Fig. 1: Genetic identification of resistances to the blast fungus by k-mer-based association mapping on an R-gene enriched sequencing panel of wheat landraces.

a,b, k-mers associated with resistance to (Br48 + PWT3 mapped to Chinese Spring (a) and Br48 + PWT4 mapped to Jagger (b). c,d, k-mer-based phylogeny of wheat landraces showing the phenotype of an accession after inoculation with: Br48 + PWT3 (c) and Br48 + PWT4 (d), and the predicted presence of the putative resistances. Phenotype of an accession after inoculation with a blast isolate is indicated by the colour used to highlight the label of that accession, while the presence and absence of allele-specific polymorphisms is indicated by filled symbols with black/grey and white, respectively. e,f, k-mers significantly associated with resistance to Br48 + PWT3 in the absence of the Rwt3 candidate gene on chromosome 1D leads to the identification of a resistance on chromosome 2A when mapped to the assembly of wheat cultivar SY Mattis (e), and chromosome 7A when mapped to wheat cultivar Jagger (f). g, k-mers significantly associated with resistance to Br48 + PWT4 in the absence of Rwt4 candidate gene on chromosome 1D leads to the identification of a resistance on a region of chromosome 1B containing the homoeologue of Rwt4 when mapped to Jagger. h, Box plots showing variation for resistance to Br48 + PWT3 in Watkins lines predicted to carry Rwt3, 2A resistance, 7A resistance and none of them. i, Box plots showing variation for resistance to Br48 + PWT4 in Watkins lines predicted to carry Rwt4-1D, Rwt4-1B, 2A resistance, 7A resistance and none of them. In the box plots of h and i, boxes denote the interquartile range with the horizontal bar inside representing the median. Whiskers extend to 1.5 times the interquartile range, values outside of which are considered outliers and shown as individual points. Number of Watkins lines belonging to each class is indicated at the top of the corresponding box plot. In the association plots of a and b and e–g: points on the y axis depict k-mers positively associated with resistance in blue and negatively associated with resistance in red. Point size is proportional to the number of k-mers. The association score is defined as the –log₁₀ of the P value obtained using the likelihood ratio test for nested models. The threshold of significant association scores is adjusted for multiple comparisons using the Bonferroni approximation. Arrows indicate regions with significant association scores.