Mapping stem rust (Puccinia graminis f. sp. secalis) resistance in self-fertile winter rye populations

Rye stem rust caused by Puccinia graminis f. sp. secalis can be found in all European rye growing regions. When the summers are warm and dry, the disease can cause severe yield losses over large areas. To date only little research was done in Europe to trigger resistance breeding. To our knowledge, all varieties currently registered in Germany are susceptible. In this study, three biparental populations of inbred lines and one testcross population developed for mapping resistance were investigated. Over 2 years, 68–70 genotypes per population were tested, each in three locations. Combining the phenotypic data with genotyping results of a custom 10k Infinium iSelect single nucleotide polymorphism (SNP) array, we identified both quantitatively inherited adult plant resistance and monogenic all-stage resistance. A single resistance gene, tentatively named Pgs1, located at the distal end of chromosome 7R, could be identified in two independently developed populations. With high probability, it is closely linked to a nucleotide-binding leucine-rich repeat (NB-LRR) resistance gene homolog. A marker for a competitive allele-specific polymerase chain reaction (KASP) genotyping assay was designed that could explain 73 and 97% of the genetic variance in each of both populations, respectively. Additional investigation of naturally occurring rye leaf rust (caused by Puccinia recondita ROEBERGE) revealed a gene complex on chromosome 7R. The gene Pgs1 and further identified quantitative trait loci (QTL) have high potential to be used for breeding stem rust resistant rye.