Identification of selection signatures in livestock species

Abstract

The identification of regions that have undergone selection is one of the principal goals of theoretical and applied evolutionary genetics. Such studies can also provide information about the evolutionary processes involved in shaping genomes, as well as physical and functional information about genes/genomic regions. Domestication followed by breed formation and selection schemes has allowed the formation of very diverse livestock breeds adapted to a wide variety of environments and with special characteristics. The advances in genomics in the last five years have enabled the development of several methods to detect selection signatures and have resulted in the publication of a considerable number of studies involving livestock species. The aims of this review are to describe the principal effects of natural/artificial selection on livestock genomes, to present the main methods used to detect selection signatures and to discuss some recent results in this area. This review should be useful also to research scientists working with wild animals/non-domesticated species and plant biologists working with breeding and evolutionary biology.

Whole-Genome Signatures of Selection in Sport Horses Revealed Selection Footprints Related to Musculoskeletal System Development Processes

“…However, assuming the sport performance as a simple trait that is controlled by a few genes can be unrealistic [7], and, thus, signatures of selection studies may identify novel candidate genes related to this complex trait. Additionally, combining the results of different signatures of selection approaches can increase the reliability, because different methods can focus on different genomic selective signals that have been subjected to selection in varied time scales [40]. Our main selection signature tests in this study were fixation index [26] and pairwise nucleotide diversity [27] based on population differentiation and allele frequency spectrum, respectively.…”

Genome-wide analysis reveals genetic diversity, linkage disequilibrium, and selection for milk traits in Chinese buffalo breeds

“…These methods mainly based on the linkage disequilibrium (LD), spectra of allele frequencies, and characteristics of haplotype structures in the studied populations [28]. Notably, identifying signatures of selection could provide insight into the genomic response to domestication and selection for production traits, which help in the design of more efficient selection schemes [29]. To date, numbers selective sweep regions associated with production traits has been identified in domesticated animals, such as milk production traits [30], reproductive traits [31], feed efficiency [32], elongation of the back [33], and lack of horns [34].…”

GBS Data Identify Pigmentation-Specific Genes of Potential Role in Skin-Photosensitization in Two Tunisian Sheep Breeds

“…The most significant genomic region under selection wasregion1, located on OAR 14, containing the Melanocortin 1 receptor MC1R gene, a key candidate gene for coat color pigmentation. Indeed, the MC1R gene played a central role in the regulation of eumelanin (black-brown) and phaeomelanin (red-yellow) synthesis within the mammalian melanocyte and is often found under selection in several sheep breeds [38,39]. Moreover, previous sequence analysis studies evidenced those mutations, within the MC1R gene, which are responsible for the dominant black-color in sheep [40,41] and pigs [42].…”