Location: Cool and Cold Water Aquaculture ResearchTitle: Development and validation of a SNP panel for parentage assignment in rainbow trout
Submitted to: Aquaculture
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/1/2015
Publication Date: 11/10/2015
Citation: Liu, S., Palti, Y., Gao, G., Rexroad III, C.E. 2015. Development and validation of a SNP panel for parentage assignment in rainbow trout. Aquaculture. 452:178–182. doi: 10.1016/j.aquaculture.2015.11.001.
Interpretive Summary: Pedigree information is essential for breeding to improve production efficiency of rainbow trout. Use of physical tags for pedigree tracking can be expensive and cannot be used with small fish. Fortunately, molecular markers offer an alternative approach to track pedigrees. In this study, we developed a molecular marker panel that can be used to accurately assign offspring to their parents. The results were validated with fish with known pedigrees. Thus, the marker panel is robust and is a useful tool for rainbow trout breeding.
Technical Abstract: In salmonids aquaculture, family-based selective breeding programs rely on accurate pedigree information for estimating genetic merits. The pedigree information can be tracked through the use of Passive Integrated Transponder (PIT) tags. However, PIT tags can be expensive, and cannot be used with small fish. DNA markers offer an alternative approach for pedigree tracking and microsatellites have been previously used for parentage assignments in rainbow trout. Recently, single nucleotide polymorphism (SNP) have become the markers of choice as they are highly abundant and are amenable for high throughput genotyping. The objectives of this study were to develop a SNP panel for parentage assignment in rainbow trout and to evaluate the accuracy of parentage assignment using fish with known pedigrees. Two groups of SNPs were targeted: 1) genome SNPs distributed across all 29 chromosomes; and 2) previously identified trait-associated SNPs. Among the 128 SNPs selected for assay development, 102 (79.7%) working assays were developed. A panel of 95 SNP assays including 68 genome SNPs and 27 trait-associated SNPs was used to genotype 499 fish with known pedigrees from Troutlodge Inc. and from the USDA/ARS National Center for Cool and Cold Water Aquaculture. Parentage assignments matched perfectly with the known pedigrees when all 95 SNPs were used. Near perfect parentage assignment was obtained with the 68 genome SNPs, and the accuracy of parentage assignment was over 98% with a subset of 48 genome SNPs. Therefore, these SNP assays are robust and enable accurate parentage analysis in populations that are typically used in rainbow trout breeding programs.