ARS | Publication request: The genetics of winterhardiness in barley: Perspectives from genome-wide association mapping

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 31, 2011
Publication Date: March 1, 2011
Citation: Zitzewitz, J., Condon, F., Corey, A., Cuesta-Marcos, A., Filichkin, T., Haggard, K., Fisk, S.P., Smith, K.P., Muehlbauer, G.J., Karsai, I., Veisz, O., Chao, S., Castro, A.J., Gutierrez, L., Hayes, P.M. 2011. The genetics of winterhardiness in barley: Perspectives from genome-wide association mapping. The Plant Genome. 4:76-91.

Interpretive Summary: To survive the winter conditions (winter hardiness), it is critical that plants are able to withstand and remain healthy under the cold temperatures. Winterhardiness is a complex trait that involves three main components, low temperature (LT) tolerance, vernalization (VRN) sensitivity and photoperiod (PPD) sensitivity. VRN is a process that allows winter-sown plants to flower in the spring after being exposed to a long period of cold temperatures. The transition from a vegetative state to a reproductive state can also be influenced by seasonal changes in day length or PPD. In barley, previous genetic studies have identified and characterized candidate genes controlling the winterhardiness traits using bi-parental mapping populations constructed using two parents with contrasting phenotypes. These results also showed that genes involved in the pathways underlying the expression of these traits are highly interconnected. In this research, an alternative mapping approach known as genome-wide association (GWA) mapping was used to detect genes that have significant genetic effects on the winterhardiness traits. The GWA approach permits the use of samples derived from a wider genetic base, and can complement the bi-parental crosses approach. The study included a set of 148 lines consisting of advanced breeding lines from the Oregon (USA) barley breeding program and selected cultivars that were extensively phenotyped and genotyped with single nucleotide polymorphism markers. Using these data for GWA mapping the same genes were detected that have been systematically characterized using bi-parental populations over nearly two decades of intensive research. Our results also showed that in this sample of germplasm, maximum LT tolerance can be achieved with facultative growth habit, i.e., the barley lines that are LT tolerant, are not responsive to VRN, and may be PPD sensitive. These samples can be predicted based on a genotype of variants at three genes including FR-H1, FR-H2 (both influencing the cold tolerance), and VRN-H2 (affecting the VRN responsiveness). In particular, the FR-H1 and FR-H2 LT tolerance genes explained 25% of the phenotypic variation, offering the prospect that additional gains from selection can be achieved once favorable variants are fixed at these genes.

Technical Abstract: Winterhardiness is a complex trait that involves low temperature (LT) tolerance, vernalization sensitivity and photoperiod sensitivity. Quantitative trait loci (QTL) for these traits were first identified using biparental mapping populations; candidate genes for all loci have since been identified and characterized. In this research we used a set of 148 accessions consisting of advanced breeding lines from the Oregon (USA) barley breeding program and selected cultivars that were extensively phenotyped and genotyped with single nucleotide polymorphisms. Using these data for genome-wide association mapping we detected the same QTL and genes that have been systematically characterized using biparental populations over nearly two decades of intensive research. In this sample of germplasm, maximum LT tolerance can be achieved with facultative growth habit, which can be predicted using a three-locus haplotype involving FR-H1, FR-H2, and VRN-H2. The FR-H1 and FR-H2 LT tolerance QTL explained 25% of the phenotypic variation, offering the prospect that additional gains from selection can be achieved once favorable alleles are fixed at these loci.