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 because of selection by wheat cultivars with leaf rust resistance genes. The objective of this study was to genotype collections of P. triticina from 2011 to 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 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 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 phenotypes, and the overall population had high levels of heterozygosity and high levels of linkage disequilibria, which were all indicators of clonality. Two new genotype groups were described, thereby raising the possibility of new introductions of P. triticina; however, genotypes in these groups may have also originated from somatic nuclear exchange and recombination. A genome-wide association study detected 19 single nucleotide polymorphisms that were highly associated with virulence to 11 resistance genes in the Thatcher near-isogenic lines.