Extraction Of Key Genes Associated With The Black-headed Trait In Sheep Through Selected Signals And GWAS Analysis

Sheep is one of the earliest domesticated animals in the world,playing a crucial role in the development of global agricultural economy,and also serving as a significant source of meat,wool,and dairy products.The wide variety of sheep breeds has provided a resource foundation for the study of mammalian coat color,and the coat color diversity of sheep is an excellent model studying the genetic mechanism of mammalian coat color,and it is also one of the most obvious phenotypic traits.The intuitiveness and descriptiveness of coat color can be used as an important marker to distinguish breeds.The black-headed phenotype is a unique coat color of sheep,such as the Bayinbuluke sheep from Asia and the black-headed Dorper sheep from Africa,in which the pigmentation extends from the face to the neck.At present,there is currently limited research on how the black-headed phenotype in sheep is formed.In this study,the genome sequences of Bayinbuluke sheep（black-headed）and Small Tail Han sheep（all-white）,as well as black-headed Dorper sheep and white-headed Dorper sheep,were compared to explore the genes and causative mutations that influence the sheep black-headed phenotype,including genomic genetic diversity,population genetic structure,selective signal detection and genome-wide association studies.Additionally,the whole genome sequence data from460 sheep with different coat colors all over the world were integrated to investigate the relationship between haplotypes associated with the black-headed phenotypic trait and pigment deposition changes.The results are as follows:1.Analysis of genomic genetic diversity and population genetic structureThrough the study of single nucleotide genomic variation and genetic diversity,it was found that wild Moufion sheep exhibits the highest number of SNP variations,nucleotide diversity,and the fastest Linkage Disequilibrium（LD）decay rate,demonstrating that Moufion sheep possess greater genome diversity;And Principal Component Analysis（PCA）,Neighbor-Joining（NJ）tree and ancestral component analysis showed that wild Moufion sheep and domestic sheep were separated significantly,and the genomes of black-headed Dorper and white-headed Dorper had higher homology.2.Detection of genome-wide selection signals for the black-headed trait in sheepThrough the utilization of F_ST,π ratio and haplotype analysis,the MC1R gene located on chromosome 14 was found to have a significant association with the black-headed phenotype in Bayinbuluke sheep and black-headed Dorper sheep.Within this genomic region,two missense mutations have been detected,specifically referred to as g.14251947T>A（p.M73K）and g.14252090G>A（p.D121N）.Notably,the derived allele A was not present in Moufion sheep,Bighorn sheep and Argali sheep,indicating that the mutations occurred after domestication.Furthermore,the convergent evolution in the MC1R gene region may be responsible for this unique black-headed phenotype,and different pigmentation is also controlled by other loci.3.Genome-wide association analysis of the black-headed trait in sheepThrough combining selective signal detection with genome-wide association studies,it was found that two missense mutations,g.14251947T>A（p.M73K）and g.14252090G>A（p.D121N）,in MC1R gene were the potential causative mutations affecting the black-headed phenotype in Bayinbuluke sheep and black-headed Dorper sheep.Additionally,the TCF25 gene was identified as a potential contributor to the development of the black-headed phenotype in sheep.In conclusion,the study utilized selection signal detection and genome-wide association analysis to investigate the black-headed phenotype in sheep.The findings identified that two missense mutations,g.14251947T>A（p.M73K）and g.14252090G>A（p.D121N）,in the MC1R gene as the potential causative mutations for the black-headed phenotype in Bayinbuluke sheep and black-headed Dorper sheep,and the TCF25 gene was also identified as a candidate gene associated with the black-headed phenotype in sheep.The findings of this study advance our comprehension of the relationship between various pigmentation patterns in sheep and the MC1R gene.Moreover,it provides novel insights into the genetic mechanisms underlying coat color in sheep,making it an invaluable resource for investigating the genetic foundations of coat color diversity and convergent evolution in mammals.