title: Genome Wide Association Study Identifies New Loci Associated with Undesired Coat Color Phenotypes in Saanen Goats.
abstract: This paper reports a quantitative genetics and genomic analysis of undesirable coat color patterns in goats. Two undesirable coat colors have routinely been recorded for the past 15 years in French Saanen goats. One fifth of Saanen females have been phenotyped "pink" (8.0%) or "pink neck" (11.5%) and consequently have not been included in the breeding program as elite animals. Heritability of the binary "pink" and "pink neck" phenotype, estimated from 103,443 females was 0.26 for "pink" and 0.21 for "pink neck". Genome wide association studies (using haplotypes or single SNPs) were implemented using a daughter design of 810 Saanen goats sired by 9 Artificial Insemination bucks genotyped with the goatSNP50 chip. A highly significant signal (-log10pvalue = 10.2) was associated with the "pink neck" phenotype on chromosome 11, suggesting the presence of a major gene. Highly significant signals for the "pink" phenotype were found on chromosomes 5 and 13 (-log10p values of 7.2 and, 7.7 respectively). The most significant SNP on chromosome 13 was in the ASIP gene region, well known for its association with coat color phenotypes. Nine significant signals were also found for both traits. The highest signal for each trait was detected by both single SNP and haplotype approaches, whereas the smaller signals were not consistently detected by the two methods. Altogether these results demonstrated a strong genetic control of the "pink" and "pink neck" phenotypes in French Saanen goats suggesting that SNP information could be used to identify and remove undesired colored animals from the breeding program.
authors.affiliation: INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France.|Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France.|Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France.
authors.forename: Pauline Marie
authors.initials: PM
authors.lastname: Martin
authors.affiliation: INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France.|Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France.|Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Palhière
authors.affiliation: INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France.|Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France.|Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Ricard
authors.affiliation: INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France.|Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France.|Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France.
authors.forename: Gwenola
authors.initials: G
authors.lastname: Tosser-Klopp
authors.affiliation: INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France.|Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France.|Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France.
authors.forename: Rachel
authors.initials: R
authors.lastname: Rupp
mesh_terms: D000818:Animals; D001947:Breeding; D005260:Female; D056426:Genetic Loci; D055106:Genome-Wide Association Study; D006041:Goats / Q000235:genetics*; D006200:Hair Color / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA