title: The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout.
abstract: In this study, 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 (Affymetrix). 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 are 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 suggests 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 that has not been previously anchored to chromosomes.
authors.affiliation: National Center for Cool and Cold Water Aquaculture, ARS-USDA, 11861 Leetown Road, Kearneysville, WV, 25430, USA.
authors.forename: Y
authors.initials: Y
authors.lastname: Palti
authors.forename: G
authors.initials: G
authors.lastname: Gao
authors.forename: S
authors.initials: S
authors.lastname: Liu
authors.forename: M P
authors.initials: MP
authors.lastname: Kent
authors.forename: S
authors.initials: S
authors.lastname: Lien
authors.forename: M R
authors.initials: MR
authors.lastname: Miller
authors.forename: C E
authors.initials: CE
authors.lastname: Rexroad
authors.forename: T
authors.initials: T
authors.lastname: Moen
mesh_terms: D000818:Animals; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods; D060005:Genotyping Techniques / Q000379:methods*; D017686:Oncorhynchus mykiss / Q000145:classification* / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results
keywords: genetic diversity; linkage analysis; rainbow trout; single nucleotide polymorphism chip