Characterising diversity in Zymoseptoria tritici field isolates from across the UK

The causes of aggressiveness and pathogenicity within a species are often encoded by a subset of strains. The ability to compare multiple genomes of the same pathogenic species is therefore vital to gain insights into variations in virulence. Zymoseptoria tritici is one of the most damaging pathogens of wheat. In this thesis, 175 isolates of Z. tritici were extracted from STB-diseased leaves from 4 sites across the UK over a 3 year period. These were examined for their virulence and the diversity present within them. Co-infection disease assays comparing plants infected with single isolate inocula and those infected with site-specific mixture inocula found evidence of an overall reduction in STB symptoms in co-infections equivalent to the least aggressive isolate in a single isolate infection, and further investigation found evidence of defence gene induction on distal, uninfected leaves. Disease assays on the STB-resistant cv. KWS Extase using 120 isolates showed a gene-for-gene like reaction. A GWAS using SNP data from the isolates was carried out to identify the gene responsible for this interaction. Twenty-four SNPs on chromosomes 1, 3, 8, and 11 were marked as highly correlated with mean PLACP. Investigation of the effector gene candidates surrounding these sites did not identify changes specific to the virulent isolates and the results were inconclusive. A deeper investigation of the genes associated with the most strongly correlated SNPs identified in the GWAS (Mycgr3G87038, Mycgr3G74453, Zt09 00112, and Zt09 00114) and two genes of known effector candidates (ZtSSP2 and Zt-11), across all 175 isolates extracted from the field sites was undertaken. High levels of diversity and selection pressure were detected for five of the genes, particularly Mycgr3G87038. Examination of the effector/candidate proteins by Blastp and Phyre2 found no significant similarity or predictions for three of the genes (Zt09 00112, ZtSSP2, and Zt-11), similarity with proteins associated with nuclear morphology for one gene (Zt09 00114), and two genes with functions that suggest they are likely effector genes (Mycgr3G87038 a predicted oxidoreductase, and Mycgr3G74453, a beta -1,3-glucanase).