Three host-associated subpopulations of <i>Colletotrichum sublineola</i> cause anthracnose of <i>Sorghum halepense</i> and <i>S. bicolor</i> in the southeastern United States

<i>Colletotrichum sublineola</i> Henn. causes anthracnose disease on grain, forage, and sweet sorghum [<i>Sorghum bicolor</i> (L.) Moench], and on the related weed Johnsongrass [<i>S. halepense</i> (L.) Pers.]. Previous genetic fingerprinting studies using neutral markers indicated <i>C. sublineola</i> in the southeastern United States comprises two divergent populations mostly associated with the Sorghum host species. In the current study, we further characterized these populations by evaluating restriction fragment length polymorphisms (RFLPs) in fourteen putative pathogenicity-related genes (twelve small secreted-protein effector genes and two secondary metabolite-associated protein genes), and by sequencing polymorphic regions of a subset of these genes. These analyses identified three clades: one (clade A) corresponded to the previously defined population isolated mostly from <i>S. bicolor</i>; the other two (clades B and C) revealed further subdivision within the population recovered mostly from <i>S. halepense</i>. Evidence for reticulation among the gene trees suggested that the three clades correspond to genetically distinct subpopulations within <i>C. sublineola</i>. In greenhouse pathogenicity assays, representatives of the A clade caused disease only on <i>S. bicolor</i>, while clade B members caused disease only on <i>S. halepense</i>, and isolates belonging to clade C were pathogenic to both host species. Estimates of genetic variation indicated that the B clade was the most diverse. Members of the three subpopulations were morphologically similar but could be differentiated by single-nucleotide polymorphisms (SNPs) within a subset of the pathogenicity gene alleles, and several phylogenetic sequence markers. These SNPS could be used to identify members of the three subpopulations for future diagnostic, breeding, and research purposes.