Phylogeography and Genotype-Symptom Associations in Early and Late Season Infections of Canola by Sclerotinia sclerotiorum.

ABSTRACT Both typical late season stem infections and atypical early season rosette infections of canola, a relatively new crop in the southeastern United States, were caused by Sclerotinia sclerotiorum. The 51 DNA fingerprints (from 71 isolates) did not match any fingerprints from previous studies of canola or other crops. Single locus haplotypes from nuclear DNA sequences included 18 in the intergenic spacer (IGS) of the rRNA repeat, four in 44.11, six in translation elongation factor 1alpha, three in calmodulin (CAL), and two in chitin synthase 1. Contingency permutation testing for associations of infection type with DNA fingerprint, single- or multilocus haplotype, or hierarchically nested clades based on single locus haplotypes found significant association of haplotype with mycelial compatibility group and DNA fingerprint for all loci except CAL. Significant association of IGS haplotypes with symptom type was detected in one pathogen population. Southeastern U.S. canola was infected by both recently evolved, geographically dispersed pathogen genotypes and older, indigenous genotypes (Carbone and Kohn, 2001. Mol. Ecol. 10:947-964). Indigenous haplotypes are infection-type generalists, and the most frequently isolated from rosette infections. In contrast, haplotypes from the most recently evolved, dispersed population were associated one-to-one with infection type, with only the most recently evolved haplotypes infecting rosettes.