Table 1.
Breeds collected for pool sequencing (pool-seq).
Fig 1.
Manhattan plots showing −ZHp values from 20 diverse goat breeds.
The red horizontal line indicates the chosen significance threshold of −ZHp = 4. Each dot represents a 150 kb window. Each plot contains 29 autosomes and two unplaced scaffolds representing the X chromosome. Selection signatures co-localizing with known coat color genes are marked with arrows.
Fig 2.
The coverage plot of bezoars (BEZ) does not show any copy number variation and represents the wildtype allele. In the Pak Angora breed (ANG), the coverage plot shows a triplication of ~100 kb downstream of the KIT gene. In the Barbari breed (BAR), the same region is duplicated. The Barbari allele shows a complex rearrangement involving the insertion of a ~23 kb genome segment originating at 89.2 Mb into the duplicated sequence at ~70.9 Mb with the simultaneous deletion of ~16 kb of KIT sequence. Please note that the coverage at ~89.2 Mb corresponds to three times the average. One genome equivalent corresponds to the wildtype sequence at ~89.2 Mb. Read-pair information indicated that the other two genome equivalents are inserted into the duplicated sequence at ~70.9 Mb (S4 Fig). The dashed red line indicates the average coverage across the whole genome of each pool-seq dataset.
Fig 3.
A Coverage plots of the ASIP locus in different goat breeds reveal four different CNVs. The bezoar (BEZ) coverage plot shows uniform coverage and is characteristic for the wildtype allele (Abz). Underneath, four different mutant ASIP alleles associated with different CNVs are illustrated. The line on top of each plot schematically indicates the most likely configuration of these mutant alleles derived from the available short-read sequence information (S4 Fig). The dashed red line indicates the average coverage across the whole genome of each breed. B Schematic drawings and C representative photographs illustrating the coat color phenotypes of the studied breeds. The photo of the bezoar was obtained during summer, when the dark stripes at the collar and the belly are much less pronounced than in the winter coat. Note that some of the patterns show an exactly inverse distribution of eumelanin and pheomelanin. For example, goats with the Asm allele have white (pheomelanistic) facial stripes and legs, while goats with the Ab or Apc alleles have black (eumelanistic) facial stripes and legs.
Fig 4.
ASIP mRNA expression and identified transcripts in skin.
A Representative photographs of the five sampled goat breeds. The biopsy sites are numbered and indicated by red circles. B Trimmed mean of M (TMM) values of ASIP mRNA expression were determined from RNA-seq data for each sample. The colors of the bars correspond to the pigmentation of the skin samples. Please note that the Valais Blackneck goat (VAG) has a black base color that is independent of the ASIP gene. This goat has a white spotting phenotype and lacks melanocytes in its caudal half. The low ASIP expression in the unpigmented white skin sample of this goat underscores the difference to the pheomelanistic pale white pigmentation in other goats. C ASIP transcript isoforms in pheomelanistic skin samples from goats with different ASIP alleles. Transcript isoforms X1 and X2 correspond to the RefSeq accessions XM_018057735.1 and XM_018057736.1. CNV breakpoints of the Ab, AWt, and Apc alleles are indicated.