Whole-genome resequencing identifies candidate genes and SNPs in genomic regions associated with shell color selection in the Pacific oyster, Crassostrea gigas

The various shell colors of bivalves not only result in a better visual perception but also show great commercial value as a highly potential breeding trait. Four shell color strains of Pacific oyster (Crassostrea gigas) characterized by black (SB), white (SW), gold (SG), and orange (SO) were bred purposefully for more than ten generations. In this study, whole-genome resequencing was performed on 20 oysters from each of the four strains, and a total of 14.67 million single nucleotide polymorphisms (SNPs) were obtained after stringent filtering, with an average sequencing depth of >10×. The population structure analysis provided support for the subdivision of all samples into four major genetic clusters corresponding to shell color phenotypes, indicating a high level of genomic differentiation driven by artificial selection. Then, a composite measure of fixation index (FST) and cross-population composite likelihood ratio (XP-CLR) allowed us to identify 336 to 414 candidate divergent regions (CDRs) in pairwise comparisons of different shell colors, with a total of 480 to 614 corresponding genes distributed. Of particular interest were tyrosinase (TYR) and perilipin2 (PLIN2) occurring with extremely high frequency, which participates in shell color determination by regulating melanin production and carotenoid metabolism, respectively. In addition, two genes, namely porphobilinogen deaminase (PBGD) and hephaestin (HEPH), may have a potential function in the accumulation of specific porphyrin in orange shells, while the kynurenine 3-monooxygenase (KMO) gene, known to be involved in ommochrome biosynthesis, may contribute to the darker coloration in black shells. Further, a total of 304 SNPs were extracted from the exons of candidate genes mentioned above, of which 25 loci had highly significant differences among populations (p-value ≤0.01). After Sanger sequencing in another population, 14 SNPs were successfully validated as specific loci closely linked to different shell colors of black, white, gold, and orange, respectively. All in all, the results of this study shed light on the molecular basis of pigmentation and facilitate the selective breeding of C. gigas with desired phenotypic color.