title: Copy number variation at the HvCBF4-HvCBF2 genomic segment is a major component of frost resistance in barley.
abstract: A family of CBF transcription factors plays a major role in reconfiguring the plant transcriptome in response to low-freezing temperature in temperate cereals. In barley, more than 13 HvCBF genes map coincident with the major QTL FR-H2 suggesting them as candidates to explain the function of the locus. Variation in copy number (CNV) of specific HvCBFs was assayed in a panel of 41 barley genotypes using RT-qPCR. Taking advantage of an accurate phenotyping that combined Fv/Fm and field survival, resistance-associated variants within FR-H2 were identified. Genotypes with an increased copy number of HvCBF4 and HvCBF2 (at least ten and eight copies, respectively) showed greater frost resistance. A CAPS marker able to distinguish the CBF2A, CBF2B and CBF2A/B forms was developed and showed that all the higher-ranking genotypes in term of resistance harbour only CBF2A, while other resistant winter genotypes harbour also CBF2B, although at a lower CNV. In addition to the major involvement of the HvCBF4-HvCBF2 genomic segment in the proximal cluster of CBF elements, a negative role of HvCBF3 in the distal cluster was identified. Multiple linear regression models taking into account allelic variation at FR-H1/VRN-H1 explained 0.434 and 0.550 (both at p < 0.001) of the phenotypic variation for Fv/Fm and field survival respectively, while no interaction effect between CNV at the HvCBFs and FR-H1/VRN-H1 was found. Altogether our data suggest a major involvement of the CBF genes located in the proximal cluster, with no apparent involvement of the central cluster contrary to what was reported for wheat.
authors.affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad.Besta, 42122, Reggio Emilia, Italy. enrico.francia@unimore.it.|Center for Genome Research (CGR), University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy. enrico.francia@unimore.it.
authors.forename: Enrico
authors.identifier: http://orcid.org/0000-0001-8709-1002
authors.initials: E
authors.lastname: Francia
authors.affiliation: Genomics Research Centre (GPG), Council for Agricultural Research and Economics, Via San Protaso 302, 29017, Fiorenzuola d'Arda, Italy.
authors.forename: Caterina
authors.initials: C
authors.lastname: Morcia
authors.affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad.Besta, 42122, Reggio Emilia, Italy.|Department of Crop Genetics, John Innes Centre (JIC), Norwich Research Park, Norwich, NR4 7UH, UK.
authors.forename: Marianna
authors.initials: M
authors.lastname: Pasquariello
authors.affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad.Besta, 42122, Reggio Emilia, Italy.
authors.forename: Valentina
authors.initials: V
authors.lastname: Mazzamurro
authors.affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad.Besta, 42122, Reggio Emilia, Italy.|Center for Genome Research (CGR), University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy.
authors.forename: Justyna Anna
authors.initials: JA
authors.lastname: Milc
authors.affiliation: Genomics Research Centre (GPG), Council for Agricultural Research and Economics, Via San Protaso 302, 29017, Fiorenzuola d'Arda, Italy.
authors.forename: Fulvia
authors.initials: F
authors.lastname: Rizza
authors.affiliation: Genomics Research Centre (GPG), Council for Agricultural Research and Economics, Via San Protaso 302, 29017, Fiorenzuola d'Arda, Italy.
authors.forename: Valeria
authors.initials: V
authors.lastname: Terzi
authors.affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Pad.Besta, 42122, Reggio Emilia, Italy.|Center for Genome Research (CGR), University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy.|Cereal Research Centre, Council for Agricultural Research and Economics, 71122, Foggia, Italy.
authors.forename: Nicola
authors.initials: N
authors.lastname: Pecchioni
mesh_terms: D003080:Cold Temperature; D056915:DNA Copy Number Variations / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D001467:Hordeum / Q000235:genetics* / Q000502:physiology*; D010940:Plant Proteins / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D010940:Plant Proteins
keywords: Barley; CBF genes; CNV; FR-H2 locus; Frost resistance; RT-qPCR