Two novel SNP variants at ASIP and SNAI2 genes are associated with yellow coat color in rabbits

Rabbits display a wide range of coat colors, with yellow being a particular phenotype that aids in exploring the molecular mechanisms of coat pigmentation. The Fujian yellow (FJY) rabbit, as China's only indigenous breed with a yellow coat, serves as a valuable genetic resource. Fujian yellow rabbits have predominantly yellow fur, with a diluted white hue on the distal limbs and tail. However, the genetic mechanism underlying yellow coat color remains unclear. To address this, we conducted selection signature analysis to identify candidate genes and potential casual mutations underlying the yellow phenotype in rabbits. Utilizing whole-genome resequencing, a total of 22 486 177 high-quality SNPs were identified from 30 individuals belonging to three Chinese indigenous rabbit breeds featured with yellow or non-yellow phenotype. The results revealed that the ASIP gene on chromosome 4 and the SNAI2 gene on chromosome 3 were under strong selection pressure, both of which play pivotal roles in determining coat color phenotypes. The ASIP gene is involved in melanogenesis across various livestock species, while the SNAI2 gene is linked to hypopigmentation in the distal regions such as the limbs and tail. We further identified two SNP variants, g.23870943C>T in the fourth intron of the ASIP gene, which is closely associated with the yellow phenotype, and g.73725380A>G downstream of the SNAI2 gene, probably contributing to the white shading in Fujian yellow rabbits’ limb and tail regions. These variants are key determinants in the development of the yellow coat color in rabbits. These findings advance the understanding of coat color pigmentation in domestic animals.