Different methods of selecting animals for genotyping to maximize the amount of genetic information known in the population

¹ Animal and Dairy Science Department, University of Georgia, Athens, Georgia 30602-2771
² USDA-ARS, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT 59301
³ Animal and Dairy Science Department; Department of Statistics; Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602-2771

^* To whom correspondence should be addressed. E-mail: rrekaya{at}uga.edu.

	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 (AK_P), the probability of assigning true alleles (AK_G), 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 AK_P and AK_G 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.

Key Words: genotype sampling, marker-assisted selection, simulation