Although tagging of individuals with physical tags is difficult in most fish species due to their mass spawning and tiny larvae, the introduce of molecular tools makes it feasible for fish pedigree traceability. Since mixed breeding system is often adopted in aquaculture breeding programs, accurate pedigree information is the basis of sustainable genetic selection and hatchery management. The development of molecular markers and sequencing technologies over the past decades has brought great innovations for aquaculture. This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean H o = 0.821, mean PIC = 0.651). CERVUS, PAPA and COLONY were used for mutually verification. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper ( Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Pedigree information is necessary for the maintenance of diversity for wild and captive populations.
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