A reference-anchored oat linkage map reveals quantitative trait loci conferring adult plant resistance to crown rust (Puccinia coronata f. sp. avenae)

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

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/13/2022
Publication Date: 8/27/2022
Citation: Nazareno, E.S., Fiedler, J.D., Miller, M.E., Figueroa, M., Kianian, S. 2022. A reference-anchored oat linkage map reveals quantitative trait loci conferring adult plant resistance to crown rust (Puccinia coronata f. sp. avenae). Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-022-04128-6.
DOI: https://doi.org/10.1007/s00122-022-04128-6

Interpretive Summary: Crown rust is an important disease of oat and has the potential to cause significant yield losses worldwide. The identification and deployment of new durable genetic resistance genes is crucial as the crown rust pathogen quickly adapts to overcome currently used varieties. Adult plant resistance was previously discovered in five oat lines and in this study, we crossed these lines with a common susceptible parent, Otana, to develop new research populations for gene discovery. We used extensive trait analysis and genetic analysis to identify three new gene regions that confer adult oat crown rust resistance. We also developed genetic tools to help breeders check their breeding material for inclusion of the resistance gene regions. This information is important for researchers investigating plant disease resistance mechanisms and breeders to aid in developing new oat lines with durable crown rust resistance.

Technical Abstract: Sources of durable disease resistance are needed to minimize yield losses in cultivated oat caused by crown rust (Puccinia coronata f. sp. avenae). In this study, we developed five oat recombinant inbred line (RIL) mapping populations to identify important genomic regions for adult plant resistance (APR) from crosses between five APR donors and Otana, a susceptible variety. The preliminary bulk segregant mapping based on allele frequencies showed two regions in linkage group Mrg21 (Chr4D), associated with the APR phenotype in all five populations. Six markers from these regions were converted to high-throughput allele specific PCR assays and were used to genotype all individuals in each population. Simple interval mapping showed two peaks in Chr4D, named QPc.APR-4D.1 and QPc.APR-4D.2, detected in the OtanaA/CI4706-2 and OtanaA/CI9416-2 and in the Otana/PI189733, OtanaD/PI260616, and OtanaA/CI8000-4 populations, respectively. These results were validated by mapping two entire populations, Otana/PI189733 and OtanaA/CI9416, genotyped using Illumina HiSeq, in which polymorphisms were called against the OT3098 oat reference genome. Composite interval mapping results confirmed the presence of the two quantitative trait loci (QTL) located on oat chromosome 4D and an additional QTL with a smaller effect located on chromosome 6C. This mapping approach also narrowed down the physical intervals to between 5 and 19 Mb, and indicated that QPc.APR-4D.1, QPc.APR-4D.2, and QPc.APR-6C explained 43.4%, 38.5%, and 21.5% of the phenotypic variation, respectively. In a survey of the gene content of each QTL, several clusters of disease resistance genes were identified as putative candidate APR genes.