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Title: Transcriptome profiling and expression analyses of genes critical to wheat adaptation to low temperature

item L Chingcuanco, Debbie
item GANESHAN, SEEDHABADEE - University Of Saskatchewan
item YOU, FRANK - University Of California
item FOWLER, BRIAN - University Of Saskatchewan
item CHIBBAR, RAVINDRA - University Of Saskatchewan
item MCGUIRE, PATRICK - University Of California
item Anderson, Olin

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/7/2011
Publication Date: 6/7/2011
Citation: Chingcuanco, D.L., Ganeshan, S., You, F., Fowler, B., Chibbar, R., Mcguire, P., Anderson, O.D. 2011. Transcriptome profiling and expression analyses of genes critical to wheat adaptation to low temperature. Biomed Central (BMC) Genomics. 1:299.

Interpretive Summary: Low temperature (LT) is a major abiotic stress that limits the growth, productivity and geographical distribution of agricultural crops. Even in established agricultural production areas, seasonal or episodic freezing events can lead to significant crop loss. In the U.S., ten percent of the sources for claims filed under the Federal crop insurance since 1988 have been due to frost, freeze and cold weather ( Clearly, the development of crops with better adaptation to cold could save billions of dollars. Crops with improved LT tolerance also have a role to play in the goal towards multiple land use and sustainable production systems. Greater LT tolerance allows more flexibility in farm management choices thereby increasing the opportunity to create more environmentally friendly production systems, reduce herbicide costs, increase crop moisture utilization, lower energy requirements, and increase productivity. Identifying and understanding the mechanisms of LT adaptation is crucial to the development of cold-tolerant crops. In this paper, the response of a set of wheat cultivars that vary in sensitivity to cold was evaluated and was coupled with microarray analyses to identify and assess the relative expression patterns of cold-responsive genes and their association with the development of wheat tolerance to low temperature. We report the impact of the Vrn-A1 locus, a major determinant of flowering in wheat, on global gene expression during vernalization and low temperature acclimation. We compared low temperature induced gene expression in tender and cold hardy genetic backgrounds when the effect of the Vrn-A1 locus has been neutralized.

Technical Abstract: Background: 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 Vrn-A1 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 crown of 3-leaf stage seedlings cold-treated at 6oC for 0, 2, 14, 21, 38, 42, 56 and 70 days was examined. Results: Analysis of variance of gene expression separated the samples by genetic background and by the developmental stage before or after vernalization saturation is reached. Using gene-specific ANOVA we identified 12,901 genes (at p < 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) which expression is 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 are up-regulated 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 are highly influenced by the initial rate a! nd the duration of the gene’s response to cold. We show that the Vrn-A1 locus controls the duration of gene expression but not its initial rate of response to cold-treatment. Furthermore, we provide evidence that Ta.Vrn-A1 pattern of expression is distinct from Ta.Vrt1. Conclusion: Our data supports the developmental model of LT tolerance in wheat. It provides novel insights into the underlying mechanisms in the regulation of the expression of cold-responsive genes.