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CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals

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Abstract

Frost Resistance-1 (FR-1) and FR-2 are two loci affecting freezing tolerance and winter hardiness of the temperate-climate cereals. FR-1 is hypothesized to be due to the pleiotropic effects of VRN-1. FR-2 spans a cluster of C-Repeat Binding Factor (CBF) genes. These loci are genetically and functionally linked. Recent studies indicate CBF transcripts are downregulated by the VRN-1 encoded MADS-box protein or a factor in the VRN-1 pathway. Here, we report that barley genotypes ‘Dicktoo’ and ‘Nure’ carrying a vrn-H1 winter allele at VRN-H1 harbor increased copy numbers of CBF coding sequences relative to Vrn-H1 spring allele genotypes ‘Morex’ and ‘Tremois’. Sequencing bacteriophage lambda genomic clones from these four genotypes alongside DNA blot hybridizations indicate approximately half of the eleven CBF orthologs at FR-H2 are duplicated in individual genomes. One of these duplications discriminates vrn-H1 genotypes from Vrn-H1 genotypes. The vrn-H1 winter allele genotypes harbor tandem segmental duplications through the CBF2A–CBF4B genomic region and maintain two distinct CBF2 paralogs, while the Vrn-H1 spring allele genotypes harbor single copies of CBF2 and CBF4. An additional CBF gene, CBF13, is a pseudogene interrupted by multiple non-sense codons in ‘Tremois’ whereas CBF13 is a complete uninterrupted coding sequence in ‘Dicktoo’ and ‘Nure’. DNA blot hybridization with wheat DNAs reveals greater copy numbers of CBF14 also occurs in winter wheats than in spring wheats. These data indicate that variation in CBF gene copy numbers is widespread in the Triticeae and suggest selection for winter hardiness co-selects winter alleles at both VRN-1 and FR-2.

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Acknowledgments

We thank Erik R. Rowley for technical assistance. We thank David M. Francis, Esther van der Knaap, Ning Jiang (Michigan State University), and an anonymous reviewer for critical reading and suggestions on how to improve the manuscript. This work was supported by the National Science Foundation Plant Genome Program (DBI 0110124). Salaries and research support provided by state and federal funds appropriated to The Ohio State University, Ohio Agricultural Research and Development Center. Support for A.T. came from the Italian National Research Project MIPAAF Sistema Integrato per lo sviluppo della Cerealicoltura Meridionale.

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  1. Hongmei Cheng

    Present address: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

  2. Andrea K. Knox

    Present address: Department of Biology, Thompson Biology Laboratory, 59 Lab Campus Drive, Williams College, Williamstown, MA, 01267, USA

Authors and Affiliations

  1. Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center (OARDC), 1680 Madison Ave, Wooster, OH, 44691, USA

    Andrea K. Knox, Taniya Dhillon, Hongmei Cheng, Alessandro Tondelli & Eric J. Stockinger

  2. Dipartimento di Scienze Agrarie, Università degli Studi di Modena e Reggio Emilia, 42100, Reggio Emilia, Italy

    Nicola Pecchioni

  3. CRA Genomic Research Centre, 29017, Fiorenzuola d’Arda, Italy

    Alessandro Tondelli

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Knox, A.K., Dhillon, T., Cheng, H. et al. CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals. Theor Appl Genet 121, 21–35 (2010). https://doi.org/10.1007/s00122-010-1288-7

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