Abstract
Coat colour is one of the most important economic traits of sheep and is mainly used for breed identification and characterization. This trait is determined by the biochemical function, availability and distribution of phaeomelanin and eumelanin pigments. In our study, we conducted a genome-wide association study to identify candidate genes and genetic variants associated with coat colour in 75 Chinese Tan sheep using the ovine 600K SNP BeadChip. Accordingly, we identified two significant SNPs (rs409651063 at 14.232 Mb and rs408511664 at 14.228 Mb) associated with coat colour in the MC1R gene on chromosome 14 with −log10(P) = 2.47E-14 and 1.00E-13, respectively. The consequence of rs409651063 was a missense variant (g.14231948 G>A) that caused an amino acid change (Asp105Asn); however, the second SNP (rs408511664) was a synonymous substitution and is an upstream variant (g.14228343G>A). Moreover, our PCR analysis revealed that the genotype of white sheep was exclusively homozygous (GG), whereas the genotypes of black-head sheep were mainly heterozygous (GA). Interestingly, allele-specific expression analysis (using the missense variant for the skin cDNA samples from black-head sheep) revealed that only the G allele was expressed in the skin covered with white hair, while both the G and A alleles were expressed in the skin covered with black hair. This finding indicated that the missense mutation that we identified is probably responsible for white coat colour in Tan sheep. Furthermore, qPCR analysis of MC1R mRNA level in the skin samples was significantly higher in black-head than white sheep and very significantly higher in GA than GG individuals. Taken together, these results help to elucidate the genetic mechanism underlying coat colour variation in Chinese indigenous sheep.
Highlights
Animal coat colour is one of the most important economic traits, for animal breeds that are kept for skin and wool production
In addition to melanocortin 1 receptor (MC1R) and agouti signalling protein (ASIP), there are other genes involved in coat colour variation such as melanocyte inducing transcription factor (MITF), tyrosinase related protein-1 (TYRP1) and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homologue (KIT) [6, 11,12,13,14,15]
GWAS: after quality control was performed using missing genotype data (0.1), Hardy-Weinberg equilibrium (1e-5) and minor allele frequency (0.05), a total of 366,991 single nucleotide polymorphism (SNP) remained for the genome-wide association study
Summary
Animal coat colour is one of the most important economic traits, for animal breeds that are kept for skin and wool production. Animal coat colour variation is mainly regulated by genetic and environmental factors [6]. Coat colour variation is determined by the biochemical function, distribution and availability of phaeomelanin and eumelanin pigments [8]. The relative amount of eumelanin and phaeomelanin colours in melanocytes is regulated by the interactions of agouti signalling protein (ASIP) and melanocortin 1 receptor (MC1R) genes [9, 10]. In addition to MC1R and ASIP, there are other genes involved in coat colour variation such as melanocyte inducing transcription factor (MITF), tyrosinase related protein-1 (TYRP1) and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homologue (KIT) [6, 11,12,13,14,15]
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