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.

Additional file 2: Table S1. Information on rye accessions used in the study, including genebank accession number, name, source, taxon, improvement status, country of origin, geographic region, group memberships based on STRUCTURE anaysis and NJ clustering, and sweep detection set membership. Table S2. List of 12486 HQ DArTseq markers used in this study, including their sequences and position in the Lo7 reference genome. Table S3. Chromosomal distribution of SNPs by germplasm group. Table S4. Pairwise population FST values for accessions groups based on NJ clustering. Table S5. Values of genetic diversity indices for the collection of 478 rye accessions and each established germplasm group. Table S6. Information on common outliers and sweeps detected by all three methods (SweeD, OmegaPlus and RAiSD) in groups of cultivated rye accessions. Table S7. List of putative candidate genes targeted by selection in cultivated rye. Table S8. Enriched GO terms for putative candidate genes from the selective sweep regions. Table S9. Literature based list of known cereal domestication/improvement genes and locations of their putative homologues in the Lo7 genome.

Additional file 2: Table S1. Information on rye accessions used in the study, including genebank accession number, name, source, taxon, improvement status, country of origin, geographic region, group memberships based on STRUCTURE anaysis and NJ clustering, and sweep detection set membership. Table S2. List of 12486 HQ DArTseq markers used in this study, including their sequences and position in the Lo7 reference genome. Table S3. Chromosomal distribution of SNPs by germplasm group. Table S4. Pairwise population FST values for accessions groups based on NJ clustering. Table S5. Values of genetic diversity indices for the collection of 478 rye accessions and each established germplasm group. Table S6. Information on common outliers and sweeps detected by all three methods (SweeD, OmegaPlus and RAiSD) in groups of cultivated rye accessions. Table S7. List of putative candidate genes targeted by selection in cultivated rye. Table S8. Enriched GO terms for putative candidate genes from the selective sweep regions. Table S9. Literature based list of known cereal domestication/improvement genes and locations of their putative homologues in the Lo7 genome.