Genetic diversity and phylogeny of strains of Clavibacter nebraskensis associated with recent and historic Goss’s wilt epidemics in the North Central U.S

Goss's wilt and blight of maize, caused by Clavibacter nebraskensis, is an important disease in the USA and Canada. The re‐emergence of Goss's wilt in the mid‐2000s and the subsequent spread of this disease probably resulted from changes in crop management practices and possibly changes in the pathogen population. The objectives of this study were to determine the genetic diversity and phylogeny of strains of C. nebraskensis associated with recent and historic Goss's wilt epidemics in the north Central USA, to measure the effects of collection period on population structure, and to identify the phylogenetic status of avirulent strains of C. nebraskensis. Multilocus sequence analysis and typing were used to address these objectives. Bayesian analysis of the sequences of atpD, dnaK, and kdpA separated the type strain of C. nebraskensis from type or reference strains of three other Clavibacter spp. The 125 strains of C. nebraskensis used in this study formed a monophyletic taxon. Four lineages were identified. Clades I, II, and IV contained a high proportion of highly virulent strains from the Upper Midwest. Clade III contained a high proportion of strains from Nebraska, Colorado, and South Dakota collected between 1969 and 1998. A significant substructure was detected between subpopulations from historic outbreaks in Nebraska and Colorado and more recent outbreaks in Minnesota. Virulence or avirulence in maize was not correlated with a particular MLSA clade. The results support the hypothesis that genetic changes in the population of C. nebraskensis were correlated with recent area expansions of Goss's wilt.