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

Authors: Kolmer, James; HERMAN, ADAM - University Of Minnesota; Fellers, John

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/14/2021
Publication Date: 3/1/2022
Citation: Kolmer, J.A., Herman, A.C., Fellers, J.P. 2022. Genotype groups of the wheat leaf rust fungus Puccinia triticina in the United States as determined by genotyping by sequencing. Phytopathology. 112(3):653-662. https://doi.org/10.1094/phyto-03-21-0125-r.
DOI: https://doi.org/10.1094/phyto-03-21-0125-r

Interpretive Summary: Leaf rust, caused by the fungus Puccinia triticina, is a major disease of wheat in the U.S. and world-wide. There are many different variants or races of leaf rust that are virulent to resistance genes in wheat cultivars. The objective of this study was to characterize recent races of leaf rust in the United States using molecular DNA markers to determine if new races of leaf rust were derived by mutation from the previous races or if the new races were introduced from other continental regions. The DNA markers based on single nucleotide polymorphism (SNP) were derived using the genotype by sequence method. The recent collections of P. triticina from the U.S. were grouped into nine different genotype groups. Races and SNP genotypes in eight of the groups were virulent to bread wheat, and races in one group were virulent to durum wheat. Races within each group were highly related for SNP genotype and races in different groups were more distant. Two of the groups had SNP genotypes and races that were new to the United States. SNP genotypes in one of the groups may have originated from a mixture of races from two other groups. A large majority of the collections were in two groups that are found throughout the Great Plains, Ohio Valley, and southeastern states. There were many different races in these two groups, with virulence to the important leaf rust resistance genes in the current soft red winter wheat cultivars, and the hard red winter and spring wheat cultivars. Nineteen DNA markers were highly associated virulence to 11 leaf rust resistance genes. These markers may be linked to genes that control the ability of the leaf rust fungus to attack wheat plants. These results have provided further insight into the biology of P. triticina and how new races and variants evolve in the United States. These results can be used to help wheat breeders and plant pathologists develop wheat cultivars with long lasting resistance to leaf rust.

Technical Abstract: 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 sequence (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 to the United States, although one of the groups may have 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.