Genomic amplification of the caprine EDNRA locus might lead to a dose dependent loss of pigmentation

Abstract

The South African Boer goat displays a characteristic white spotting phenotype, in which the pigment is limited to the head. Exploiting the existing phenotype variation within the breed, we mapped the locus causing this white spotting phenotype to chromosome 17 by genome wide association. Subsequent whole genome sequencing identified a 1 Mb copy number variant (CNV) harboring 5 genes including EDNRA. The analysis of 358 Boer goats revealed 3 alleles with one, two, and three copies of this CNV. The copy number is correlated with the degree of white spotting in goats. We propose a hypothesis that ectopic overexpression of a mutant EDNRA scavenges EDN3 required for EDNRB signaling and normal melanocyte development and thus likely lead to an absence of melanocytes in the non-pigmented body areas of Boer goats. Our findings demonstrate the value of domestic animals as reservoir of unique mutants and for identifying a precisely defined functional CNV.

A combined genome-wide approach identifies a new potential candidate marker associated with the coat color sidedness in cattle

“…Similar results have been also reported by Menzi et al (2016) and by Kumar et al (2018), which in studies for coat color in goat, clearly demonstrated that a single SNP controls the phenotype. Matukumalli et al (2009) exploited the black/red coat color phenotype to demonstrate the utility of the Illumina BovineSNP50 assay for genome-wide association studies in cattle by localizing known variation for the phenotype.…”

Population structure, genetic diversity and selection signatures within seven indigenous Pakistani goat populations

“…The windows contained a newly identified coat colour‐related gene ( EDNRA , chromosome 17, 10.10–10.71 Mb) (Menzi et al . ), which was also significant in KAMO and PATE (Fig. c,d, Table ).…”

“…A similar pattern was found in Boer goats, as described in a recent publication (Menzi et al . ). Therefore, we performed an allele genome‐wide association study (GWAS) for a case–control group pair (KAMO vs.…”

“…), endothelin receptor A ( EDNRA ) (Menzi et al . ) and tyrosinase‐related protein 1 ( TRYP1 ) (Becker et al . ).…”

A structural variant in the 5’-flanking region of the TWIST2 gene affects melanocyte development in belted cattle

“…Modern domestic animals thus constitute a unique reservoir of spontaneous pigmentation mutants. Their favorable population structure facilitates the discovery of functional genetic variation including some interesting non-coding structural variants with regulatory effects [10][11][12][13][14][15].…”