A Genomic and Economic Analysis of Utilizing Pooled Genotypes in a Commercial Beef Cattle Feedlot Setting

Genotyping individual animals, the primary way to identify the genetic makeup of the animal, comes at a fiscal and logistical cost commercial beef cattle feedlots cannot afford in current markets. The purpose of this study was to utilize DNA pooling and a pooled genome-wide association study (GWAS) to allow the commercial feedlot setting to ascertain the benefits of genomic testing and make predictions contingent on these tests, as well as determine its economic feasibility.

A total of 1,956 commercial feedlot cattle (1,715 steers; 241 heifers) completed the project with receival information, carcass data, and tissue samples. DNA was stratified into 79 pools (mean size = 25 individuals) based on receival weight within lot and arrival date and genotyped via GGP Bovine 100K array (Illumina). Data preparation with outlier filtering (OF) and repeated measures (RM) reduced phenotypic variation within pools by removing outlier-driven pools and replicating the pool genotype to an individual level, respectively. Pool average and individual calculated yield grade (CYG) and marbling (MARB), both essential carcass value determinants, served as phenotype data. A cost comparison of pooled and individual genotyping and a cost-benefit analysis of prospective pooling displayed the economic advantage and potential economic feasibility of the process.

The RM CYG, OF CYG, RM MARB, and OF MARB trial GWAS identified 20, 10, 27, and 16 significant (p ≤ 0.001) SNPs, respectively. The estimated cost of individually genotyping the study ($105,354) was 4.5 times greater than the estimated pooled genotyping cost ($23,460). Utilizing pooled genotypes to make marketing decisions had a potential benefit-cost ratio of 2.33 (SD = 1.91).

This research identified biologically logical associations despite high genetic variability between pools, signifying success in utilizing prospectively pooled DNA in GWAS. Further research and exploration are necessary for developing a successful strategy for its application. With potential benefits that outweigh the cost, the pooled genetic processing and analysis should be further evaluated in additional commercial feedlot settings.