Identity-by-descent genomic selection using selective and sparse genotyping.
BACKGROUND
Genomic selection methods require dense and widespread genotyping data, posing a particular challenge if both sexes are subject to intense selection (e.g., aquaculture species). This study focuses on alternative low-cost genomic selection methods (IBD-GS) that use selective genotyping with sparse marker panels to estimate identity-by-descent relationships through linkage analysis. Our aim was to evaluate the potential of these methods in selection programs for continuous traits measured on sibs of selection candidates in a typical aquaculture breeding population.


METHODS
Phenotypic and genomic data were generated by stochastic simulation, assuming low to moderate heritabilities (0.10 to 0.30) for a Gaussian trait measured on sibs of the selection candidates in a typical aquaculture breeding population that consisted of 100 families (100 training animals and 20 selection candidates per family). Low-density marker genotype data (~ 40 markers per Morgan) were used to trace genomic identity-by-descent relationships. Genotyping was restricted to selection candidates from 30 phenotypically top-ranking families and varying fractions of their phenotypically extreme training sibs. All phenotypes were included in the genetic analyses. Classical pedigree-based and IBD-GS models were compared based on realized genetic gain over one generation of selection.


RESULTS
Genetic gain increased substantially (13 to 32%) with IBD-GS compared to classical selection and was greatest with higher heritability. Most of the extra gain from IBD-GS was obtained already by genotyping the 5% phenotypically most extreme sibs within the pre-selected families. Additional genotyping further increased genetic gains, but these were small when going from genotyping 20% of the extremes to all phenotyped sibs. The success of IBD-GS with sparse and selective genotyping can be explained by the fact that within-family haplotype blocks are accurately traced even with low-marker densities and that most of the within-family variance for normally distributed traits is captured by a small proportion of the phenotypically extreme sibs.


CONCLUSIONS
IBD-GS was substantially more effective than classical selection, even when based on very few markers and combined with selective genotyping of small fractions of the population. The study shows that low-cost GS programs can be successful by combining sparse and selective genotyping with pedigree and linkage information.
AquaGen AS, P,O, Box 1240, Sluppen, NO-7462 Trondheim, Norway. jorgen.odegard@nmbu.no.
Jørgen
J
Odegård
Theo H E
TH
Meuwissen
D000465:Algorithms; D000818:Animals; D017756:Aquaculture / Q000379:methods*; D001947:Breeding / Q000379:methods*; D003198:Computer Simulation; D005260:Female; D016678:Genome; D023281:Genomics / Q000379:methods; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D008297:Male; D008957:Models, Genetic; D010641:Phenotype; D012641:Selection, Genetic