Genome-Wide Association Mapping of Low Temperature Tolerance (LTT) in Barley (Hordeum vulgare L.) to Improve Crop Efficiency Under Climate Change

Low temperature tolerance can be an indirect path to greater water use efficiency (WUE) in environments with winter precipitation. In such environments, the grain yields of fall-sown barley are typically 20% greater than those of spring-sown barley. The challenge is achieving sufficient LTT, aka winter survival. We assembled a very large GWAS panel (n = 941) which was evaluated at 14 locations around the world in 2013/2014. The panel includes 300 lines from the TCAP Facultative-Winter 6 row set derived from elite lines at Oregon State University and University of Minnesota Breeding programs, and originally developed to map QTLs for nitrogen use efficiency (NUE) and water use efficiency. Additionally, the panel contains winter/facultative accessions submitted by breeders from around the world and collections assembled by the AGOUEB and ExBarDiv Projects led by the James Hutton Institute and University of Dundee, UK. Genotyping was done with the Illumina 9K chip in several separate runs based on accession collections. After combining all the information available and filtering for data quality we currently have 6683 SNPs in 883 lines. Differential winter survival was observed in four of the test environments: ID, MN, OH (USA) and Alberta, Canada. One environment experienced complete winter kill (NE, USA), while there was 100% survival in the remaining 9 environments which generated useful data on a range of biotic stress resistance, morphology, and phenology phenotypes. The GWAS validated the effects of know LTT-related genes (FR-H1, FR-H2, FR-H3, PPD-H2) and identified significant QTLs on all other chromosomes.  Interestingly, VRN-H2 was not a significant determinant of LTT. Characterization of these novel QTLs in terms of the physiological bases and candidate genes is underway.