Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat

• Published in: BMC bioinformatics 2017-03, Vol.18 (1), p.174-174, Article 174
• Main Authors: Tchagang, Alain B, Fauteux, François, Tulpan, Dan, Pan, Youlian
• Format: Article
• Language: English
• Subjects: Abiotic stress; Acclimation; Acclimatization; Adaptation, Physiological; Algorithms; Bioinformatics; Circadian rhythm; Cold; Cold acclimation; Cold shock; Cold Temperature; Cold tolerance; Cold weather construction; Computational Biology - methods; Computer applications; Cultivars; Datasets; Gene expression; Gene Expression Regulation, Plant; Gene Regulatory Networks; Gene silencing; Genes; Genomes; Identification; Kinases; Linear Models; Low temperature; Low temperature resistance; Ontology; Plant breeding; Plant Proteins - genetics; Plant Proteins - metabolism; Seasons; Signal transduction; Spring (season); Spring wheat; Stress; Stress, Physiological; Studies; Target recognition; Temperature tolerance; Time series; Transcription; Transcription factors; Triticeae; Triticum - genetics; Triticum - metabolism; Triticum aestivum; Wheat; Winter wheat
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-017-1596-x

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. 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. 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.