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Background  In cattle, the gene coding for the melanocortin receptor 1 ( MC1R ) is known to be the main regulator of the switch between the two coat colour pigments: eumelanin (black pigment) and phaeomelanin (red pigment). Some breeds, such as Charolais and Simmental, exhibit a lightening of the original pigment over the whole body. The dilution mutation in Charolais ( Dc ) is responsible for the white coat colour of this breed. Using an F2-Backcross Charolais × Holstein population which includes animals with both pigment backgrounds, we present a linkage mapping study of the Charolais dilution locus.    Results  A Charolais × Holstein crossbred population was investigated for genetic effects on coat colour dilution. Three different traits representing the dilution of the phaeomelanin, eumelanin, and non-pigment-specific dilution were defined. Highly significant genome-wide associations were detected on chromosome 5 for the three traits analysed in the marker interval [ETH10-DIK5248]. The  SILV  gene was examined as the strongest positional and functional candidate gene. A previously reported non-synonymous mutation in exon 1 of this gene,  SILV  c.64A>G, was associated with the coat colour dilution phenotype in this resource population. Although some discrepancies were identified between this mutation and the dilution phenotype, no convincing recombination events were found between the  SILV  c.64A>G mutation and the  Dc  locus. Further analysis identified a region on chromosome 28 influencing the variation in pigment intensity for a given coat colour category.    Conclusion  The present study has identified a region on bovine chromosome 5 that harbours the major locus responsible for the dilution of the eumelanin and phaeomelanin seen in Charolais crossbred cattle. In this study, no convincing evidence was found to exclude  SILV  c.64A>G as the causative mutation for the Charolais dilution phenotype, although other genetic effects may influence the coat colour variation in the population studied. A region on chromosome 28 influences the intensity of pigment within coat colour categories, and therefore may include a modifier of the  Dc  locus. A candidate gene for this effect,  LYST , was identified.

Genetic effects on coat colour in cattle: dilution of eumelanin and phaeomelanin pigments in an F2-Backcross Charolais × Holstein population