Manhattan plots for frost tolerance in barley in the Foradada (Spain) location where the frost episode was long and severe (A) and in the Fiorenzuola (Italy) location where accessions experienced less severe cold conditions (B). (i) ”Uncorrected” naive analysis. (ii) EIGENSTRAT and (iii) Kinship analysis. The -log10(p-values) from a genome-wide scan are plotted against the position on each of the 7 barley chromosomes. The horizontal line indicates the genome-wide significance threshold (−log10p ≥ 3). Three amongst the top ‘uncorrected’ hits fail to reach the significance threshold in the kinship analysis despite being genetically close to FLT-2L-linked ’frost sensitivity in reproductive tissues’ locus (downward purple arrow), ICE2 regulatory gene (downward green arow) and the Fr-H1 locus (downward red arow), known to be involved with cold tolerance. (red circle) Association hits previously reported in the literature . (down ward light blue arrow) Top hit in the ‘uncorrected’ analysis also significant in the kinship analysis.