MC1R residue 223 is a convergent target for coat-colour lightening in domestic and wild bovids

Abstract

Whether similar phenotypes evolve through shared substitutions or alternative molecular routes is a central question in evolutionary genomics. Grey-coated taurine cattle provide a powerful system for investigating this question using geographically distinct Podolian and Alpine lineages. We combined whole-genome resequencing data, complementary selection scans (hapFLK, DCMS and FST) and contrasts between grey-coated and non-grey-coated breeds to investigate the molecular evolution of grey coat colour. Selection analyses identified candidate regions associated with Podolian/steppe divergence and a prominent pigmentation-related signal on BTA18 contaning FANCA, MC1R, and SPIRE2. Most grey breeds shared a BTA18 haplotype containing MC1R p.Arg223Trp and additional candidate variants. Tyrolean Grey cattle lacked this predominant haplotype but carried the coding duplication p.Gly220_Arg223dup, together with differentiation near the ASIP regulatory region. Thus, different candidate coding changes affect the same MC1R residue in different cattle lineages. Haplotype comparisons supported independent Podolian and Alpine origins for p.Arg223Trp and p.Gly220_Arg223dup insertion, respectively. Ancient-genome screening yielded no validated evidence of either variant except p.Arg223Trp in medieval cattle. Comparisons across 1,108 mammalian taxa identified independent recurrence of p.Arg223Trp in the white-coated mountain goat, Oreamnos americanus, where the derived allele was fixed in surveyed individuals (JTT-based neutral probability = 0.0043). Our findings support a model in which grey coat colour in cattle evolved through at least two partially distinct molecular routes within interacting pigmentation pathways. More broadly, they identify MC1R residue 223 as a candidate recurrent target of coat-colour lightening and illustrate how domesticated and wild lineages can repeatedly target constrained functional positions during phenotypic evolution.