker, Randy Kutcher, Lester Young
    • Funding: $839,301
    • Funding source: Canadian Agricultural partnership – AAFC/Diversified Field Crop Cluster (managed by AgWest Bio)
    • Time: 2018-2023
  • Exploring the extent and potential of epigenetic variation in wheat
    • Lead: Steve Robinson
    • Collaborators: Sylvie Cloutier, Curtis Pozniak, Andrew Sharpe
    • Funding: $524,000
    • Funding source: Canadian Wheat Alliance
    • Time: 2016-2021
  • Characterization of rust resistance genes of flax
    • Lead: Helen Booker
    • Collaborators: Sylvie Cloutier, Frank You, Khalid Rashid, Lester Young, Randy Kutcher
    • Funding: $357,139
    • Funding source: Agricultural Development Funds, Western Grains Research Foundation and Saskatchewan Flax Development Commission
    • Time: 2017-2020

Research and/or project statements

  • 4DWheat:
    • To produce reference genome assemblies for six Aegilops species;
    • To perform pan-genome analyses of 50 Aegilops and Triticum genomes using long-range reference-guided assemblies;
    • To perform SNP discovery and diversity analyses using low coverage short reads;
    • To produce genomic data and bioinformatics analyses of five backcross populations and 25 Nested Association Mapping (NAM) populations derived from 30 synthetic wheats to improve cross design and selection to increase the genetic diversity of the D genome from Ae. tauschii.
  • Wheat Pre-Breeding Platform:
    • To genotype and phenotype a collection of wheat, progenitors, synthetics and wild relatives for leaf rust, stripe rust, Fusarium head blight and powdery mildew;
    • To perform a genome wide association study for all traits and identify genes and markers for wheat improvement.
  • Flax Cadmium:
    • To sequence high and low cadmium accessions and to perform GWAS analysis for cadmium accumulation in flax.
  • Flax Diseases:
    • To develop markers and isolate genes for resistance to pasmo, powdery mildew and Fusarium wilt in flax.
  • Wheat Epigenetics:
    • To study gene expression mechanisms in synthetic wheats through RNASeq and  microRNAs.
  • Recent Publications:
    • Walkowiak S, Gao L, Monat C, Haberer G, Kassa MT, Brinton J, Ramirez-Gonzalez RH, Kolodziej MC, Delorean E, Thambugala D, Klymiuk V, Byrns B, Gundlach H, Bandi V, Siri JN, Nilsen K, Aquino C, Himmelbach A, Copetti D, Ban T, Venturini L, Bevan M, Clavijo B, Koo D-H, Ens J, Wiebe K, N’Diaye A, Fritz AK, Gutwin C, Fiebig A, Fosker C, Fu BX, Accinelli GG, Gardner KA, Fradgley N, Gutierrez-Gonzalez J, Halstead-Nussloch G, Hatakeyama M, Koh CS, Deek J, Costamagna AC, Fobert P, Heavens D, Kanamori H, Kawaura K, Kobayashi F, Krasileva K, Kuo T, McKenzie N, Murata K, Nabeka Y, Paape T, Padmarasu S, Percival-Alwyn L, Kagale S, Scholz U, Sese J, Juliana P, Singh R, Shimizu-Inatsugi R, Swarbreck D, Cockram J, Budak H, Tameshige T, Tanaka T, Tsuji H, Wright J, Wu J, Steuernagel B, Small I, Cloutier S, Keeble-Gagnère G, Muehlbauer G, Tibbets J, Nasuda S, Melonek J, Hucl PJ, Sharpe AG, Clark M, Legg E, Bharti A, Langridge P, Hall A, Uauy C, Mascher M, Krattinger SG, Handa H, Shimizu KK, Distelfeld A, Chalmers K, Keller B, Mayer KFX, Poland J, Stein N, McCartney CA, Spannagl M, Wicker T, Pozniak CJ (2020) Multiple wheat genomes reveal global variation in modern breeding. Nature (
    • Fatima F, McCallum BD, Pozniak CJ, Hiebert C, McCartney C, Fedak G, You FM, Cloutier S (2020) Resistance gene cloning from a wild crop relative by sequence capture and association genetics. Frontiers Plant Sci (doi: 10.3389/fpls.2020.583738)
    • Sertse D, You FM, Ravichandran S, Soto-Cerda BJ, Duguid S, Cloutier S (2020) Loci harboring genes with important role in drought and related abiotic stress responses in flax revealed by multiple GWAS models. Theor Appl Genet Online first Oct 12 (doi: 10.1007/s00122-020-03691-0)
    • Khan N, You FM, Datla R, Ravichandran S, Jia B, Cloutier S (2020) Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.). BMC Genomics 21:722 (doi: 10.1186/s12864-020-07121-9)
    • Rajagopalan N, Lu Y, Burton IW, Monteil-Rivera F, Halasz A, Reimer E, Tweidt R, Brule-Babel A, Kutcher HR, You FM, Cloutier S, Cuperlovic-Culf M, Hiebert CW, McCallum BD, Loewen MC*(2020) A phenylpropanoid diglyceride associates with the leaf rust resistance Lr34res gene in wheat. Phytochemistry 178:112456 (
    • You FM, Cloutier S (2020) Mapping quantitative trait loci onto chromosome-scale pseudomolecules in flax. Methods Protoc 3:E28 (doi: 10.3390/mps3020028)
    • Soto-Cerda BJ, Cloutier S, Gagardo HA, Aravena G, Quian R, You FM (2020) Drought response of flax accessions and identification of quantitative trait nucleotides (QTNs) governing agronomic and root traits by genome-wide association analysis. Mol Breeding 40:15 (
    • Shafiei-Koij F, Cloutier S, Ravichandran S, Barthet V, Rodrigue N, Mirlohi A, Majidi MMM (2020) Evolution of Carthamus species revealed through sequence analyses of the fad2 gene family. Physiol Mol Biol Plant 26: 419-432 (
    • Sertse D, You FM, Ravichandran S, Cloutier S (2020) The Complex Genetic Architecture of Early Root and Shoot Traits in Flax Revealed by Genome-Wide Association Analyses. Front Plant Sci 10:1483 (

