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Copy number and haplotype variation at the VRN-A1 and central FR-A2 loci are associated with frost tolerance in hexaploid wheat

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Abstract

Key message

The interaction between VRN - A1 and FR - A2 largely affect the frost tolerance of hexaploid wheat.

Abstract

Frost tolerance is critical for wheat survival during cold winters. Natural variation for this trait is mainly associated with allelic differences at the VERNALIZATION 1 (VRN1) and FROST RESISTANCE 2 (FR2) loci. VRN1 regulates the transition between vegetative and reproductive stages and FR2, a locus including several tandemly duplicated C-REPEAT BINDING FACTOR (CBF) transcription factors, regulates the expression of Cold-regulated genes. We identified sequence and copy number variation at these two loci among winter and spring wheat varieties and characterized their association with frost tolerance. We identified two FR-A2 haplotypes—‘FR-A2-S’ and ‘FR-A2-T’—distinguished by two insertion/deletions and ten single nucleotide polymorphisms within the CBF-A12 and CBF-A15 genes. Increased copy number of CBF-A14 was frequently associated with the FR-A2-T haplotype and with higher CBF14 transcript levels in response to cold. Factorial ANOVAs revealed significant interactions between VRN1 and FR-A2 for frost tolerance in both winter and spring panels suggesting a crosstalk between vernalization and cold acclimation pathways. The model including these two loci and their interaction explained 32.0 and 20.7 % of the variation in frost tolerance in the winter and spring panels, respectively. The interaction was validated in a winter wheat F 4:5 population segregating for both genes. Increased VRN-A1 copy number was associated with improved frost tolerance among varieties carrying the FR-A2-T allele but not among those carrying the FR-A2-S allele. These results suggest that selection of varieties carrying the FR-A2-T allele and three copies of the recessive vrn-A1 allele would be a good strategy to improve frost tolerance in wheat.

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Acknowledgments

This project was supported by the National Research Initiative Competitive Grants WNR-2008-01010 and 2011-68002-30029 (Triticeae-CAP) from the USDA National Institute of Food and Agriculture, the Washington Grains Commission Project No. 5345, and USDA, ARS (in house) CWU: 5348-21220-003-00D. JD also acknowledges support from the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation.

Conflict of interest

The experiments in this manuscript comply with the current laws of the United States. The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. USDA-ARS Wheat Genetics, Quality, Physiology and Disease Research Unit, United States Department of Agricutlure, Pullman, WA, 99164-6420, USA

    Adrienne Burke, Deven Robert See, Daniel Z. Skinner & Kimberly Garland-Campbell

  2. Department of Plant Sciences, University of California, Davis, CA, 95616, USA

    Stephen Pearce & Jorge Dubcovsky

  3. Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA

    Jie Zhu, Daniel Z. Skinner & Kimberly Garland-Campbell

  4. Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA

    Deven Robert See

  5. Howard Hughes Medical Institute and Gordon and Betty Moore Foundation Investigator, Chevy Chase, MD, 28015-6789, USA

    Jorge Dubcovsky

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  1. Jie Zhu
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  2. Stephen Pearce
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  3. Adrienne Burke
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  7. Kimberly Garland-Campbell
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Corresponding authors

Correspondence to Jorge Dubcovsky or Kimberly Garland-Campbell.

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Communicated by L. Xiong.

J. Zhu and S. Pearce contributed equally to this work.

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Zhu, J., Pearce, S., Burke, A. et al. Copy number and haplotype variation at the VRN-A1 and central FR-A2 loci are associated with frost tolerance in hexaploid wheat. Theor Appl Genet 127, 1183–1197 (2014). https://doi.org/10.1007/s00122-014-2290-2

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