Detection and evaluation of selection signatures in sheep

Abstract

The recent development of genome-wide single nucleotide polymorphism (SNP) arrays made it possible to carry out several studies with different species. The selection process can increase or reduce allelic (or genic) frequencies at specific loci in the genome, besides dragging neighboring alleles in the chromosome. This way, genomic regions with increased frequencies of specific alleles are formed, caracterizing selection signatures or selective sweeps. The detection of these signatures is important to characterize genetic resources, as well as to identify genes or regions involved in the control and expression of important production and economic traits. Sheep are an important species for theses studies as they are dispersed worldwide and have great phenotypic diversity. Due to the large amounts of genomic data generated, specific statistical methods and softwares are necessary for the detection of selection signatures. Therefore, the objectives of this review are to address the main statistical methods and softwares currently used for the analysis of genomic data and the identification of selection signatures; to describe the results of recent works published on selection signatures in sheep; and to discuss some challenges and opportunities in this research field.

Genomic scan of selective sweeps in Djallonké (West African Dwarf) sheep shed light on adaptation to harsh environments

“…In scenarios of poor differentiation amongst individuals, the use of EHH-based tests to identify genomic areas under selection is preferable to F ST -based methods which need at least two different populations in dataset 1 . We further tested this running the software BayeScan v. 2.1 49 on our Djallonké genotypes.…”

Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders

“…The hapFLK package detects selection signatures based on differences in haplotype frequencies between all the populations ( Fariello et al, 2014 ). A number of studies have used iHS , Rsb , and other similar methods in the investigation of selection sweeps in sheep ( Paim et al, 2018 ; Alvarez et al, 2020 ), cattle ( Chen et al, 2016 ; Tijani et al, 2019 ), and other livestock species.…”

Video recording and vegetation classification elucidate sheep foraging ecology in species‐rich grassland

“…Animal genotypes that possess relevant behavioral adaptations, such as appropriate patterns of selectivity (Meuret & Provenza, 2015;Provenza et al, 2003), would therefore be important genetic resources, but the underlying genetics are incompletely understood. Specific regions of the sheep genome have been shown to have been under postdomestication selection (e.g., Fariello et al, 2014;Paim et al, 2018), but no such region directly relating to grazing behavior has yet been identified. However, it is clear from quantitative genetics that some behavioral components of grazing behavior are heritable (Fogarty et al, 2009;Snowder et al, 2001), supporting the contention that grazing behavior is an outcome of genotype-environment interaction (Osoro et al, 1999;Rook, Dumont, et al, 2004).…”