QTL mapping and transcriptome analysis to identify wheat resistance genes for Septoria tritici blotch disease

Resistance to Septoria tritici blotch (STB) is an economically important target trait in many wheat-breeding programs across theworld. Growing a resistant cultivar is considered as the best strategy for STB disease management as it is effective, environmentally friendly and reduces the cost of production. The pathogen population causing STB is highly dynamic overcoming resistance genes and fungicide effects rapidly. Several quantitative trait loci (QTL) for STB resistance were identified in wheat but due to the dynamic pathogen population it is necessary to continuously identify new resistance genes/QTLand determine the underlying resistance mechanism. In this work, we integrated QTL mapping and transcriptome profiling to identify candidate genes underlying QTL associated with STB resistance in bread wheat at the seedling stage. The results revealed four QTL on chromosome arms 3DL, 2BL, 1BS and 3AS that contribute to STB resistance. Among these, two QTL on 3DL and 2BL were mapped for chlorosis, necrosis and pycnidia and the other two on 1BS and 3AS were only associated with necrosis and pycnidia. Among the four identified QTL, candidate genes were only identified in three QTL (1BS, 2BL and 3DL). In total, 238 differentially expressed genes (DEGs) were localized on 1BS, 16 DEGs on 2BL and 80 DEGs on 3DL QTL region, of which, several DEGs related to F-box protein, NBS-LRR disease resistance genes and receptor-like protein kinase were most over-represented. The results emphasise the importance of integrating QTL and transcriptome analysis to accelerate the identification of key genes underlying the traits of interest.