Novel SNP isolation: Two novel SNP markers (named A316C and A376C) were screened from shell matrix genes in pearl oysters.

Association analysis: A total of 160 individuals were genotyped by Tm-shift method and used to investigate correlations between SNP markers and economic traits. A376C locus was associated with four commercial traits (P < 0.05).

Preferred genotype: For A376C locus, the AC-type individuals showed the highest trait values in the three genotypes, AC allele could be the preferred genotype in the selective breeding of a host oyster to produce high-quality pearls in Pinctada fucata martensii.