Fig 1.
Manhattan plots of association with roaning and ticking.
A) Roaning. B) Ticking. Red and blue horizontal lines are significant (P < 5 x 10−8) and suggestive (P < 1 x 10−5) associations, respectively.
Fig 2.
Normalized read depth in 5-kb sliding windows across the significant GWAS locus on CFA38 for Australian Cattle Dogs (red), German Wirehaired Pointer (pink), and Border Collies (grey).
Filled circles show the corresponding markers of the Manhattan plot shown in Fig 1A (red circle: Most significant marker).
Fig 3.
Haplotypes near the marker on CFA38 significantly associated with roaning.
Border Collies (grey), breeds with high frequency of ticking (green), breeds with high frequency of roaning (orange), and Dalmatians (red). Rows correspond to haplotypes (two rows/individual), and columns correspond to markers. The positions of the first and last markers are 11,031,835 and 11,243,237, respectively. +/-: presence and absence of the 11-kb duplication based on Manta. Red box: 11-kb duplication (CFA38:11,131,835–11,143,234). Yellow box: a core haplotype (CFA38:11,122,646–11,167,876). Red triangle: the most significant marker associated with roaning. Green triangle: markers used for defining the duplication-associated haplotypes. Photos of representative breeds are shown (from top to bottom: Border Collie, Münsterländer, German Wirehaired Pointer, and Dalmatian). Photo credit: Alison Rule, Brett Ford, Dominic Ebacher, Hanna N.
Fig 4.
PCR genotyping of the tandem duplication on CFA38 associated with roaning.
A) Schematic view of the design of the PCR genotyping assay. Yellow boxes indicate the duplicated region. Single-headed arrows indicate pairs of primers to amplify three regions. The first (black) and the third (yellow) primer pairs should produce amplicons in all dogs regardless of the presence or absence of the duplication, while the second pair in the middle should produce an amplicon only in dogs carrying the duplication. Representative coat patterns of non-roaned (top) and roaned dogs (bottom) are shown (left: non-herding group, right: herding group) B) PCR genotyping of a roaned and control dogs. Each gel lane corresponds to PCR primer pairs depicted in panel A. Photo credit: Kellina H., Fernanda Lesnau, Lisa Hayden, and L. Bray.
Fig 5.
Density distribution of the array signal intensity (ΔLRR) for the discovery panel dogs with zero, one, or two copies of the duplication-associated haplotypes (no haplotype, heterozygote, and homozygote, respectively).
Vertical ticks indicate individual ΔLRR of dogs with roaning (orange) and without roaning (grey).
Fig 6.
Signature of selection in the region on CFA38 associated with roaning.
A) Nucleotide diversity (π) for Wirehaired Pointing Griffon (orange), Border Collies (grey), and Labrador Retriever (black) in 500-kb sliding windows. B) Pairwise genetic difference (FST) for Wirehaired Pointing Griffon (orange) and Labrador Retriever (black). Border Collies were used as a reference. C) ROH in Australian Cattle Dog (orange), Dalmatians (red), and Border Collies (grey). D) XP-EHH in Australian Cattle Dog (orange), Dalmatians (red), and Labrador Retrievers (black). Border Collies were used as a reference. Wirehaired Pointing Griffons and Australian Cattle Dogs are breeds where roaning is common. Blue rectangle: position of the 11-kb duplication. π and FST are estimated by using whole-genome re-sequencing data, while ROH and XP-EHH were estimated by using Embark genotyping data.