Development and accuracy assessment of molecular markers associated with crown rust resistance genes in oat

Crown rust caused by Puccinia coronata Cda. f. sp. avenae P. Syd. (Pca) is considered the most destructive disease of oat, causing yield and grain quality losses. Over a hundred crown rust race-specific resistance genes have been identified, but the history of cultivar development has left the identity of Pc resistance genes elusive. Closely linked molecular markers may be used to identify the carrier status of a particular Pc resistance allele in any given oat line. However, elevated false positive rates could lead to misidentifying carriers, potentially excluding valuable genetic material from breeding programs. There are very few studies that examine the reliability of gene molecular markers in a diverse genetic background. In this study, molecular markers with genotype data from the T3/Oat database and map data from GrainGenes, which indicated linkage to Pc genes, were evaluated for their predictive potential. A panel of non-carrier lines for Pc genes was identified using phenotype data downloaded from T3/Oat database and pedigree records from Pedigrees of Oat Lines database. The false positive rate of the markers was calculated as the percentage of non-carriers possessing the allele associated with the Pc gene. Using the available map information, thirty SNPs associated with 15 Pc genes were selected and assessed for their predictive capabilities. Eight out of the thirty markers, linked to seven Pc genes, showed potential in predicting carrier status with a false positive rate of ≤25% in non-carrier lines. Particularly, markers for Pc38 and Pc68 perfectly corresponded to carrier status across all lines. Furthermore, validation of published predictive markers for four Pc genes in this non-carrier panel demonstrated consistency with published data, with only a 6-17% genotyping error observed for three markers. Such markers have potential to identify Pc genes present in germplasm with resistance of unknown derivation, thereby enhancing the marker assisted selection process for oat breeding.