title: Copy number variations of CBF genes at the Fr-A2 locus are essential components of winter hardiness in wheat.
abstract: Winter hardiness is important for the adaptation of wheat to the harsh winter conditions in temperate regions and is thus also an important breeding goal. Here, we employed a panel of 407 European winter wheat cultivars to dissect the genetic architecture of winter hardiness. We show that copy number variation (CNV) of CBF (C-repeat Binding Factor) genes at the Fr-A2 locus is the essential component for winter survival, with CBF-A14 CNV being the most likely causal polymorphism, accounting for 24.3% of the genotypic variance. Genome-wide association mapping identified several markers in the Fr-A2 chromosomal region, which even after accounting for the effects of CBF-A14 copy number explained approximately 15% of the genotypic variance. This suggests that additional, as yet undiscovered, polymorphisms are present at the Fr-A2 locus. Furthermore, CNV of Vrn-A1 explained an additional 3.0% of the genotypic variance. The allele frequencies of all loci associated with winter hardiness were found to show geographic patterns consistent with their role in adaptation. Collectively, our results from the candidate gene analysis, association mapping and genome-wide prediction show that winter hardiness in wheat is a quantitative trait, but with a major contribution of the Fr-A2 locus.
authors.affiliation: State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Würschum
authors.affiliation: State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany.
authors.forename: C Friedrich H
authors.initials: CF
authors.lastname: Longin
authors.affiliation: State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany.
authors.forename: Volker
authors.initials: V
authors.lastname: Hahn
authors.affiliation: School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Tucker
authors.affiliation: State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany.
authors.forename: Willmar L
authors.initials: WL
authors.lastname: Leiser
mesh_terms: D032461:Chromosomes, Plant; D056915:DNA Copy Number Variations / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D055106:Genome-Wide Association Study; D005838:Genotype; D010940:Plant Proteins / Q000235:genetics* / Q000502:physiology; D040641:Quantitative Trait Loci / Q000235:genetics / Q000502:physiology; D012621:Seasons; D014908:Triticum / Q000235:genetics* / Q000502:physiology
chemical_list: D010940:Plant Proteins
keywords: 
  Fr-A2
  ; 
  Vrn-A1
  ; association mapping; copy number variation; wheat; winter hardiness