Genetic and physical mapping of oat adult plant resistance loci against Puccinia coronata f. sp. avenae

Authors: NAZARENO, ERIC - University Of Minnesota; Fiedler, Jason; NAAKORKOI, ARDAYFIO - North Dakota State University; MILLER, MARISA - University Of Minnesota; FIGUEROA, MELANIA - Commonwealth Scientific And Industrial Research Organisation (CSIRO); Kianian, Shahryar

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/26/2023
Publication Date: 1/31/2023
Citation: Nazareno, E., Fiedler, J.D., Naakorkoi, A., Miller, M., Figueroa, M., Kianian, S. 2023. Genetic and physical mapping of oat adult plant resistance loci against Puccinia coronata f. sp. avenae. Phytopathology. https://doi.org/10.1094/phyto-10-22-0395-r.
DOI: https://doi.org/10.1094/phyto-10-22-0395-r

Interpretive Summary: Crown rust is an important disease of oat that has the potential to cause significant yield losses worldwide. The identification and deployment of new durable genetic resistance genes is crucial as the pathogen quickly adapts to overcome currently used genetic sources. Previously, three oat resource lines were identified as resistant and in this study, we developed mapping populations with a common susceptible parent, Otana. With extensive genetic analysis, we identified five new gene regions that confer resistance to oat crown rust resistance as adult plants. This is the preferred mode of action as adult plant resistance is typically more durable. We developed high-throughput molecular markers to rapidly screen new lines to put these three different gene regions together in a single line for maximum effectiveness. This information is important for researchers investigating resistance mechanisms and breeders to aid in developing new oat lines with durable crown rust resistance.

Technical Abstract: Six quantitative trait loci (QTL) for adult plant resistance (APR) against oat crown rust (Puccinia coronata f. sp. avenae) were identified from mapping three recombinant inbred populations (RILs). Using genotyping-by-sequencing with markers called against the OT3098 v1 reference genome, the QTL were mapped in six different chromosomes, namely: Chr1D, Chr4D, Chr5A, Chr5D, Chr7A, and Chr7C. Composite interval mapping with marker cofactor selection showed that the phenotypic variance explained by all identified QTL for coefficient of infection range from 12.2 to 46.9%. The significant regions were narrowed down to intervals of 3.9 to 25 cM, equivalent to physical distances of 11 to 133 Mb. At least two flanking SNP markers were identified within 10 cM of each QTL to assist in the introgression, pyramiding, and selection. The additive effects of the QTL based on SNP haplotypes range from 10.3 to 21.3, indicating a modest decrease in CI in lines homozygous for the resistant alleles. Analysis of pairwise linkage disequilibrium also revealed high correlation of markers and presence of linkage blocks in the significant regions. To further facilitate marker-assisted breeding, Polymerase Chain Reaction Allelic Competitive Extension (PACE) markers for the APR loci were developed. Putative candidate genes were identified in each of the significant regions, which reveal that the gene content of the APR loci include resistance gene clusters, such as those that encode for kinases, ligases, resistance gene analogs, and predicted receptors of avirulence proteins from pathogens.