A Loss-of-Function Mutation in bco1l Underlies Yellow Coloration in Large Yellow Croaker (Larimichthys crocea)

Carotenoid-based coloration significantly influences the ornamental appeal and market value of aquatic species. This study identifies the genetic basis of yellow body coloration in the large yellow croaker (<i>Larimichthys crocea</i>), a commercially important aquaculture species in China. Through a genome-wide association study (GWAS), we identified a 10 bp deletion (<i>bco1l-Δ10</i>) in the <i>bco1l</i> gene, a critical enzyme in carotenoid metabolism. This deletion, located in exon 10, causes a frameshift mutation and premature stop codon, resulting in loss of the enzymatic function essential for carotenoid cleavage. Sanger sequencing confirmed that all yellow juveniles were homozygous for the deletion, while none of the wild-type juveniles harbored this mutation. Functional assays demonstrated that the recombinant Bco1l-Δ10 protein failed to catalyze β-carotene cleavage, validating the genetic association with the yellow phenotype. The <i>bco1l-Δ10</i> mutation was detected only in a limited number of juvenile individuals, indicating it is a rare occurrence in the population. Our findings provide a valuable genetic marker for marker-assisted selection (MAS) to enhance yellow pigmentation in aquaculture breeding programs, offering a potential strategy to improve the market value of <i>L. crocea</i>.