Tchagang Alain B, Fauteux François, Tulpan Dan, Pan Youlian
Information and Communications Technologies, National Research Council Canada, Ottawa, ON, K1A 0R6, Canada.
Information and Communications Technologies, National Research Council Canada, Moncton, NB, E1A 7R1, Canada.
BMC Bioinformatics. 2017 Mar 16;18(1):174. 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.
小麦族的表型研究表明，低温诱导的保护机制受到发育调控，并涉及动态驯化过程。了解这些机制对于培育抗寒小麦品种至关重要。在本研究中，我们结合了三种计算技术来分析来自春小麦和冬小麦品种经低温处理后的基因表达数据。我们的主要目标是构建一个全面的小麦冷响应转录事件网络，并鉴定小麦中新型的耐寒候选基因。
我们为35个小麦基因赋予了与冷胁迫相关的新功能，发现了新的转录因子（TF）-基因相互作用，并鉴定出127个代表已知和新型候选靶点的基因，这些靶点与小麦的耐寒性相关。我们的结果还表明，不同小麦品种中相同基因激活或抑制的延迟在冬小麦和春小麦品种的表型差异以及对低温胁迫、冷休克和冷驯化的适应中起关键作用。
通过三种计算方法，我们鉴定出了新型的假定冷响应基因和TF-基因相互作用。这些结果为调控小麦冷响应基因表达的复杂机制提供了新的见解。
