Studying Stem Rust and Leaf Rust Resistances of Self-Fertile Rye Breeding Populations

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 DArTseqTM. 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.