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

Abstract

Simple Summary: Maintaining the flexibility of the genetic resources of native animals to face local environment constraints is still a major challenge. In Tunisia, the Noire de Thibar breed is a local sheep, typically with black coloration, known for its ability to tolerate "hypericum perforatum", which causes skin photosensitization in white colored sheep. The goal of this study was to perform a genome scan, by considering genotyping-by-sequencing (GBS) markers that were genotyped in divergent coat colored sheep (black vs. white) to identify strong, and recent, artificial selection that is involved in skin-photosensitization. Interestingly, the genomic differentiation analysis identified F ST markers within genomic regions containing key pigmentation and photosensitivity related-genes. These findings help in understanding the background of coat color genetics and its potential role in adaptation to local environment constraints.Abstract: The Tunisian Noire de Thibar sheep breed is a composite breed, recently selected to create animals that are uniformly black in order to avoid skin photosensitization after the ingestion of toxic "hypericum perforatum" weeds, which causes a major economic loss to sheep farmers. We assessed genetic differentiation and estimated marker F ST using genotyping-by-sequencing (GBS) data in black (Noire de Thibar) and related white-coated (Queue fine de l'ouest) sheep breeds to identify signals of artificial selection. The results revealed the selection signatures within candidate genes related to coat color, which are assumed to be indirectly involved in the mechanism of photosensitization in sheep. The identified genes could provide important information for molecular breeding.

Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes

“…In this study, white-coated and red-coated animals were homozygous for the E + allele, whereas black-coated animals carried at least one copy of the E D allele [ 87 ]. In a study performed to identify pigmentation-specific genes associated with skin photosensitization, MC1R was also the most significant genomic region under selection, and a number of other genes were also suggested to be potentially associated with this trait, including KIT , PDGFRA , IRF4 , SOX10 , PICK1 , and EDN3 [ 88 ]. Moreover, a GWAS using the OvineSNP600K Beadchip was performed on 75 Chinese Tan sheep individuals (29 black-headed and 46 white-coated; see Additional file 1 : Fig.…”

Genomic analysis of GBS data reveals genes associated with facial pigmentation in Xinyang blue-shelled layers

“…In order to detect superior signals based on the allele frequency difference, markers were ranked according to raw F ST values and plotted according to their genomic position based on the Gallus_gallus-5.0 assembly genome using R software (version 2.13.2). In addition, Haploview v4.2 software was used to analyze linkage disequilibrium and haplotype (Barrett et al, 2005).…”

“…Mutations in this gene and EDNRB have been as-sociated with Hirschsprung disease (HSCR) (Gabriel et al, 2002) and Waardenburg syndrome (WS) (Amiel et al, 2008). The gene may also be related to pigmentation of sheep skin (Fariello et al, 2014;Baazaoui et al, 2019). Recently, a combined analysis of genomic and transcriptomic data suggests that the candidate gene related to the black-bone trait, EDN3, might interact with the upstream ncRNA LOC101747896 to generate black skin color during melanogenesis (Li et al, 2020).…”

“…The advent of next-generation sequencing (NGS) has reduced the cost of genome sequencing to a level where genotyping by sequencing (GBS) is now considered a powerful tool for inquiring into a large number of genomic variations (SNPs). A large number of candidate genes related to different economic traits of livestock and poultry have been identified by this method, such as the coat color of sheep (Baazaoui et al, 2019), the fatty acid biosynthesis and litter traits of pigs (Kai et al, 2018;Wu et al, 2018), and the body weight of chicken (Fuwei et al, 2018). The combined analysis of genome-wide association study (GWAS) and selection signatures can effectively reveal agronomic traits of crops (You et al, 2018;Lu et al, 2019) and livestock economic traits (Yang et al, 2017).…”

Reproductive behavior of Pantaneiros sheep, Mato Grosso do Sul, Brazil

“…Patterns of genetic flow at domestic animals variation processes in domestic animals have long proven insightful for the domestication study, breed formation, population structure, and the selection consequences. Natural and artificial selection processes in domestic animals play crucial roles in maintaining the flexibility of animal genetic resources in facing local environment constraints (Baazaoui et al, 2020).…”