Background Selective breeding programs must maintain pedigree information to help increase production efficiency. • Estimate genetic parameters and breeding values • Minimize inbreeding Single-nucleotide polymorphism (SNP) assays: • High-throughput • Easy to standardize • Low error rates • Proven in terrestrial animals for parentage assignment • 60–100 SNPs adequate for accurate large-scale parentage assignment
Methods Lab: Fin clip samples • Offspring previously genotyped on 57K array • DNA concentration >30 ng/µL SNP Type assays • SNPs across 29 chromosomes, MAF >0.45 • Included additional trait-associated SNPs (stress, growth, disease resistance) • 128 SNP assays designed, 95 selected for panel Default SNP Type™ assay protocol in 96.96 GT IFC with specific target amplification (STA)
Offspring to parent matching: • All 95 SNPs = 100% accuracy • 48 SNPs = 98% accuracy • 36 SNPs = 92% accuracy • Accuracy consistent with prior research Conclusions • SNP assays compatible for parentage assessment, low-cost, high-throughput, flexible assay choice to include trait-associated SNPs for rainbow trout populations studied
Results and conclusions