Topology of a trait-associated bubble upstream of the KIT gene. (A) Bandage plots showing the paths traversed for the three observed alleles (two for white-headed breeds and one for color-headed) through the pangenome. Unless stated otherwise, n = 1 for the breed. The gray arrow paths indicate the segmental duplication regions, whereas the green and red arrow paths, respectively, indicate the sequence preceding and following the segmental duplication. (B) Repeat structure within the candidate SV region, for five classes of genomic elements. The start and end sequences are taken from A, whereas the full copy refers to the 14.3 kb segmental duplication copy found in all three Simmental assemblies. The arrow direction denotes the strand of the repeat element (+/forward and −/reverse).
