The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds

Abstract

Domestication and the subsequent selection of animals for either economic or morphological features can leave a variety of imprints on the genome of a population. Genomic regions subjected to high selective pressures often show reduced genetic diversity and frequent runs of homozygosity (ROH). Therefore, the objective of the present study was to use 42,182 autosomal SNPs to identify genomic regions in 3,191 sheep from six commercial breeds subjected to selection pressure and to quantify the genetic diversity within each breed using ROH. In addition, the historical effective population size of each breed was also estimated and, in conjunction with ROH, was used to elucidate the demographic history of the six breeds. ROH were common in the autosomes of animals in the present study, but the observed breed differences in patterns of ROH length and burden suggested differences in breed effective population size and recent management. ROH provided a sufficient predictor of the pedigree inbreeding coefficient, with an estimated correlation between both measures of 0.62. Genomic regions under putative selection were identified using two complementary algorithms; the fixation index and hapFLK. The identified regions under putative selection included candidate genes associated with skin pigmentation, body size and muscle formation; such characteristics are often sought after in modern-day breeding programs. These regions of selection frequently overlapped with high ROH regions both within and across breeds. Multiple yet uncharacterised genes also resided within putative regions of selection. This further substantiates the need for a more comprehensive annotation of the sheep genome as these uncharacterised genes may contribute to traits of interest in the animal sciences. Despite this, the regions identified as under putative selection in the current study provide an insight into the mechanisms leading to breed differentiation and genetic variation in meat production.

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.

Fig 5. Matrix of scatter plots for different measures of inbreeding calculated from runs of homozygosity (F_ROH) versus inbreeding estimated from A) pedigree analysis (F_PED), B) genomic relationship matrix (F_GRM) and C) the observed versus expected homozygotes (F_HOM) 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).

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 F_ST 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.

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.