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.

Mapping and validating stem rust resistance genes directly in self-incompatible genetic resources of winter rye.

KEY MESSAGE: Individual stem rust resistance genes could be directly mapped within self-incompatible rye populations. Genetic resources of rye (Secale cereale L.) are cross-pollinating populations that can be highly diverse and are naturally segregating. In this study, we show that this segregation could be used for mapping stem rust resistance. Populations of pre-selected donors from the Russian Federation, the USA and Austria were tested on a single-plant basis for stem rust resistance by a leaf-segment test with three rust isolates. Seventy-four plants per population were genotyped with a 10 K-SNP chip. Using cumulative logit models, significant associations between the ordinal infection score and the marker alleles could be found. Three different loci (Pgs1, Pgs2, Pgs3) in three populations were highly significant, and resistance-linked markers could be validated with field experiments of an independent seed sample from the original population and were used to fix two populations for resistance. We showed that it is possible to map monogenically inherited seedling resistance genes directly in genetic resources, thus providing a competitive alternative to linkage mapping approaches that require a tedious and time-consuming inbreeding over several generations.

Perennial Rye: Genetics of Perenniality and Limited Fertility.

Perenniality, the ability of plants to regrow after seed set, could be introgressed into cultivated rye by crossing with the wild relative and perennial Secale strictum. However, studies in the past showed that Secale cereale × Secale strictum-derived cultivars were also characterized by reduced fertility what was related to so called chromosomal multivalents, bulks of chromosomes that paired together in metaphase I of pollen mother cells instead of only two chromosomes (bivalents). Those multivalents could be caused by ancient translocations that occurred between both species. Genetic studies on perennial rye are quite old and especially the advent of molecular markers and genome sequencing paved the way for new insights and more comprehensive studies. After a brief review of the past research, we used a basic QTL mapping approach to analyze the genetic status of perennial rye. We could show that for the trait perennation 0.74 of the genetic variance in our population was explained by additively inherited QTLs on chromosome 2R, 3R, 4R, 5R and 7R. Fertility on the other hand was with 0.64 of explained genetic variance mainly attributed to a locus on chromosome 5R, what was most probably the self-incompatibility locus S5. Additionally, we could trace the Z locus on chromosome 2R by high segregation distortion of markers. Indications for chromosomal co-segregation, like multivalents, could not be found. This study opens new possibilities to use perennial rye as genetic resource and for alternative breeding methods, as well as a valuable resource for comparative studies of perennation across different species.

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.