Fig. 4: GWAS and QTL mapping identify a common locus on B. g. tritici chromosome 8 controlling virulence on Pm4b and Pm4a.

a,b, GWAS analysis using 473,887 SNPs across the 11 B. g. tritici chromosomes, based on phenotypes of 78 isolates of the Pm4b NIL W804/8*Fed (a) and the Pm4a NIL Khapli/8*CC (b). The red dashed line indicates the significance threshold at P < 0.05 after Bonferroni correction. The genomic position of AvrPm4 is indicated by a grey dashed line. c, Results of a QTL analysis on Pm4a NIL Khapli/8*CC, using 118 F₁ progenies of the biparental mapping population CHE_96224 (avirulent) × THUN-12 (partially virulent). The virulence phenotypes of the parental isolates on the Pm4a NIL are shown in the top left corner. The dashed line indicates the significance threshold logarithm of the odds (LOD) value at P < 0.05, determined by 1,000 permutations. d, Depiction of the genomic locus on chromosome 8 identified via GWAS and QTL analysis. Locus borders were defined on the basis of the GWAS analysis on the Pm4b NIL (W804/8*Fed). Candidate secreted effector genes are represented by yellow arrows, and non-effector genes by white arrows. Red triangles indicate candidate effectors exhibiting non-synonymous sequence polymorphisms between Pm4b/Pm4a virulent and avirulent reference isolates. The grey box indicates the location of the 13 best associated SNPs with the phenotype on Pm4b (W804/8*Fed) with an identical P value of 8.660015 × 10⁻¹². Gene names are based on the gene annotation published for B. g. tritici reference isolate CHE_96224 (ref. ³⁴). Gene models are not drawn to scale. Genomic confidence intervals identified by GWAS on Pm4b (blue), GWAS on Pm4a (dark green) or QTL mapping on Pm4a (light green) are indicated by coloured bars.