Genome-Wide Association study in a US soft winter wheat population reveals novel and known sources of resistance to the Septoria tritici blotch pathogen Zymoseptoria tritici

Key message GWAS of 337 soft winter wheat genotypes from a breeding program in Indiana, USA identified marker-trait associations that likely correspond with existing and novel resistances to Septoria tritici blotch disease. Abstract Septoria tritici blotch (STB), caused by the ascomycete fungus Zymoseptoria tritici, is a major disease of wheat worldwide. To find additional sources of resistance, Genome-Wide Association (GWA) was used to analyze 337 soft winter wheat genotypes from Indiana, USA, by inoculating seedlings with two isolates of Z. tritici in a complete randomized design. Necrosis and pycnidia development were assessed at 14, 18 and 22 days post inoculation, enabling the calculation of area under the disease progress curve (AUDPC) for each parameter. Adjusted necrosis and pycnidia AUDPC scores were compared with 14,341 high-quality SNPs in a GWA analysis using the FarmCPU and GAPIT CMLM models to identify markers associated with the resistance. Significant (p < 0.05) isolate {xi} genotype interactions were identified, confirming that the phenotypic variation was caused by isolate-specific resistance genes. Overall, 12 marker-trait associations (MTAs) were identified with Z. tritici necrosis and pycnidia resistance. All mapped MTAs were isolate and necrosis/pycnidia specific. Distinct MTAs were mapped for necrosis and pycnidia on chromosome 6A, and for pycnidia on chromosomes 1A, 1D, 3B, 4A, 5B, 6A and 7A. MTAs on chromosomes 5B, 4A, 6A, and 1D likely corresponded with the known genes Stb1, Stb7, Stb15 and Stb19, respectively. MTAs on chromosomes 1A, 3B, 4A, 6A and 7A were not associated with previously known Stb genes and may be novel. Candidate genes near the marker locations have been identified for further investigations. The GWAS showed that Indiana soft winter wheat germplasm segregates for novel and known Stb genes and constitutes a valuable breeding resource for Z. tritici resistance.