Natural variation in CBF gene sequence, gene expression and freezing tolerance in the Versailles core collection of Arabidopsis thaliana

Carine Gery,Ellen Zuther,Dirk K Hincha,Evelyne Teoule,Heather I Mckhann,S De Mita,Aurelie Berard,Dominique Brunel,Sylvie Leveque

doi:10.1186/1471-2229-8-105

Carine Gery, Ellen Zuther

Open Access

https://doi.org/10.1186/1471-2229-8-105

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Abstract

BackgroundPlants from temperate regions are able to withstand freezing temperatures due to a process known as cold acclimation, which is a prior exposure to low, but non-freezing temperatures. During acclimation, a large number of genes are induced, bringing about biochemical changes in the plant, thought to be responsible for the subsequent increase in freezing tolerance. Key regulatory proteins in this process are the CBF1, 2 and 3 transcription factors which control the expression of a set of target genes referred to as the "CBF regulon".ResultsTo assess the role of the CBF genes in cold acclimation and freezing tolerance of Arabidopsis thaliana, the CBF genes and their promoters were sequenced in the Versailles core collection, a set of 48 accessions that maximizes the naturally-occurring genetic diversity, as well as in the commonly used accessions Col-0 and WS. Extensive polymorphism was found in all three genes. Freezing tolerance was measured in all accessions to assess the variability in acclimated freezing tolerance. The effect of sequence polymorphism was investigated by evaluating the kinetics of CBF gene expression, as well as that of a subset of the target COR genes, in a set of eight accessions with contrasting freezing tolerance. Our data indicate that CBF genes as well as the selected COR genes are cold induced in all accessions, irrespective of their freezing tolerance. Although we observed different levels of expression in different accessions, CBF or COR gene expression was not closely correlated with freezing tolerance.ConclusionOur results indicate that the Versailles core collection contains significant natural variation with respect to freezing tolerance, polymorphism in the CBF genes and CBF and COR gene expression. Although there tends to be more CBF and COR gene expression in tolerant accessions, there are exceptions, reinforcing the idea that a complex network of genes is involved in freezing tolerance and that the CBF genes alone cannot explain all differences in phenotype. Our study also highlights the difficulty in assessing the function of single transcription factors that are members of closely related gene families.

Highlights

Plants from temperate regions are able to withstand freezing temperatures due to a process known as cold acclimation, which is a prior exposure to low, but non-freezing temperatures
Sequencing of the CBF genes in the Arabidopsis core collection We surveyed the sequence diversity of the CBF genes to understand their role in gene expression variation, and to determine if these genes exhibit atypical patterns of polymorphism that are suggestive of recent selection
The entire coding regions of the CBF1, 2 and 3 genes as well as 1200–1400 bp upstream of the ATG were sequenced in the 48 accessions of the Versailles core collection

Summary

Introduction

Plants from temperate regions are able to withstand freezing temperatures due to a process known as cold acclimation, which is a prior exposure to low, but non-freezing temperatures. The CBF proteins in turn activate expression of a set of target effector genes by binding to a core sequence in their promoter, alternatively called the C-repeat (CRT), the dehydration-responsive element (DRE) or the low temperature response element (LTRE), that is involved in cold responsiveness [11,12]. Genes containing this motif are known as COR (cold regulated), (E)RD ((early) responsive to dehydration), KIN (cold induced) or LTI (low temperature-induced) genes, and are collectively referred to as the "CBF regulon"

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