Fields of Science

Learn more about my research and how it impacts you by visiting Fields of Science, a campaign featuring 11 Agriculture and Agri-Food Canada scientists from coast to coast.

Professional activities / interests

  • Co-Lead of the Genome Canada project 4DWheat
  • Co-Lead of the Genome Canada project TUFGEN
  • Co-Lead of the Canadian Wheat Pre-Breeding Platform

Education and awards


  • Ph.D. Molecular Genetics, University of Montréal, 1994
  • M.Sc. Plant Biotechnology, Univeristy of Guelph, 1990
  • B.Sc.Appl. Agronomy, Laval University, 1987


  • Farm Credit Canada Rosemary Davis Award for leadership in agriculture, 2013

International experience and/or work

International consortium

  • Walkowiak S, … Cloutier S, et al. (2020) Multiple wheat genomes reveal global variation in modern breeding. Nature (
  • McCouch S, … Cloutier S, et al. (2013) Agriculture: Feeding the future. Nature 499:23-24


  • Rosewarne GM, … Cloutier S, McFadden H, Lagudah ES (2006) Leaf tip necrosis, molecular markers and beta1-proteasome subunits associated with the slow rusting resistance genes Lr46/Yr29. Theor Appl Genet 112(3):500-508


  • Soto-Cerda BJ, Cloutier S, … Quian R (2019) Identifying drought-resilient flax genotypes and related-candidate genes based on stress indices, root traits and selective sweep. Euphytica 215:41
  • Soto-Cerda BJ, Cloutier S, et al. (2019) Genome-wide association analysis identifies QTL and candidate genes governing seed mucilage content and hull content in flax (Linum usitatissimum L.). Int J Mol Sci 19:2870


  • Zhu Z, … Cloutier S, Xia X, He Z (2019) Management of wheat Fusarium head blight through cultivar resistance in the Global North: China, USA and Canada. Crop J 7:730-738


  • Saha D, … Cloutier S, You FM (2018) Genome-wide regulatory gene-derived hypervariable SSRs reveal genetic differentiation and population structure in fibre flax genotypes. J Appl Genet 60:13-25


  • Shafiei-Koij F, Cloutier S, … Majidi MMM (2020) Evolution of Carthamus species revealed through sequence analyses of the fad2 gene family. Physiol Mol Biol Plant 26: 419-432
  • Asgarinia P, Cloutier S, … Saeidi G (2013) Mapping QTL for powdery mildew resistance in flax (Linum usitatissimum L.). Crop Sci 53:2462-2472
  • Malihipour A, … Cloutier S (2012) Molecular phylogenetic analysis, trichotecene chemotype patterns, and variation in aggressiveness among Fusarium graminearum isolates from different sources. Plant Dis 96:1016-1025


