A SNP in the MdWRKY11 promoter controls the segregation of Glomerella leaf blotch susceptibility in apple

Glomerella leaf blotch (GLB), a severe fungal disease caused by Colletotrichum gloeosporioides, threatens the apple (Malus domestica Borkh.) industry worldwide. The susceptibility of apple to GLB is controlled by a single dominant locus. Although several markers for GLB susceptibility have been developed, the causal genes and their functional variations have not been explored. In this study, we used MapQTL and fine mapping to identify SNP544 C/G in the MdWRKY11 promoter as the major factor underlying the variation in GLB susceptibility in apple. The SNP544 G allele generates a W-box motif that is directly bound by MdWRKY29 and activates MdWRKY11 expression during C. gloeosporioides infection. In turn, MdWRKY11 binds to the MdDMR6.1 promoter and activates its expression, leading to salicylic acid degradation and leaf necrosis. The MdWRKY11 SNP544 G allele was strongly associated with GLB susceptibility, with a prediction accuracy of 96.2% in 767 Malus accessions. In addition to SNP544, we identified nine allelic variations in MdWRKY11 across 29 Malus accessions, with a combined prediction accuracy for GLB susceptibility of 99.6%. These findings shed light on the genetic control of GLB susceptibility in apple and provide an efficient molecular marker for breeding GLB-resistant cultivars.