Genotype Imputation to Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon ...

• Main Authors: Tsai, Hsin-Yuan, Matika, Oswald, Edwards, Stefan McKinnon, Antolín–Sánchez, Roberto, Hamilton, Alastair, Guy, Derrick R, Tinch, Alan E, Gharbi, Karim, Stear, Michael, Taggart, John B, Bron, James E, Hickey, John M, Houston, Ross D
• Format: Text
• Language: unknown
• Published: La Trobe 2022
• Subjects: Atlantic salmon
• Online Access: https://dx.doi.org/10.26181/17205902.v1; https://opal.latrobe.edu.au/articles/journal_contribution/Genotype_Imputation_to_Improve_the_Cost-Efficiency_of_Genomic_Selection_in_Farmed_Atlantic_Salmon/17205902/1

Genomic selection uses genome-wide marker information to predict breeding values for traits of economic interest, and is more accurate than pedigree-based methods. The development of high density SNP arrays for Atlantic salmon has enabled genomic selection in selective breeding programs, alongside high-resolution association mapping of the genetic basis of complex traits. However, in sibling testing schemes typical of salmon breeding programs, trait records are available on many thousands of fish with close relationships to the selection candidates. Therefore, routine high density SNP genotyping may be prohibitively expensive. One means to reducing genotyping cost is the use of genotype imputation, where selected key animals (e.g., breeding program parents) are genotyped at high density, and the majority of individuals (e.g., performance tested fish and selection candidates) are genotyped at much lower density, followed by imputation to high density. The main objectives of the current study were to assess ...