  • Wicker T, … Cloutier S, … Keller B (2009) Analysis of intraspecies diversity in wheat and barley genomes identifies breakpoints of ancient haplotypes and provides insight in the structure of diploid and hexaploid Triticeae gene pools. Plant Physiol 149:258-270
  • Cloutier S, … Wicker T, Feuillet C, Keller B, Jordan MC (2007) A leaf rust resistance gene, Lr1, isolated from bread wheat wheat (Triticum aestivum L.), is a member of the large psr567 gene family. Plant Mol Biol 65:93-106


  • Wang Z, … Paterson AH, Cloutier S (2017) Tandem duplications of receptor-like kinase genes reshaped the homologous regions in Oryza sativa ssp. indica and japonica sub-genomes and their possible ancestral genomes. Mol Breeding 37:3
  • Shi G, … Cloutier S, … Faris JD (2016) Marker development, saturation mapping and high-resolution mapping of the Septoria nodorum blotch susceptibility gene Snn3-B1 in wheat. Mol Genet Genomics 291:107-119
  • Faris JD, … Cloutier S, et al. (2010) A unique wheat disease resistance-like gene governs effector-triggered susceptibility to necrotrophic pathogens. Proc Natl Acad Sci USA 107:13544-13549

Key publications

  1. Wenguang Cao, Gavin Humphreys, Minkyung Kang-Choi, Linda Langille, Sylvie Cloutier, Allen Xue, Barbara Blackwell and Maria Antonia Henriquez (2020) Evaluation for new sources of Fusarium head blight resistance in hexaploid and tetraploid wheat Proceedings of the 6th International Symposium on Fusarium Head Blight. Banff, Canada March 23-26 2020

    2020 - View publication details

  2. Fatima F, McCallum B, Hiebert C, McCartney C, Fedak G, Pozniak C, Edwards T, Ravichandran S, You FM, Cloutier S (2020) Single and multi-locus genome-wide association study for leaf rust resistance in cultivated, progenitor and wild wheat. Proc 28th Plant and Animal Genome Conference, San Diego, USA, Jan 11-15, PO0937

    2020 - View publication details

  3. Cloutier S, You F, Rashid K, Zheng C, Lam S, Khan N, He L, Xiao X, Yao J, Li P (2020) Insights into genetic structure and genomic prediction of powdery mildew resistance in flax (Linum usitatissimum L.). Proc 28th Plant and Animal Genome Conference, San Diego, USA, Jan 11-15, PO0499

    2020 - View publication details

  4. Till BJ, Aravena Abarzua GA, Howard-Till R, Qian R, Gajardo H, Cloutier S, Fofana B, Soto-Cerda BJ (2020) Genomic improvement of flax using natural variation and induced mutations. Proc 28th Plant and Animal Genome Conference, San Diego, USA, Jan 11-15, W436

    2020 - View publication details

  5. Goodman E (2020) Serious support for grain science. GrainsWest , Winter 2020, pp7-8 (

    2020 - View publication details

  6. You FM, Cloutier S (2019) Assembly of the Flax Genome into Chromosomes. In: Genetics and Genomics of Linum, Plant Genetics and Genomics: Crops and Models 23, Cullis CA (ed), Springer Nature, Switzerland, Chap 5,

    2019 - View publication details

  7. Cloutier S, You FM, Soto-Cerda BJ (2019) Linum Genetic Markers, Maps and QTL Discovery. In: Genetics and Genomics of Linum, Plant Genetics and Genomics: Crops and Models 23, Cullis CA (ed), Springer Nature, Switzerland, Chap 7,

    2019 - View publication details

  8. CBCNews (2019) $24M in funding announced for 3 U of Sask-led agriculture research projects. , July 23

    2019 - View publication details

  9. Humphreys G, Cao W, Kalikililo A, Langille L, Henriquez MA, Blackwell B, Fedak G, Cloutier S (2019) Uncovering useful variability for agronomics and disease resistance within a diverse wheat collection. Proc 1st International Wheat Congress, Saskatoon, July 21-27, P 447 (poster)

