Location: Range and Livestock ResearchTitle: Different Methods of Selecting Animals for Genotyping to Maximize the Amount of Genetic Information Known in the Population Author
Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/15/2008
Publication Date: 4/25/2008
Citation: Spangler, M.L., Sapp, R.L., Bertrand, J.K., MacNeil, M.D., Rekaya, R. 2008. Different Methods of Selecting Animals for Genotyping to Maximize the Amount of Genetic Information Known in the Population. Journal of Animal Science 86:2471-2479. Interpretive Summary: Interest in identifying QTL and genes of economic importance for marker-assisted selection (MAS) in livestock populations has increased greatly in the past decade. Yet, it may not be viable to genotype each animal. A method that would allow for a selected sample (e.g. 5%) of the population to be genotyped and at the same time inferring with high probability genotypes for the remaining animals in the population could be beneficial. Objectives of the current study were to investigate sampling techniques for genotyping a selection of animals and to determine the impact of estimating allele frequencies of selected animals. Results of the current study show that random selection is not desirable and numerous alternatives exist. Selection of animals based on their diagonal element of the inverse of the relationship matrix appears to be the most desirable solution. The proportion of males and females selected may depend on the particular pedigree. Every pedigree will offer its own challenges due to its intrinsic structure and the application of the methods presented here may be limited to the pedigrees used in the current study.
Technical Abstract: It is possible to predict genotypes of some individuals based on genotypes of relatives. Different methods of sampling individuals to be genotyped from populations were evaluated using simulation. Simulated pedigrees included 5,000 animals and were assigned genotypes based on assumed allelic frequencies for a Single Nucleotide Polymorphism (SNP) (favorable/unfavorable) of 0.3/0.7, 0.5/0.5, and 0.8/0.2. A field data pedigree (29,101 animals), and a research pedigree (8,688 animals) were used to test selected methods using simulated genotypes with allelic frequencies of 0.3/0.7 and 0.5/0.5. For the simulated pedigrees, known and unknown allelic frequencies were assumed. The methods used included random sampling, selection of males, and selection of both sexes based on the diagonal element of the inverse of the relationship matrix (A-1) and absorption of either the A or A-1 matrix. For random sampling, scenarios included selection of 5 and 15% of the animals while all other methods presented concentrated on the selection of 5% of the animals for genotyping. The methods were evaluated based on the percentage of alleles correctly assigned after peeling (AKP), the probability of assigning true alleles (AKG) and the average probability of correctly assigning the true genotype (APTG). As expected random sampling was the least desirable method. The most desirable method in the simulated pedigrees was selecting both males and females based on their diagonal element of A-1. Increases in AKP and AKG ranged from 26.58 to 29.11% and 2.76 to 6.08%, respectively, when males and females (equal to 5% of all animals) were selected based on their diagonal element of A-1 compared with selecting 15% of the animals at random. In the case of a real beef cattle pedigree, selection of males only or males and females yielded similar results and both selection methods were superior to random selection.