ICE genes in Arabidopsis thaliana: clinal variation in DNA polymorphism and sequence diversification

Natural accessions of Arabidopsis thaliana exhibit a clinal variation in freezing tolerance following temperature changes across the natural habitat. Here we performed molecular evolution and population genetic analyses of homologous INDUCER OF CBF EXPRESSION1 (ICE1) and ICE2 genes, the master regulators of plant cold response. A study of ICE genes polymorphism was performed using 60 A. thaliana ecotypes grouped according to their geographic origin. The genetic diversity of ICE2 was characterized by a high number of haplotypes and an overall high diversity. The levels of nonsynonymous nucleotide polymorphism increased from a northern group southward. On the contrary, the ICE1 gene sequence was less diverse and there was no clinal variation in the sequence polymorphism. Thus, different selection forces acting on the ICE2 gene might be one of the reasons of clinal variation in freezing tolerance. This clinal variation also indicates that ICE2 is more important for a cold response than ICE1. The study of the ratio of numbers of nonsynonymous to synonymous substitutions (Ka/Ks) between A. thaliana paralogs shows that the sequence diversification and emergence of two new ICE2-specific motifs could contribute to the functional diversification of the duplicates. The Ka/Ks for ICE2 of A. thaliana and A. lyrata orthologs was an order of magnitude greater than that for the ICE1 orthologs, which suggests that the protein sequence of ICE2, an early duplicate, evolved under a weaker selective constraint. A relaxed selection on ICE2 in southern populations and more stringent in northern populations also confirmed its role in a cold resistance. The selection pressure on ICE1 might be caused by its role in the control of more essential than cold response functions.