Whole genome sequencing of multiple isolates of Puccina triticina reveals asexual lineages evolving by recurrent mutations.

Authors: Fellers, John; SAKTHIKUMAR, SHARADHA - Broad Institute Of Mit/harvard; CUOMO, CHRISTINA - Broad Institute Of Mit/harvard; HE, FEI - Kansas State University; MCRELL, KATIE - Kansas State University; BAKKEREN, GUUS - Agriculture And Agri-Food Canada; Kolmer, James

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/1/2021
Publication Date: 7/8/2021
Citation: Fellers, J.P., Sakthikumar, S., Cuomo, C., He, F., McRell, K., Bakkeren, G., Kolmer, J.A. 2021. Whole genome sequencing of multiple isolates of Puccina triticina reveals asexual lineages evolving by recurrent mutations. G3, Genes/Genomes/Genetics. https://doi.org/10.1093/g3journal/jkab219.
DOI: https://doi.org/10.1093/g3journal/jkab219

Interpretive Summary: Worldwide wheat production is continually confronted with new races of the leaf rust pathogen (Puccinia triticina). New high throughput genomic sequencing methods may help our understanding of how the pathogen evolves to overcome particular disease resistance genes in wheat. An international collection of 121 isolates was sequenced using next-generation sequencing technology. Their sequences were compared to the Race 1 reference genome sequence, and differences were tallied. Overall, the genomes were highly variable, with over 284,000 nucleotide differences in each isolate. Using this information, the 121 isolates were grouped into eleven discrete lineages correlating with the wheat species and geographic origin. The differences also suggested that many lineages are unique and have appeared in North America as new introductions and not derived from races already present. Mutations were found evenly across the genome without concentration in genes related to infection. This research suggests that new races appear by the process of recurrent mutation within the clonal lineage.

Technical Abstract: The wheat leaf rust fungus, Puccinia triticina Erikss. is a worldwide pathogen of tetraploid durum and hexaploid wheat. Many races of P. triticina differ for virulence to specific leaf rust resistance genes and are found in most wheat-growing regions of the world. Wheat cultivars with effective leaf rust resistance exert selection pressure on P. triticina populations for virulent race types, thus eroding cultivar resistance. The objectives of this study were to examine whole-genome sequence data of 121 P. triticina isolates comprising many different race phenotypes collected worldwide from common wheat in the U.S. and the European Union together with isolates from durum wheat. One isolate from the wild wheat relative Aegilops speltoides, and two from Ae. cylindrica were also included for comparison. Based on 121,907 variants identified relative to the reference race 1-1 genome, the isolates were clustered into 11 major lineages with 100% bootstrap support. The isolates were also grouped based on variation in approximately 1400 secreted resistance interactor candidate proteins. Based on total variation or variation in the secreted protein genes, isolates grouped the same indicating that variants were distributed across the entire genome. In gene-coding regions, all groups had high ratios of non-synonymous to synonymous mutations and nonsense to readthrough mutations, which indicated the role of recurrent mutation and selection in differentiation within the clonal lineages.