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A 14-bp motif in the KIT active promoter region is critical for melanin accumulation in yaks, mice, and humans

Liu Xinfeng,Wang Tongcheng,Zheng Zeyu,Dong Congcong,Liu Wenyu,Niu Zhimin,Yang Yingbo,Wu Xiaoyun,Qiu Qiang,Yang Yongzhi,Li Kexin,Lenstra Johannes A.,Yan Ping,Kang Minghui,Li Bowen,Fang Lingzhao,Liu Jianquan

Background Animal pigmentation serves as an excellent model for studying genetics, development, and evolution. Among yak breeds, the all-white yak breed ( Bos grunniens ) is the only indigenous variety with pristine white fur, in stark contrast to the black coat color of the wild yak and most domesticated yaks. Results Using whole-genome sequencing data from 387 yaks, we analyzed the population genetic structure of all-white yaks and discovered that they clustered into two distinct genetic groups. Further, by conducting a genome-wide association study (GWAS) based on whole-genome variants (SNPs and indels) between all-white and wild-type yaks, we identified a 14-bp deletion in the promoter of KIT , which decreased its expression in all-white yaks. The following knock-in experiments in mouse confirmed that the absence of the yak 14-bp motif decreases the expression of KIT . Deletion of a human orthologue of the yak 14-bp motif by using the CRISPR/Cas9 system reduces the melanin accumulation in human melanoma cells. Conclusions Overall, our study revealed the genetic basis of all-white yaks and underscored the importance of studying livestock phenotypes to uncover conserved genetic regulators in mammals.