Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat (Triticum aestivum L.)

<p>Abstract</p> <p>Background</p> <p>To identify the genes involved in the development of low temperature (LT) tolerance in hexaploid wheat, we examined the global changes in expression in response to cold of the 55,052 potentially unique genes represented in the Affymetrix Wheat Genome microarray. We compared the expression of genes in winter-habit (winter Norstar and winter Manitou) and spring-habit (spring Manitou and spring Norstar)) cultivars, wherein the locus for the vernalization gene <it>Vrn-A1 </it>was swapped between the parental winter Norstar and spring Manitou in the derived near-isogenic lines winter Manitou and spring Norstar. Global expression of genes in the crowns of 3-leaf stage plants cold-acclimated at 6°C for 0, 2, 14, 21, 38, 42, 56 and 70 days was examined.</p> <p>Results</p> <p>Analysis of variance of gene expression separated the samples by genetic background and by the developmental stage before or after vernalization saturation was reached. Using gene-specific ANOVA we identified 12,901 genes (at <it>p </it>< 0.001) that change in expression with respect to both genotype and the duration of cold-treatment. We examined in more detail a subset of these genes (2,771) where expression was highly influenced by the interaction between these two main factors. Functional assignments using GO annotations showed that genes involved in transport, oxidation-reduction, and stress response were highly represented. Clustering based on the pattern of transcript accumulation identified genes that were up or down-regulated by cold-treatment. Our data indicate that the cold-sensitive lines can up-regulate known cold-responsive genes comparable to that of cold-hardy lines. The levels of expression of these genes were highly influenced by the initial rate and the duration of the gene's response to cold. We show that the <it>Vrn-A1 </it>locus controls the duration of gene expression but not its initial rate of response to cold treatment. Furthermore, we provide evidence that <it>Ta.Vrn-A1 </it>and <it>Ta.Vrt1 </it>originally hypothesized to encode for the same gene showed different patterns of expression and therefore are distinct.</p> <p>Conclusion</p> <p>This study provides novel insight into the underlying mechanisms that regulate the expression of cold-responsive genes in wheat. The results support the developmental model of LT tolerance gene regulation and demonstrate the complex genotype by environment interactions that determine LT adaptation in winter annual cereals.</p

Localization of QTLs and candidate genes involved in the regulation of frost tolerance in cereals

The recent advances in the molecular investigation of the stress response have led to the identification of a great number of genes whose expression is associated to cold acclimation. In the model species Arabidopsis thaliana, a crucial role in the regulation of the gene set involved in cold tolerance has been clearly demonstrated for a family of transcription factors named C-repeat binding factor (CBF). Genes similar to the Arabidopsis CBF genes were identified in the EST database of many crop species including barley and wheat. In Triticeae, CBF is a multigene family with more than six members per genome and most of the CBF-cereal homologous sequences are clustered together on the long arm of chromosome 5. On the other hand, parallel genetic studies have identified several major genes and QTLs responsible for frost resistance or for components associated to frost restistance on each member of the 5th homoeologous chromosome of Triticeae. Soon after the discovery of the CBF transcription factors it was suggested that the CBF-cereal homologous genes might represent candidate genes for the loci controlling stress tolerance in cereals. Recent findings have demonstrated that the CBF locus cosegregates with one of the major QTLs for frost tolerance in barley and einkorn. This result represent one of the best successful examples of candidate gene approach for unraveling a complex phenotype such as the tolerance to abiotic stress