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Table 1 Description of (type 1) loci with a large effects on breed-defining traits, such as coat colour, in in domestic cattle and likely to be segregating in our populations

From: Selection for complex traits leaves little or no classic signatures of selection

Locus Location Description
POLLED BTA11.71 Mbp Determines the presence and absence of horns. Two identified alleles: P C (Celtic-origin) a 212 bp insertion-deletion at 1.706 Mbp; and P F (Holstein Friesian-origin) which segregates as a 260 kb haplotype (from 1.649 – 1.989 Mbp) in Holstein and Jersey [18, 19]. No known associated gene. Most domestic cattle are horned but Angus and Murray Grey breeds are exclusively polled and the POLLED locus segregates in other breeds.
MC1-R BTA18 14.75 Mbp The main determinant of coat colour in cattle [20]. Two identified alleles: ED (p.L99P) which produces a black coat; and e (inducing a premature stop codon) which is recessive produces a red coat when homozygous [21].
PMEL BTA5 57.67 Mbp Coat colour dilution mutation (c.64G > A) identified in Charolais [22]. Different PMEL mutations segregate in Highland and Charolais cattle [23].
KIT BTA6 71.85 Mbp Locus associated with piebald colour in Hereford [24] and degree of white-spotting in Holstein [25]. No known causative mutations but the different coat colour patterns in these breeds, suggests different KIT mutations.
KITLG BTA5 18.34 Mbp A SNP mutation (p.A193D) identified in Shorthorn and Belgian Blue as causative for the roan phenotype [26]. KITLG is also associated with pigmentation surrounding the eyes in Fleckvieh cattle [27].