A microsatellite marker tool for parentage assessment in gilthead seabream (Sparus aurata)

Eleven microsatellite loci previously described in Sparid species were evaluated for their suitability in paternity assignment of gilthead seabream (Sparus aurata). Nine hundred and ninety six offspring obtained by natural spawning from 159 potential breeders maintained in 8 different tanks were genotyped for this set of 11 loci. Given their high potential for parentage exclusion (Excl1 = 0.9999; Excl2 = 1) all offspring could be traced back to a single couple of parents. The families identified were used to analyze the performances of these loci for parentage analysis. Null alleles were the main source of false exclusions (70.1% of single mismatches) and were detected in five loci at frequencies between 4.9 × 10− 3 and 0.084. The average mutation rate estimated over 21,912 gametes was 1.8 × 10− 4 in the range reported within fish. All the loci analyzed conformed to Mendelian segregation. However, significant genotypic linkage disequilibrium was detected between SaGT1 and SaGT32, SaGT41a and SaGT41b, SaGT31 and PbMS6, and PbMS1 and PbMS16. A subset of five highly polymorphic and easily genotyped microsatellite loci, SaGT1, SaGT26, SaGT41a, PbMS2 and PbMS16, were selected for parentage assessment in S. aurata. In spite of their high combined exclusion potential (> 0.997), the actual exclusion power was 0.933, mostly due to the high relatedness between some parents in the broodstock. Exclusion and maximum likelihood-based strategies were compared for paternity inference using the data obtained. The former approach performed better in the context of this study, where a set of highly polymorphic microsatellites with the lowest genotyping error were selected.