Ergot caused by Claviceps purpurea is a problem for food and feed security in rye due to the occurrence of toxic ergot alkaloids (EAs). For grain elevators and breeders, a quick, easy-to-handle, and cheap screening assay would have a high economic impact. The study was performed to reveal (1) the covariation of ergot severity (= percentage of sclerotia in harvested grain) and the content of 12 EAs determined by high performance liquid chromatography (HPLC) and (2) the covariation between these traits and results of one commercial enzyme linked immunosorbent assays (ELISA). In total, 372 winter rye samples consisting of a diverse set of genotypes, locations from Germany, Austria, and Poland over two years, and three isolates were analyzed. Ergocornine and α-ergocryptine were detected as major EAs. Ergocristinine occurred as a minor component. Claviceps isolates from different countries showed a similar EA spectrum, but different quantities of individual EAs. A moderate, positive covariation between ergot severity and EA content determined by HPLC was observed across two years (r = 0.53, p < 0.01), but large deviation from the regression was detected. ELISA values did neither correlate with the HPLC results nor with ergot severity. In conclusion, a reliable prediction of the EA content based on ergot severity is, at present, not possible.

Contamination by ergot caused by the phytopathogenic fungus Claviceps purpurea is a constant threat to the whole rye value chain. Ergot alkaloids (EA) produced within the fungal sclerotia are toxic for humans and animals and are subjected to strict regulations in human food. Our main objective was to analyze whether less susceptible rye cultivars with a lower content of sclerotia also contain fewer ergot alkaloids (EA). We analyzed 15 factorial single crosses in multi-environmental trials with artificial inoculation for their ergot severity, the content of twelve EAs by HPLC, and the total ergot content by ELISA. The genotypes displayed a wide range of pollen shedding from fully sterile to fully fertile, of ergot severity expressed as percentage of sclerotia relative to the harvest (0.22–11.47%), and of EA contents when analyzed by HPLC (0.57–45.27 mg/kg. Entry-mean heritabilities were high throughout (0.87–0.98). The factorial analysis yielded a preponderance of male general combining ability (GCA) variances, the estimates for the females were smaller, although significant. EA contents measured by ELISA were, on average, seven times larger. The correlation between ergot severity and EA contents determined by HPLC was r = 0.98 (p ≤ 0.01) and only somewhat lower when analyzed by ELISA. In conclusion, less ergot prone rye genotypes also support lower EA contents.

Stem rust (SR) and leaf rust (LR) are currently the two most important rust diseases of cultivated rye in Central Europe and resistant cultivars promise to prevent yield losses caused by those pathogens. To secure long-lasting resistance, ideally pyramided monogenic resistances and race-nonspecific resistances are applied. To find respective genes, we screened six breeding populations and one testcross population for resistance to artificially inoculated SR and naturally occurring LR in multi-environmental field trials. Five populations were genotyped with a 10K SNP marker chip and one with DArTseq^TM. In total, ten SR-QTLs were found that caused a reduction of 5–17 percentage points in stem coverage with urediniospores. Four QTLs thereof were mapped to positions of already known SR QTLs. An additional gene at the distal end of chromosome 2R, Pgs3.1, that caused a reduction of 40 percentage points SR infection, was validated. One SR-QTL on chromosome 3R, QTL-SR4, was found in three populations linked with the same marker. Further QTLs at similar positions, but from different populations, were also found on chromosomes 1R, 4R, and 6R. For SR, additionally seedling tests were used to separate between adult-plant and all-stage resistances and a statistical method accounting for the ordinal-scaled seedling test data was used to map seedling resistances. However, only Pgs3.1 could be detected based on seedling test data, even though genetic variance was observed in another population, too. For LR, in three of the populations, two new large-effect loci (Pr7 and Pr8) on chromosomes 1R and 2R were mapped that caused 34 and 21 percentage points reduction in leaf area covered with urediniospores and one new QTL on chromosome 1R causing 9 percentage points reduction.