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Title: The development and characterization of a 57K SNP array for rainbow trout

item Palti, Yniv
item Gao, Guangtu
item MOEN, THOMAS - Aquagen
item Liu, Sixin
item KENT, MATTHEW - Centre For Integrative Genetics (CIGENE)
item SIGBJORN, LIEN - Centre For Integrative Genetics (CIGENE)
item MILLER, MICHAEL - University Of California
item Rexroad, Caird

Submitted to: Molecular Ecology Resources
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/26/2014
Publication Date: 5/1/2015
Citation: Palti, Y., Gao, G., Moen, T., Liu, S., Kent, M., Sigbjorn, L., Miller, M., Rexroad III, C.E. 2015. The development and characterization of a 57K SNP array for rainbow trout. Molecular Ecology Resources. 15:662-672.

Interpretive Summary: Rainbow trout is one of the most important aquaculture species in the United States and around the world, but not enough research tools and resources are available to study the genetics of this species. Recent biotechnological advancements has enhanced productivity gains in dairy cattle and poultry through the utilization of molecular genetics for improving selective breeding. To this end, an assay called high-density single nucleotide polymorphism (SNP) chip is used to assess relationships between the DNA make-up of the animal and desired production traits, which enables accurate prediction of the genetic merit and breeding potential of the animal. Here we report on the design, development and characterization of a high-density SNP chip assay for genetic analyses in rainbow trout. The new high density genetic assay has passed the standard quality control standards accepted for similar application by the Biotechnology industry and has been commercialized by Affymetrix. It is highly informative for rainbow trout strains used by the aquaculture industry and will also be useful for genetic analyses of wild populations to aid in fishery management decisions. This resource will facilitate the identification of genes affecting important aquaculture production traits and enhance strategies targeting the genetic improvement of this species for production efficiency.

Technical Abstract: In this paper we describe the development and characterization of the first high density single nucleotide polymorphism (SNP) genotyping array for rainbow trout. The SNP array is publically available from a commercial vendor. The SNP genotyping quality was high and validation rate was close to 90%. This is comparable to other farm animals and is much higher than previous smaller scale SNP validation studies in rainbow trout. High quality and integrity of the genotypes is evident from sample reproducibility and from nearly 100% agreement in genotyping results from other methods. The array is very useful for rainbow trout aquaculture populations with more than 40,900 polymorphic markers per population. For wild populations that were confounded by a smaller sample size the number of polymorphic markers was between 10,577 and 24,330. Comparison between genotypes from individual populations suggest good potential for identifying candidate markers for populations' traceability. Linkage analysis and mapping of the SNPs to the reference genome assembly provide strong evidence for a wide distribution throughout the genome with good representation in all 29 chromosomes. A total of 68% of the genome scaffolds and contigs were anchored through linkage analysis using the SNP array genotypes, including ~20% of the genome assembly has not been previously anchored to chromosomes.