Characterization of novel EST-SSR markers and their correlations with growth and nacreous secretion traits in the pearl oyster Pinctada martensii (Dunker)

The pearl oyster Pinctada martensii Dunker is the primary cultured species of marine pearls in southern China. To facilitate marker-assisted selection in genetic improvement of this species, twenty-nine novel polymorphic microsatellite markers were developed from twenty thousand expressed sequence tags (ESTs) of mantle and pearl sac of P. martensii, and were characterized in a wild Nanshan population and in a mapping CI5 family. We further analyzed the correlations between these makers and growth and nacreous secretion traits in the CI5 family and in a hatchery population. These 29 markers showed polymorphism in the wild population, with the number of alleles ranged from four to eighteen (mean 7.5 ± 3.3) per locus. Observed and expected heterozygosities ranged from 0.30 to 0.93 (mean 0.50 ± 0.24) and from 0.10 to 0.95 (mean 0.71 ± 0.14), respectively. Ten loci (34.5%) deviated significantly (P < 0.05 after Bonferroni correction) from Hardy-Weinberg equilibrium, of which nine loci showed heterozygote deficiency. Seventeen of these 29 validated microsatellites segregated in the CI5 family, with eight (47%) deviating significantly (P < 0.05) from Mendelian ratios and six (35%) remaining significant after Bonferroni correction. Null alleles were observed at four loci. A GLM procedure of SPSS software was used to analyze the correlations between those 17 microsatellite loci and means of shell measurements. The results show that two loci (PmartE05 and PmartE35) were significantly (P < 0.05) correlated with shell height and weight, and one locus PmartE64 was significantly (P < 0.05) correlated with shell nacre thickness in the CI5 family. Locus PmartE05 was also significantly correlated with shell height in the hatchery population. Therefore, these EST-SSRs markers developed here are useful for pedigree management and assistant selection in genetic breeding in this species.