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Abstract Background During domestication and subsequent improvement plants were subjected to intensive positive selection for desirable traits. Identification of selection targets is important with respect to the future targeted broadening of diversity in breeding programmes. Rye (Secale cereale L.) is a cereal that is closely related to wheat, and it is an important crop in Central, Eastern and Northern Europe. The aim of the study was (i) to identify diverse groups of rye accessions based on high-density, genome-wide analysis of genetic diversity within a set of 478 rye accessions, covering a full spectrum of diversity within the genus, from wild accessions to inbred lines used in hybrid breeding, and (ii) to identify selective sweeps in the established groups of cultivated rye germplasm and putative candidate genes targeted by selection. Results Population structure and genetic diversity analyses based on high-quality SNP (DArTseq) markers revealed the presence of three complexes in the Secale genus: S. sylvestre, S. strictum and S. cereale/vavilovii, a relatively narrow diversity of S. sylvestre, very high diversity of S. strictum, and signatures of strong positive selection in S. vavilovii. Within cultivated ryes we detected the presence of genetic clusters and the influence of improvement status on the clustering. Rye landraces represent a reservoir of variation for breeding, and especially a distinct group of landraces from Turkey should be of special interest as a source of untapped variation. Selective sweep detection in cultivated accessions identified 133 outlier positions within 13 sweep regions and 170 putative candidate genes related, among others, to response to various environmental stimuli (such as pathogens, drought, cold), plant fertility and reproduction (pollen sperm cell differentiation, pollen maturation, pollen tube growth), and plant growth and biomass production. Conclusions Our study provides valuable information for efficient management of rye germplasm collections, which can help to ensure proper safeguarding of their genetic potential and provides numerous novel candidate genes targeted by selection in cultivated rye for further functional characterisation and allelic diversity studies.

Powdery mildew is one of the most devastating diseases of wheat which significantly decreases yield and quality. Identification of new sources of resistance and their implementation in breeding programs is the most effective way of disease control. Two major powdery mildew resistance loci conferring resistance to all races in seedling and adult plant stages were identified in the emmer wheat landrace GZ1. Their positions, effects, and transferability were verified using two linkage maps (1,510 codominant SNP markers) constructed from two mapping populations (276 lines in total) based on the resistant GZ1 line. The dominant resistance locus QPm.GZ1-7A was located in a 90 cM interval of chromosome 7AL and explains up to 20% of the trait variation. The recessive locus QPm.GZ1-2A, which provides total resistance, explains up to 40% of the trait variation and was located in the distal part of chromosome 2AL. The locus was saturated with 14 PCR-based markers and delimited to a 0.99 cM region which corresponds to 4.3 Mb of the cv. Zavitan reference genome and comprises 55 predicted genes with no apparent candidate for the QPm.GZ1-2A resistance gene. No recessive resistance gene or allele was located at the locus before, suggesting the presence of a new powdery mildew resistance gene in the GZ1. The mapping data and markers could be used for the implementation of the locus in breeding. Moreover, they are an ideal base for cloning and study of host–pathogen interaction pathways determined by the resistance genes.

Resistance to powdery mildew (Blumeria graminis (DC.) E. O. Speer f.sp. tritici Em. Marchal) in Aegilops crassa Boiss., Ae. ventricosa Tausch, Ae. biuncialis Vis., Ae. triuncialis L. and Ae. cylindrica Host was tested at the stage of primary leaves in the years 2000 and 2001. All plants of Ae. ventricosa, Ae. biuncialis and sample No. 9 of Ae. cylindrica repeatedly showed a susceptible reaction after being inoculated by all powdery mildew isolates used. In contrast, plants of Ae. crassa, sample No. 8 of Ae. cylindrica and all samples (No. 13, 21, 22, 24 and 26) of Ae. triuncialis were resistant to all isolates. Samples No. 5, 6, 7, 19 and 23 of Ae. cylindrica contained resistant and susceptible plants in both years. Virulence to these samples ranged from 3% to 18%. Cluster analysis using DNA microsatellite markers showed that the accessions are arranged in groups based on taxonomic relationship but not on basis of resistance. Plants susceptible to powdery mildew at the juvenile stage showed satisfactory adult plant resistance.

The objective of the study was to identify genes for resistance to powdery mildew in wheat cultivars and land races from Poland, Slovakia and Hungary. The presence and distribution of resistance genes was compared to powdery mildew virulence structure in these countries. The different strategies in breeding for resistance were expressed in a different distribution of resistance genes, especially among Polish and Hungarian cultivars. In 20 of the 29 Hungarian common wheat cultivars the resistance gene Pm8 was found. Of the 32 Polish cultivars investigated, 16 possess a combination of genes Pm2+6. Resistance gene Pm4b did not occur in any Hungarian cultivar tested, and resistance gene pm5 was not detected in any Polish cultivar. Virulence in wheat powdery mildew populations was influenced by differences in distribution of resistance genes in host genotypes. The most significant difference was found between Polish and Hungarian powdery mildew populations. The two populations differed mainly in virulence against Pm2. Resistance gene MlAr was detected in three old Slovak cultivars.