Genome-wide association study and gene editing reveals the causal gene responsible for abnormal red skin color in Yellow River carp

Skin color is an important trait for aquaculture species, serving as an important visual quality criterion determining the market value. Individuals with abnormal red skin color were found in the aquaculture population of Yellow River carp, which is a remarkable strain of common carp in China. To investigate the genetic basis underlying the abnormal skin color and identify the causal gene(s), genome-wide association analysis was conducted by utilizing a previously designed common carp 250 K SNP array for genotyping. A total of 18 significant SNPs were identified, all of which were located on Chr.11. Combined with Fst scanning, a significantly associated genomic region was identified, spanning approximate 5.3 Mb, from 5,708,740 bp to 11,047,520 bp. Five pigmentation-related candidate genes were found, including mitf, oca2, ap1m1, apoeb and lrp8. Quantitative analysis of gene expression of the five genes showed that oca2 was the only gene significantly down-regulated in the skin of red Yellow River carp comparing to that of wildtype individuals. Further disruption of oca2 by CRISPR/Cas9 gene editing system generated abnormal red individuals, and the DNA sequencing exhibited perturbation of peaks in the sgRNA targeted region, confirming the key function of oca2 gene in coloration of Yellow River carp. Our study revealed that oca2 gene was the causal gene responsible for the abnormal red skin color of Yellow River carp. Our findings would not only unravel the genetic basis of abnormal skin color in common carp, but also advance our knowledge of skin color genetics in teleost, and would speed up the molecular selection of fish species with consumer's favorite skin color.