Association between novel EST-SNPs and commercial traits in Pinctada fucata martensii

• 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.

To facilitate marker-assisted selection for genetic improvement of the pearl oyster Pinctada fucata martensii, two novel single nucleotide polymorphism (SNP) markers (A376C and A316C) were screened from two shell matrix genes (prismalin-14 and N19 gene), and genotyped to investigate their correlations to five commercial traits, including shell width (SW), shell length (SL), shell height (SH), hinge length (HL) and total weight (TW) in 160 pearl oysters. Both of the two loci showed AC heterozygous. The highest trait values of the five commercial traits measured were the CC genotype in the A316C SNP locus and the AC genotype in the A376C SNP locus, respectively. Significant differences in the trait values were detected between AA- and AC-type individuals (P = 0.005 for SW, P = 0.037 for SH, P = 0.031 for HL and P = 0.007 for TW), but not for SL (P = 0.057) in the A376C locus. These results indicated that AC-type at locus A376C from prismalin-14 gene could be used as a preferred genotype for future selection in breeding program of pearl oyster.