Reduced height (Rht) genes are widely used in modern wheat breeding although some confer higher susceptibility to Fusarium head blight (FHB) caused by F. graminearum and other species. Our objective was to test whether the recently identified Rht24b dwarfing allele has a neutral effect on FHB response as reported previously from a single mapping population when unrelated winter wheat cultivars were analyzed. We artificially infected a panel of 420 cultivars divided into four genotypic groups (Rht24a + Rht-D1a, Rht24b + Rht-D1a, Rht24a + Rht-D1b, Rht24b + Rht-D1b) with Fusarium culmorum in five location-year combinations. High and significant (P ≤ 0.001) genetic variance for FHB severity and plant height (PH) was found in the entire panel as well as within the four Rht groups and both traits showed high entry-mean heritabilities of 0.92 and 0.98, respectively. Rht24b had no significant effect on FHB severity whereas Rht-D1b increased FHB susceptibility by 37%. The 29 most resistant cultivars either had the tallness alleles of the above mentioned Rht-D1 gene or Rht24b alone. The Rht24b + Rht-D1b combination had no significantly higher FHB severity than Rht-D1b alone. However, Rht24b reduced average PH only by 6.8 cm, whereas Rht-D1b conferred a reduction of 13.6 cm. For breeding short, FHB-resistant germplasm the neutral Rht24 gene must be complemented by further QTL or other FHB-neutral Rht genes.

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.

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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.

Key message Individual stem rust resistance genes could be directly mapped within self-incompatible rye populations. Abstract 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.