Genotype groups of the wheat leaf rust fungus Puccinia triticina in the United States as determined by genotyping by sequencing.

Wheat leaf rust caused by Puccinia triticina, is a widespread disease of wheat in the United States and worldwide. Populations of P. triticina are characterized by virulence phenotypes that change rapidly due to selection by wheat cultivars with leaf rust resistance genes. The objective of this study was to genotype collections of P. triticina from 2011-2018 in the United States, using restriction site associated genotyping by sequencing (GBS), to determine if recently identified new virulence phenotypes belong to established genotype groups or belong to groups previously not detected. A total of 158 isolates were phenotyped for virulence on 20 lines of Thatcher wheat that are isogenic for leaf rust resistance genes and were also genotyped for single nucleotide polymorphism. Eight distinct groups of P. triticina genotypes from common wheat were described based on coancestry, nucleotide divergence, and principal coordinate plots. A separate genotype group had isolates with virulence to durum wheat. Isolates within groups had similar virulence phenotype, and the overall population had high level of heterozygosity and a high level of linkage disequilibria, which were all indicators of clonality. Two new genotype groups were described, raising the possibility of new introductions of P. triticina, although genotypes in these groups may have also originated from somatic nuclear exchange and recombination. A genome wide association study detected 19 SNPs that were highly associated with virulence to 11 resistance genes in the Thatcher near isogenic lines.