Genes within virulence QTL regions, excluding genes with no sequence variation or with synonymous SNP only. No sequence variation other than SNP (e.g., indels) was detected in these genes.

aNon-synonymous SNP were classified as conservative if the BLOSUM80 score was 0 or higher for the substitution, or radical if the BLOSUM80 score was negative [74].bOther SNP include SNP in introns, untranslated regions (UTR) and within 100 bp upstream or downstream of the transcript. Synonymous SNP in coding regions are not included.cProtein domains for conserved hypothetical proteins were identified by a BLAST search of the Broad Institute database [38].dThere are 3 SNP, but 2 affect the same codon.eNo clear polymorphism, but ambiguity due to low sequence coverage for strain A91.fPremature stop codon.