title: Genetic variants of HvCbf14 are statistically associated with frost  tolerance in a European germplasm collection of Hordeum vulgare.
abstract: Two quantitative trait loci (Fr-H1 and Fr-H2) for frost tolerance (FT) have been discovered on the long arm of chromosome 5H in barley. Two tightly linked groups of CBF genes, known to play a key role in the FT regulatory network in A. thaliana, have been found to co- segregate with Fr-H2. Here, we investigate the allelic variations of four barley CBF genes (HvCbf3, HvCbf6, HvCbf9 and HvCbf14) in a panel of European cultivars, landraces and H. spontaneum accessions. In the cultivars a reduction of nucleotide and haplotype diversities in CBFs compared with the landraces and the wild ancestor H. spontaneum, was evident. In particular, in cultivars the loss of HvCbf9 genetic variants was higher compared to other sequences. In order to verify if the pattern of CBF genetic variants correlated with the level of FT, an association procedure was adopted. The pairwise analysis of linkage disequilibrium (LD) among the genetic variants in four CBF genes was computed to evaluate the resolution of the association procedure. The pairwise plotting revealed a low level of LD in cultivated varieties, despite the tight physical linkage of CBF genes analysed. A structured association procedure based on a general liner model was implemented, including the variants in CBFs,of Vrn-H1, and of two reference genes not involved in FT (alpha-Amy1 and Gapdh) and considering the phenotypic data for FT. Association analysis recovered two nucleotide variants of HvCbf14 and one nucleotide variant of Vrn-H1 as statistically associated to FT.
authors.affiliation: CERSA, Parco Tecnologico Padano, Loc. Cascina Codazza, 26900 Lodi, Italy. agostino.fricano@tecnoparco.org
authors.forename: Agostino
authors.initials: A
authors.lastname: Fricano
authors.forename: Fulvia
authors.initials: F
authors.lastname: Rizza
authors.forename: Primetta
authors.initials: P
authors.lastname: Faccioli
authors.forename: Donata
authors.initials: D
authors.lastname: Pagani
authors.forename: Paolo
authors.initials: P
authors.lastname: Pavan
authors.forename: Alessandra
authors.initials: A
authors.lastname: Stella
authors.forename: Laura
authors.initials: L
authors.lastname: Rossini
authors.forename: Pietro
authors.initials: P
authors.lastname: Piffanelli
authors.forename: Luigi
authors.initials: L
authors.lastname: Cattivelli
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000483:Alleles; D001483:Base Sequence; D032461:Chromosomes, Plant; D003080:Cold Temperature; D005060:Europe; D017343:Genes, Plant; D008040:Genetic Linkage; D014644:Genetic Variation; D006239:Haplotypes; D001467:Hordeum / Q000235:genetics*; D016014:Linear Models; D015810:Linkage Disequilibrium; D040641:Quantitative Trait Loci