Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement

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 Se..., GBS genotyping (DArTseq) was performed at Diversity Array Technology Pty Ltd., Bruce ACT, Australia (http://diversityarrays.com) on DNA isolated from leaf tissue. Genome complexity reduction involved PstI-HpaII digestion. Two adaptors corresponding to two different restriction enzyme (RE) overhangs were used in ligation. The PstI-compatible adapter was designed to include Illumina flowcell attachment sequence, sequencing primer sequence and ‘‘staggered’’, varying length barcode region. Sequences generated from each lane were processed using proprietary DArT analytical pipelines., Excel, text editor