A genome-wide association study identifies SNPs and candidate genes associated with nacre color of pearl oyster Pinctada fucata martensii

Molluscan shell color polymorphism as a major economic factor in aquaculture has been of increasing interest to scientists. In pearl oyster, the trait of shell nacre color is abundant and play a major role in color during the pearl production process. To understand the genetic effect and potential underlying genes of nacre color trait, a genome-wide association study (GWAS) was performed in 830 individuals based our previous resequencing data. After GWAS, a total of 464 significantly associated SNP loci were identified and were mapped primarily onto chromosomes 14. In the 100-kb regions of the peak SNPs, some candidate genes may involve in the formation of shell golden nacre color were annotation, including LDR2, RDH12, BCOL, FN3–2 and CHI3L1, which have been reported to be involved in coloration. In addition, 11 haplotypes related nacre color were constructed. Successfully, one haplotype was verified in another population. In the block 6 of quantitative trait, the b* value (yellowness) of the haplotype ACA was significantly higher than that of the haplotype TGG in the validation population 1. The results should contribute to understanding of the molecular mechanisms of nacre coloration and useful for SNP-based genomic selection breeding in pearl oyster culture.