Abstract
BackgroundFrost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. Three main frost tolerance QTL (Fr-H1, Fr-H2 and Fr-H3) have been identified from bi-parental genetic mapping but it can be argued that those mapping populations only capture a portion of the genetic diversity of the species. A genetically broad dataset consisting of 184 genotypes, representative of the barley gene pool cultivated in the Mediterranean basin over an extended time period, was genotyped with 1536 SNP markers. Frost tolerance phenotype scores were collected from two trial sites, Foradada (Spain) and Fiorenzuola (Italy) and combined with the genotypic data in genome wide association analyses (GWAS) using Eigenstrat and kinship approaches to account for population structure.ResultsGWAS analyses identified twelve and seven positive SNP associations at Foradada and Fiorenzuola, respectively, using Eigenstrat and six and four, respectively, using kinship. Linkage disequilibrium analyses of the significant SNP associations showed they are genetically independent. In the kinship analysis, two of the significant SNP associations were tightly linked to the Fr-H2 and HvBmy loci on chromosomes 5H and 4HL, respectively. The other significant kinship associations were located in genomic regions that have not previously been associated with cold stress.ConclusionsHaplotype analysis revealed that most of the significant SNP loci are fixed in the winter or facultative types, while they are freely segregating within the un-adapted spring barley genepool. Although there is a major interest in detecting new variation to improve frost tolerance of available winter and facultative types, from a GWAS perspective, working within the un-adapted spring germplasm pool is an attractive alternative strategy which would minimize statistical issues, simplify the interpretation of the data and identify phenology independent genetic determinants of frost tolerance.
Highlights
Frost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types
We conducted genome wide association analyses (GWAS) without any correction for population substructure, as we believed that some critical genes may well be confounded with the population sub-structure existing in our germplasm panel
Current barley genome map coverage and knowledge about the role of Fr-H1 and Inducer of C-repeat Binding Factor (CBF) expression 2, INDUCER of CBF EXPRESSION 2 (ICE2), in cold tolerance [32] suggests that the strong associations in the “uncorrected” approach tightly linked to both loci represent true genetic effects that need to be included in improvement of frost tolerance rather than false positives introduced by the absence of population structure correction in the analysis (Figure 2)
Summary
Frost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. The genetic components underlying the response of plants to the photo-thermal environmental cues affecting seasonal and local adaptation are key factors that limit crops’ geographical distribution and yield potential. A locus for frost induced sterility at the reproductive stage has been mapped distally on barley chromosome 2HL in the ‘Haruna Nijo’ (facultative) × ‘Galleon’ (spring) barley mapping population [16,17,18] All these populations involve genetically broad crosses between winter (or facultative) and spring growth habit parents, which segregate for Vrn-H1 and/or Vrn-H2 (major genes governing the vernalization requirement in the cultivated barley genepool) [19] that may obscure and complicate interpretation of the results
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