Fig 1.
Admixture analysis of six commercial sheep breeds.
The number of clusters was set to k = 5.
Fig 2.
Estimated effective population size across generations for each breed.
Fig 3.
The mean sum of runs of homozygosity (ROH) per animal within each ROH length category.
Fig 4.
Proportion of autosome covered in runs of homozygosity (ROH) per animal.
The black line indicates the median ROH sum per individual within each breed.
Table 1.
The correlation between runs of homozygosity (ROH) based inbreeding coefficients and inbreeding coefficients estimated from pedigree (FPED), the genomic relationship matrix (FGRM) and the observed versus expected homozygotes (FHOM).
Three different ROH inbreeding measures were used which corresponded to the minimum length of the ROH used in the estimation (FROH1Mb, FROH5Mb, FROH10Mb).
Fig 5.
Matrix of scatter plots for different measures of inbreeding calculated from runs of homozygosity (FROH) versus inbreeding estimated from A) pedigree analysis (FPED), B) genomic relationship matrix (FGRM) and C) the observed versus expected homozygotes (FHOM) on 843 animals with at least 6 complete generation equivalents.
Four populations were included in the analysis; Belclare (red), Suffolk (purple), Texel (blue) and Vendeen (yellow).
Table 2.
Runs of homozygosity (ROH) hotspots across all breeds, as defined as the top 1% of SNPs that occurred in a ROH.
The number of SNPs within these hotspots are listed, as well as the average recombination rate (cM/Mb) within each hotspot and the putative candidate genes under selection.
Fig 6.
Genomic regions detected to be under divergent selection across all breeds.
A) The frequency of a single nucleotide polymorphism (SNP) in a run of homozygosity (ROH) B) global FST values across all breeds where the blue line indicates SNPs that exhibited great differentiation and the red line indicates SNPs that exhibited very great differentiation C) a haplotype-based hapFLK test where the red line indicates the significance level threshold of 0.0001. SNPs highlighted in green are those identified within putative selection signatures.
Table 3.
Detected selection signatures containing the top 0.1% of SNP, ranked on FST.
Detailed are the number of significant (Sig) SNP (P-value <0.0001) within each selection signature, the maximum (Max) FST value of a SNP within this signature, the number of genes identified within the selection signature boundaries and the identified candidate gene and its function.
Fig 7.
Local population tree estimated in two selection signatures identified on OAR2 and OAR23.
A) The whole genome population tree B & D) The local population tree re-estimated using only single nucleotide polymorphisms (SNPs) identified within the putative selection signature C & E) The haplotype clusters for the selection signature.
Table 4.
Putative selective sweeps identified in the hapFLK-based analysis.