Identification of a major locus interacting with MC1R and modifying black coat color in an F2 Nellore-Angus population

Hanna, Lauren L Hulsman; Riley, David G.; Abbey, Colette A.; Gill, C. A.

doi:10.1186/1297-9686-46-4

Cited by 26 publications

(15 citation statements)

References 23 publications

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“…First, we obtained a preliminary genomic localization of the RTS locus by genome-wide quantitative trait loci (QTL) analyses as described by Hanna et al [ 18 ]. We fitted additive and additive-dominant linear regression models within the GRIDQTL software package [ 19 ] to identify regions that affect hair malformation i.e.…”

Section: Methodsmentioning

confidence: 99%

“…Subsequently, we also included the genotypes at the extension and dilution loci as fixed effects to account for potential interactions between the RTS locus and these two loci. Linkage analyses were conducted on the 6k genotyping data in 1 cM steps based on the physical positions of SNPs according to the UMD3.1 assembly of the B. taurus genome [ 20 ] and the simplistic assumption that 1 cM ~1 Mb as in [ 18 ]. Chromosome- and genome-wide significance thresholds were determined by data permutations with 10,000 replicates and 95 % confidence intervals were obtained based on 10,000 bootstrap samples.…”

Section: Methodsmentioning

confidence: 99%

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Epistatic interactions between at least three loci determine the “rat-tail” phenotype in cattle

et al. 2016

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BackgroundThe “rat-tail” syndrome (RTS) is an inherited hypotrichosis in cattle, which is exclusively expressed in diluted coloured hair. The affected animals also suffer from disturbed thermoregulation, which impairs their health and growth performance. Phenotypic features that are similar to RTS are observed in dogs with black hair follicle dysplasia.ResultsWe used a resource cross population between German Holstein and Charolais cattle breeds to prove that epistatic interactions between at least three independent genetic loci are required for the expression of the RTS phenotype. In this population, the RTS is exclusively expressed in animals with a eumelanic background that is due to the dominant ED allele at the melanocortin 1 receptor gene located on Bos taurus autosome (BTA) 18. In addition, only the individuals that are heterozygous at the dilution locus on BTA5 that corresponds to the premelanosome protein or silver gene variant c.64G>A were classified as displaying a RTS phenotype. Linkage and whole-genome association analyses using different models and different pedigrees allowed us to map a third locus (hereafter referred to as the RTS locus) that is essential for the expression of the RTS phenotype to the chromosomal region between 14 and 22 Mb on BTA5. Our findings clearly demonstrate that the RTS and dilution loci are distinct loci on BTA5.ConclusionsOur study provides evidence that the RTS locus has effects on hair conformation and coat colour dilution and that the effect on coat colour dilution is clearly independent from that of the dilution locus. Finally, our results excluded several other loci that were previously reported to be associated with or to underlie hair conformation or pigmentation traits as the causal mutations of RTS and also several major functional candidate genes that are associated with hypotrichosis in humans. Our finding on the identification of a three-locus interaction that underlies RTS provides a prime example of epistatic interaction between several independent loci that is required for the expression of a distinct phenotype.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0199-8) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Epistatic interactions between at least three loci determine the “rat-tail” phenotype in cattle

et al. 2016

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“…The KIT (the Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog) gene, which is centered in the CSS interval (71.796–71.917 Mb), explains a considerable proportion of the variation in patterned pigmentation (Hayes et al, 2010 ), such as the characteristic spotting phenotype of Holstein and other dairy breeds. Close to the KIT gene, at 71.374–71.421 Mb, PDGFRA (platelet-derived growth factor alpha receptor), has recently been identified as the strongest positional candidate for the non- MC1R -related reddening phenotype in an F2 Nellore-Angus population (Hanna et al, 2014 ). Other coat color genes were also located in Multi-breed CSSs.…”

Section: Plausible Candidate Genes Underlying Css Regionsmentioning

confidence: 99%

An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds

2015

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This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 dairy breeds, and 6 dual-purpose breeds), and four different beef-vs.-dairy comparisons, which we subsequently grouped into core selective sweep (CSS) regions, defined as consecutive signals within 1 Mb of each other. We defined a total of 409 CSSs across the 29 bovine autosomes, 232 (57%) of which were associated with a single-breed (Single-breed CSSs), 134 CSSs (33%) were associated with a limited number of breeds (Two-to-Four-breed CSSs) and 39 CSSs (9%) were associated with five or more breeds (Multi-breed CSSs). For each CSS, we performed a candidate gene survey that identified 291 genes within the CSS intervals (from the total list of 5183 BioMart-extracted genes) linked to dairy and meat production, stature, and coat color traits. A complementary functional enrichment analysis of the CSS positional candidates highlighted other genes related to pathways underlying behavior, immune response, and reproductive traits. The Single-breed CSSs revealed an over-representation of genes related to dairy and beef production, this was further supported by over-representation of production-related pathway terms in these regions based on a functional enrichment analysis. Overall, this review provides a comparative map of the selection sweeps reported in European cattle breeds and presents for the first time a characterization of the selection sweeps that are found in individual breeds. Based on their uniqueness, these breed-specific signals could be considered as “divergence signals,” which may be useful in characterizing and protecting livestock genetic diversity.

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“…To support this, several recessive genetic loss-of-function variants in the MC1R gene increase the risk of developing cutaneous melanoma [43] and have been found to be associated to phenotypic features related to sun sensitivity in European populations [44].The high signal in region 2, located on OAR 6, harbored the KIT and platelet derived growth factor receptor alpha PDGFRA genes, which are implicated and interact in the functional pathway of coat color in different mammals. For example, the gene complexes KDR, KIT, and PDGFRA were found to be associated with the reddening coat color pattern in Angus cattle [45]. In addition, KIT and PDGFRA were assumed to play important roles in determining white-coat color in Iranian goats [46].…”

Section: High Signals Of Selection In Pigmentation Candidate Genesmentioning

confidence: 99%

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

Baazaoui

McEwan

Anderson

et al. 2019

Animals

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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.

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Identification of a major locus interacting with MC1R and modifying black coat color in an F2 Nellore-Angus population

Cited by 26 publications

References 23 publications

Epistatic interactions between at least three loci determine the “rat-tail” phenotype in cattle

Epistatic interactions between at least three loci determine the “rat-tail” phenotype in cattle

An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds

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

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