Selection signatures in worldwide Sheep populations

Abstract

The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinpointing several new selection signatures in the sheep genome and distinguishing those related to modern breeding objectives and to earlier post-domestication constraints. The newly identified regions, together with the ones previously identified, reveal the extensive genome response to selection on morphology, color and adaptation to new environments.

Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds

“…Because hapFLK combines information across multiple sites, it has been shown to have better detection power than single-site statistics (Fariello et al 2013(Fariello et al , 2014. This was confirmed when applied to this data set, as we could confidently find 67 significant regions using a FDR threshold of 15%.…”

“…Detected regions spanned from a few hundred base pairs to .1 Mb with a median length of 20 kb ( Figure S9). The median size of detected regions was thus considerably smaller than that obtained in previous studies where hapFLK was applied to 60K data in sheep (Fariello et al 2014;Kijas 2014). Nineteen of the regions encompassed at least one gene while 38 contained no gene.…”

“…This comes from the fact that this approach is specifically designed to detect hard-sweep signals, while hapFLK also detects incomplete or soft sweeps (Fariello et al 2013(Fariello et al , 2014. For the 49 regions detected by hapFLK and not by the within-breed approach, the evidence of a hard sweep, measured by the statistic T OR ; was always very low in all breeds, indicating that the signal detected by hapFLK had nothing to do with a hard sweep in one of the breeds.…”

“…For instance, in taurine cattle, at least 21 genomic scans for selection have already been published and were reviewed in GutierrezGil et al (2015). Numerous genomic scans for selection have also been published in other livestock species; see de Simoni Gouveia et al (2014) for a review.The regions detected by these studies are generally convincing, because they contain interesting positional and functional candidate genes (e.g., Fariello et al 2014) and/or are statistically enriched with genes from regulation pathways related to production traits (e.g., Flori et al 2009). Nevertheless, these regions often span several megabases and typically include up to tens of genes, so determining the exact gene(s) Roux et al 2015), the advantage of using sequencing data for detecting selection signatures has still not been widely discussed.…”

Whole-Genome Sequencing of Bamei Mutton Sheep for Screening the Genes and SNPs Associated with Litter Size under Selection

“…They can help in identifying genomic signatures of domestic traits in sheep (12). By performing whole-genome resequencing on phenotypically divergent sheep populations, some selective sweeps were identi ed relating to important traits targeted by arti cial selection during domestication, such as horn (1,13), coat color (14), tail morphology and fat deposition (3,15,16) and variation of thoracic vertebrae (17).…”