title: Testing strategies for genomic selection in aquaculture breeding programs.
abstract: BACKGROUND
  Genomic selection is a selection method where effects of dense genetic markers are first estimated in a test population and later used to predict breeding values of selection candidates. The aim of this paper was to investigate genetic gains, inbreeding and the accuracy of selection in a general genomic selection scheme for aquaculture, where the test population consists of sibs of the candidates.
  
  
  METHODS
  The selection scheme started after simulating 4000 generations in a Fisher-Wright population with a size of 1000 to create a founder population. The basic scheme had 3000 selection candidates, 3000 tested sibs of the candidates, 100 full-sib families, a trait heritability of 0.4 and a marker density of 0.5N(e)/M. Variants of this scheme were also analysed.
  
  
  RESULTS
  The accuracy of selection in generation 5 was 0.823 for the basic scheme when the sib-testing was performed every generation. The accuracy was hardly reduced by selection, probably because the increased frequency of favourable alleles compensated for the Bulmer effect. When sib-testing was performed only in the first generation, in order to reduce costs, accuracy of selection in generation 5 dropped to 0.304, the main reduction occurring in the first generation. The genetic level in generation 5 was 6.35 sigma(a) when sib-testing was performed every generation, which was 72%, 12% and 9% higher than when sib-testing was performed only in the first generation, only in the first three generations or every second generation, respectively. A marker density above 0.5N(e)/M hardly increased accuracy of selection further. For the basic scheme, rates of inbreeding were reduced by 81% in these schemes compared to traditional selection schemes, due to within-family selection. Increasing the number of sibs to 6000 hardly affected the accuracy of selection, and increasing the number of candidates to 6000 increased genetic gain by 10%, mainly because of increased selection intensity.
  
  
  CONCLUSIONS
  Various strategies were evaluated to reduce the amount of sib-testing and genotyping, but all resulted in loss of selection accuracy and thus of genetic gain. Rates of inbreeding were reduced by 81% in genomic selection schemes compared to traditional selection schemes for the parameters of the basic scheme, due to within-family selection.
authors: Nofima Marine AS, As, Norway. Anna.Sonesson@nofima.no
authors: Anna K
authors: AK
authors: Sonesson
authors: Theo H E
authors: TH
authors: Meuwissen
mesh_terms: D000818:Animals; D000829:Animals, Domestic / Q000235:genetics*; D017756:Aquaculture; D005260:Female; D016678:Genome; D007178:Inbreeding; D008297:Male; D008957:Models, Genetic