Screening And Breeding Application Of Golden Coat Color Gene In Yushu Yak

Yushu yaks are a distinctive local breed of yak in China,which also includes the relatively rare golden yaks.For a long time,Yushu golden yaks have received widespread attention.Their unique golden coat colour can not only be used to develop Yushu golden yak products with ethnic characteristics but also help promote the development of the local tertiary industry.Therefore,identifying the molecular markers for the golden coat colour of Yushu yaks is crucial for breeding new strains of Yushu golden yaks.In this study,41samples of ushu golden yaks were collected,22 of which were subjected to whole-genome resequencing and the remaining 19 were used to verify the candidate genes for the golden coat colour.Combined with the published data of 80 whole-genome resequenced samples（6wild yaks,37 black yaks and 37 Tianzhu white yaks）,a joint analysis was performed on the whole-genome resequencing data of 102 yaks with black,white and golden coat colours.At the same time,skin tissue samples from 4 Yushu golden yaks were collected for transcriptome sequencing.By analyzing the genetic diversity,population genetic structure and selection analysis of the autosomal genome and performing genome-wide association analysis,combined with transcriptome analysis,molecular markers for the golden coat colour trait of Yushu yaks were screened out.The main research results are as follows:1.Yushu golden yaks have rich genetic diversity and few continuous homozygous fragments with short lengths.The genetic diversity of other yak breeds from high to low is:wild yak>Yushu golden yak>black yak>white yak.2.Population structure analysis found that there is wild yak ancestry in Yushu golden yaks.Among the three domesticated yak populations,black yaks and Yushu golden yaks are closely related,while Tianzhu white yaks have a more distant relationship with Yushu golden yaks due to strong artificial selection.3.Using three selection analysis methods(F_ST,π-ratio and XP-EHH)and genome-wide association analysis methods,it was jointly identified that the MC1R gene was strongly selected in Yushu golden yaks and is the main candidate gene for the golden coat colour trait.The nonsense mutation site on the MC1R gene（CM016709.1:g.34139085 C>T,p.Gln34*）has a mutation frequency of over 95%in the Yushu golden yak population;in addition,this nonsense mutation is strongly linked with 24 other SNP sites and their combined haplotype is significantly associated with the golden coat colour of Yushu yaks（P<0.01）.4.Transcriptome analysis of skin tissue from Yushu golden yaks and black yaks identified 1,164 differentially expressed genes,of which 853 were upregulated in skin tissue from Yushu golden yaks and 311 were downregulated.The expression level of the MC1R gene in Yushu golden yaks was significantly lower than that in black yaks.This study discovered that the nonsense mutation of the MC1R gene（CM016709.1:g.34139085 C>T）is the causative mutation for the golden hair colour of Yushu yak.This can be used for the breeding of new strains of Yushu golden yak,providing a scientific basis for the rapid expansion of golden hair colour genetic resources.This has significant theoretical and practical significance.