Page Banner

United States Department of Agriculture

Agricultural Research Service

Research Project: REDUCING COST OF EFFICIENT BEEF PRODUCTION Title: Ant colony optimization as a method for strategic genotype sampling.

Authors
item Sprangler, M - U OF GEORGIA
item Robbins, K - U OF GEORGIA
item Bertrand, J - U OF GEORGIA
item Macneil, Michael
item Rekaya, R - U OF GEORGIA

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 7, 2008
Publication Date: February 1, 2009
Repository URL: http://hdl.handle.net/10113/32726
Citation: Sprangler, M.L., Robbins, K.R., Bertrand, J.K., MacNeil, M.D., Rekaya, R. 2009. Ant colony optimization as a method for strategic genotype sampling. Animal Genetics 40:308-314.

Interpretive Summary: A simulation study was carried out to develop an alternative method of selecting animals to be genotyped. Simulated pedigrees included 5000 animals, each assigned genotypes for a bi-allelic single nucleotide polymorphism (SNP) based on assumed allelic frequencies of 0.7/ 0.3 and 0.5/0.5. In addition to simulated pedigrees, two beef cattle pedigrees, one from field data and the other from a research population, were used to test selected methods using simulated genotypes. The proposed method of ant colony optimization (ACO) was evaluated based on the number of alleles correctly assigned to ungenotyped animals (AK*P*), the probability of assigning true alleles (AK*G*) and the probability of correctly assigning genotypes (APTG). The proposed animal selection method of ant colony optimization was compared to selection using the diagonal elements of the inverse of the relationship matrix (A**-1**). Comparisons of these two methods showed that ACO yielded an increase in AKP ranging from 4.98% to 5.16% and an increase in APTG from 1.6% to 1.8% using simulated pedigrees. Gains in field data and research pedigrees were slightly lower. These results suggest that ACO can provide a better genotyping strategy, when compared to A**-1**, with different pedigree sizes and structures.

Technical Abstract: A simulation study was carried out to develop an alternative method of selecting animals to be genotyped. Simulated pedigrees included 5000 animals, each assigned genotypes for a bi-allelic single nucleotide polymorphism (SNP) based on assumed allelic frequencies of 0.7/ 0.3 and 0.5/0.5. In addition to simulated pedigrees, two beef cattle pedigrees, one from field data and the other from a research population, were used to test selected methods using simulated genotypes. The proposed method of ant colony optimization (ACO) was evaluated based on the number of alleles correctly assigned to ungenotyped animals (AK*P*), the probability of assigning true alleles (AK*G*) and the probability of correctly assigning genotypes (APTG). The proposed animal selection method of ant colony optimization was compared to selection using the diagonal elements of the inverse of the relationship matrix (A**-1**). Comparisons of these two methods showed that ACO yielded an increase in AKP ranging from 4.98% to 5.16% and an increase in APTG from 1.6% to 1.8% using simulated pedigrees. Gains in field data and research pedigrees were slightly lower. These results suggest that ACO can provide a better genotyping strategy, when compared to A**-1**, with different pedigree sizes and structures.

Last Modified: 11/20/2014
Footer Content Back to Top of Page