title: Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat.
abstract: BACKGROUND
  Phenotypic studies in Triticeae have shown that low temperature-induced protective mechanisms are developmentally regulated and involve dynamic acclimation processes. Understanding these mechanisms is important for breeding cold-resistant wheat cultivars. In this study, we combined three computational techniques for the analysis of gene expression data from spring and winter wheat cultivars subjected to low temperature treatments. Our main objective was to construct a comprehensive network of cold response transcriptional events in wheat, and to identify novel cold tolerance candidate genes in wheat.
  
  
  RESULTS
  We assigned novel cold stress-related roles to 35 wheat genes, uncovered novel transcription (TF)-gene interactions, and identified 127 genes representing known and novel candidate targets associated with cold tolerance in wheat. Our results also show that delays in terms of activation or repression of the same genes across wheat cultivars play key roles in phenotypic differences among winter and spring wheat cultivars, and adaptation to low temperature stress, cold shock and cold acclimation.
  
  
  CONCLUSIONS
  Using three computational approaches, we identified novel putative cold-response genes and TF-gene interactions. These results provide new insights into the complex mechanisms regulating the expression of cold-responsive genes in wheat.
authors.affiliation: Information and Communications Technologies, National Research Council Canada, Ottawa, ON, K1A 0R6, Canada. alain.tchagang@nrc-cnrc.gc.ca.
authors.forename: Alain B
authors.initials: AB
authors.lastname: Tchagang
authors.affiliation: Information and Communications Technologies, National Research Council Canada, Ottawa, ON, K1A 0R6, Canada.
authors.forename: François
authors.initials: F
authors.lastname: Fauteux
authors.affiliation: Information and Communications Technologies, National Research Council Canada, Moncton, NB, E1A 7R1, Canada.
authors.forename: Dan
authors.initials: D
authors.lastname: Tulpan
authors.affiliation: Information and Communications Technologies, National Research Council Canada, Ottawa, ON, K1A 0R6, Canada.
authors.forename: Youlian
authors.initials: Y
authors.lastname: Pan
mesh_terms: D000222:Adaptation, Physiological; D003080:Cold Temperature; D019295:Computational Biology / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D016014:Linear Models; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D012621:Seasons; D013312:Stress, Physiological; D014908:Triticum / Q000235:genetics* / Q000378:metabolism
chemical_list: D010940:Plant Proteins
keywords: Breeding; Cold acclimation; Cold stress; Cold tolerance; Low temperature; Marker; Target; Transcriptional regulatory network; Wheat