The brown coat colour of Coppernecked goats is associated with a non‐synonymous variant at the TYRP 1 locus on chromosome 8

Summary The recent development of a goat SNP genotyping microarray enables genome‐wide association studies in this important livestock species. We investigated the genetic basis of the black and brown coat colour in Valais Blacknecked and Coppernecked goats. A genome‐wide association analysis using goat SNP 50 BeadChip genotypes of 22 cases and 23 controls allowed us to map the locus for the brown coat colour to goat chromosome 8. The TYRP 1 gene is located within the associated chromosomal region, and TYRP 1 variants cause similar coat colour phenotypes in different species. We thus considered TYRP 1 as a strong positional and functional candidate. We resequenced the caprine TYRP 1 gene by Sanger and Illumina sequencing and identified two non‐synonymous variants, p.Ile478Thr and p.Gly496Asp, that might have a functional impact on the TYRP 1 protein. However, based on the obtained pedigree and genotype data, the brown coat colour in these goats is not due to a single recessive loss‐of‐function allele. Surprisingly, the genotype distribution and the pedigree data suggest that the 496 Asp allele might possibly act in a dominant manner. The 496 Asp allele was present in 77 of 81 investigated Coppernecked goats and did not occur in black goats. This strongly suggests heterogeneity underlying the brown coat colour in Coppernecked goats. Functional experiments or targeted matings will be required to verify the unexpected preliminary findings.