    2019 - View publication details

  10. Kang-Choi M, Kalikililo A, Serajazari M, Wilker N, Langille L, Xue A, Blackwell B, Cloutier S, McCartney C, Navabi A, Humphreys G (2019) Evaluation of Fusarium Head Blight Resistance in a Canadian Winter Wheat DH population. Proc 1st International Wheat Congress, Saskatoon, July 21-27, P 268 (poster)

    2019 - View publication details

  11. Fatima F, Edwards T, Hiebert C, McCartney C, McCallum B, Henriquez MA, Humphreys G, Cao W, Fedak G, You FM, Cloutier S (2019) Diversity analysis of wheat and wild relatives using the wheat 90K Infinium array. Proc 1st International Wheat Congress, Saskatoon, July 21-27, P217 (poster)

    2019 - View publication details

  12. Bruskiewich RM, Caron CT, Kucheran LS, Jia G, Young LW, Staton SE, Légaré J-S, Wang Z, Huellas-Bruskiewicz K, Warfield A, Marden E, Bett K, Booker HM, Cloutier S, You FM and Rieseberg LH. The DivSeek Canada Initiative: out of the starting gate. XXVII Plant and Animal Genome Conference, San Diego, USA, January 12-16, 2019 (PO0035)

    2019 - View publication details

  13. Jia G, You FM, Cloutier S, Deyholos MK, and Booker H. The flax breeding database (FlaxDB). XXVII Plant and Animal Genome Conference, San Diego, USA, January 12-16, 2019. PE1082

    2019 - View publication details

  14. Young LW, Trouve J-P, Speck A, Kutcher R, Rashid KY, You FM, Cloutier S and Booker HM. Mapping rust and powdery mildew resistant genes in flax. XXVII Plant and Animal Genome Conference, San Diego, USA, January 12-16, 2019 (PO0871).

    2019 - View publication details

  15. Cloutier, S., Ravichandran, S., Edwards, T., McCallum, B., Henriquez, M.A., Humphreys, G., Cao, W., Fedak, G., Pozniak, C., You, F.M. 2018. Identifying and transferring genetic diversity from the wild to improve wheat. 9th Canadian Workshop on FHB & 4th Canadian Wheat Symposium, November 19–22, 2018 Winnipeg, Manitoba.

    2018 - View publication details

  16. Kang-Choi M, Kalikililo A, Serajazari, M Wilker N, Xue A, Cloutier S, Navabi A, Humphreys G (2018) Analysis of Fusarium Head Blight Resistance in a Canadian Winter Wheat Doubled Haploid Population. Poster and abstract presented at 9th Canadian Fusarium Workshop, Nov. 19-22, 2018 in Winnipeg, MB.

    2018 - View publication details

  17. You FM, Xiao J, Li P, Yao Z, Jia G, He L, Zhu T, Luo M-C, Wang X, Deyholos M, Cloutier S. Chromosome-scale pseudomolecules refined by optical, physical, and genetic maps in flax. Plant J. 2018,95(2):371-384. doi: 10.1111/tpj.13944.

    2018 - View publication details

  18. Cloutier S (2018) A career in agriculture. Guest speaker, March Speaker Series – Dream, Believe, Achieve, organized by Women in Science and Engineering of the University of Ottawa, March 6 (

    2018 - View publication details

  19. You FM, Rashid K, Cloutier S, Chen W, Luo M-C, Zhu (2018) High-quality genome sequences of cultivated (Linum usitatissimum) and wild (L. bienne) flax. Proc 26th Plant and Animal Genome Conference, San Diego, CA, January 13-17, P0911 (poster)

    2018 - View publication details

  20. Fofana B, Ghose K, Somalraju A, McCallum J, Cloutier S (2018) Dissecting SDG lignin biosynthetic pathways in EMS mutagenized flax using Ampliseq gene panels. Proc 26th Plant and Animal Genome Conference, San Diego, CA, January 13-17, P0117 (poster)

    2018 - View publication details

Research facility

960 Carling Avenue
Ottawa, ON K1A 0C6


  • Principal Research Scientist (SE-RES-05): Agriculture and Agri-Food Canada (1996-)
  • Adjunct professor: University of Ottawa (2015-)
  • Adjunct professor: University of Guelph (2015-)
  • Adjunct professor: University of Manitoba (1997-2016)