Data from: Population structure, genetic variation and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance

Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF] and 27 of Unselected [US]) from the second generation of the two divergently selected populations and an unselected control population were genotyped using 278 genome-wide SNPs derived from Lolium perenne L. transcriptome sequence. Our studies showed that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD) decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two Fst outlier methods; finite island model (fdist) by LOSITAN and hierarchical structure model using ARLEQUIN detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation and abiotic stress and might be the potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.Frost_278_SNPs_Genotyping_Rawdata_Kovi_et_al_2015_frontiers_PlantscienceTwo hundred and seventy-eight Lolium perenne genic SNP markers distributed across the seven linkage groups [LG1 (37); LG2 (57); LG3 (32); LG4 (40); LG5 (39); LG6 (37); and LG7 (36)] were genotyped using Sequenom MassARRAY iPLEX platform. The 'Genotype' column indicates the population labels used during the analyses. For each SNP marker, one column with a unique label (i.e. marker name) indicate the two alleles. Missing data are labelled '0'.Frost_genotype_filtering_231SNPs_Kovi_et_al_frontiers_PlantscienceTwo hundred and thirty one SNPs were obtained for data analysis after removing eleven SNPs which failed in genotyping and twenty-seven SNPs with missing data > 5% from the initial genotyping dataset. Of the remaining 231 SNPs, 181 SNPs (78.3%), 162 SNPs (70.1%), and 180 SNPs (77.9 %) were polymorphic across the HF (High frost), LF (Low frost) and US (Unselected) populations, respectively. Missing data is represented as "0".Frost_genotype_filtering_231SNPs_Kovi_et_al_2015_Frontiers_Plantscience.odsfrost_structure_excludinghomozygous_outlierSNPs_linkedmarkers_Kovi_et_al_2015_frontiers_PlantscienceStructure input file, after discarding 94 SNP markers closely linked with a minimum distance of 2 cM and 32 outlier SNP markers from the analysis. In total, 105 SNP markers were used to estimate the population structure using linkage model.frost_Kovi_et_al_2015_frontiers_PlantScienceArlequin input fil