My lab performs genome-wide association studies for biotic and abiotic stress resistance, agronomic and quality traits in wheat and flax. We are also interested in micro RNAs and their role in stress resistance. We have a strong focus on disease resistance. We investigate the genetic potential in crop wild relatives of wheat and flax. We deal with large dataset, such as Next Generation Sequencing data, and perform substantial bioinformatics analysis to test hypotheses related to agricultural traits.
Selected publications
Prof. Cloutier has published more than 80 peer-reviewed scientific publications, 7 peer-reviewed review articles and 8 book chapters. Below is a selection of a few of the scientific articles she has published.
- Cloutier S, McCallum BD, Loutre C, Banks TW, 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
- 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. Mol Genet Genomics 283:255-271
- Dakouri A, McCallum BD, Walichnowski AZ, Cloutier S (2010) Fine-mapping of the leaf rust Lr34 locus in Triticum aestivum (L.) and characterization of large germplasm collections support the ABC transporter as essential for gene function. Theor Appl Genet 121:373-384
- Ragupathy R, Rathinavelu R, Cloutier S (2011) Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome. BMC Genomics 12:217
- 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.). Theor Appl Genet 125:685-694
- Wang Z, Hobson N, Galindo L, Shilin Z, Daihu S, McDill J, Yang L, Hawkins S, Neutelings G, Datla R, Lambert G, Galbraith DW, Grassa CJ, Geraldes A, Cronk QC, Cullis C, Dash PK, Kumar PA, Cloutier S, Sharpe A, GKS Wong, Wang J, Deyholos MK (2012) The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J 72:461-473
- Cloutier S, Ragupathy R, Miranda E, Radovanovic N, Reimer R, Walichnowski A, Ward K, Rowland G, Duguid S, Banik M (2012) Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.). Theor Appl Genet 125:1783-1795
- Kumar S, You FM, Cloutier S (2012) Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries. BMC Genomics 13:684
- Ragupathy R, You F, Cloutier S (2013) Arguments for standardizing transposable element annotation in plant genomes. Trends Plant Sci 18:367-376
- Soto-Cerda B, 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. BMC Plant Biol 13:78
- McCouch S, Baute GJ, Bradeen J, Bramel P, Bretting PK, Buckler E, Burke JM, Charest D, Cloutier S, Cole G, Dempewolf H, Dingkuhn M, Feuillet C, Gepts P, Grattapaglia D, Guarino L, Jackson S, Knapp S, Langridge P, Lawton-Rauh A, Lijua Q, Lusty C, Michael T, Myles S, Naito K, Nelson RL, Pontarollo R, Richards CM, Rieseberg L, Ross-Ibarra J, Rounsley S, Sackville Hamilton R, Schurr U,Stein N, Tomooka N, van der Knaap E, van Tassel D, Toll J, Valls J, Varshney RK, Ward J, Waugh R, Wenzl P, Zamir D (2013) Agriculture: Feeding the future. Nature 499:23-24
- Thambugala D, Duguid S, Loewen E, Rowland G, Booker H, You FM, Cloutier S (2013) Genetic variation of six desaturase genes in flax and their impact on fatty acid composition. Theor Appl Genet 126:2627-2641
- Dakouri A, McCallum BD, Cloutier S (2014) Haplotype diversity and evolutionary history of the Lr34 locus of a world wheat germplasm collection. Mol Breeding 33:639-655
- Soto-Cerda BJ, Duguid S, Booker H, Rowland G, Diederichsen A, Cloutier S (2014) Association mapping of seed quality traits using the flax (Linum usitatissimum L.) core collection. Theor Appl Genet 127:881-896
- Radovanovic N, Thambugala D, Duguid S, Loewen E, Cloutier S (2014) Heterologous expression of flax fatty acid desaturase isoforms shows functional diversity. Mol Biotechnol 56:609-620
- You FM, Li P, Kumar S, Ragupathy R, Li Z, Fu Y-B, Cloutier S (2014) In silico cloning and characterization of the gene families controlling fatty acid biosynthesis in flax (Linum usitatissimum L.). J Proteomics Bioinform 7:310-326
- Soto-Cerda B, Diederichsen A, Cloutier S (2014) Molecular Diversity and Association Analyses Reveal the Potential of Pale Flax (Linum bienne Mill.), the Wild Progenitor of Cultivated Flax (Linum usitatissimum L.) as a Source of Useful Genetic Variation. Mol Breeding 34:2091-2107
- Kumar S, You FM, Duguid S, Booker H, Rowland G, Cloutier S (2015) QTL for fatty acid composition and yield in linseed (Linum usitatissimum L.). Theor Appl Genet 128:965-984
- You FM, Cloutier S, Shan Y, Ragupathy R (2015) LTRAnnotator: Automated identification and annotation of LTR retrotransposons in plant genomes. Int J Biosci Biochem Bioinform 5:165-174