Skip to main content
ARS Home » Pacific West Area » Pullman, Washington » WHGQ » Research » Publications at this Location » Publication #299780
Title: Copy number and haplotype variation at the VRN-A1 and central FR-A2 loci are associated with frost tolerance in hexaploid wheat

Author
item ZHU, JIE - Washington State University
item PEARCE, STEPHEN - University Of California
item BURKE, ADRIENNE - Washington State University
item See, Deven
item Skinner, Daniel
item DUBCOVSKY, JORGE - University Of California
item Garland-Campbell, Kimberly

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/11/2014
Publication Date: 3/14/2014
Citation: Zhu, J., Pearce, S., Burke, A., See, D.R., Skinner, D.Z., Dubcovsky, J., Garland Campbell, K.A. 2014. Copy number and haplotype variation at the VRN-A1 and central FR-A2 loci are associated with frost tolerance in hexaploid wheat. Theoretical and Applied Genetics. 127(5):1183-1197.

Interpretive Summary: Frost tolerance is a key trait to ensure winter wheat survival. Natural variation for this trait is mainly associated with allelic differences at the VERNALIZATION 1 (VRN1) and FROST RESISTANCE 2 (FR2) genes. This research identified new alleles at both genes that influence the survival of wheat during freezing. Specifically the two genes interact to affect the frost tolerance of hexaploid wheat. 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. Wheat breeders now have some good molecular tools to select for winter survival in wheat.

Technical Abstract: Frost tolerance is a key trait to ensure winter wheat survival. 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 CBF transcription factors, regulates the expression of Cold-regulated (COR) genes. In this study, we identified sequence and copy number variation at these two loci among winter and spring wheat varieties respectively and characterized their association with frost tolerance. At the FR-A2 locus, we identified two haplotypes – ‘FR-A2-S’ and ‘FR-A2-T’ – distinguished by two insertion/deletions and ten Single Nucleotide Polymorphisms (SNPs) within the CBF-A12 and CBF-A15 genes. Increased copy number of CBF-A14 was frequently associated with the FR-A2-T allele. Factorial ANOVAs revealed significant interactions between VRN1 and FR-A2 for frost tolerance in both winter and spring panels suggesting a crosstalk between the vernalization and cold-acclimation pathways. The model including these two loci and their interaction explained 32.0% of the variation in frost tolerance in the winter panel and 20.7% in the spring panel. The interaction was validated in a winter wheat F4:5 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.