Genetic gain & Inbreeding

Selecting functional alleles in purebred and composite beef cattle

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Abstract

Genetic load is caused by deleterious alleles, and alleles causing loss of gene function are generally deleterious. After observing variation in the number of loss-of-function (LOF) alleles carried by individuals with whole genome sequence (WGS), an experiment to manipulate LOF counts by selection was initiated with the idea that reducing LOF alleles would reduce genetic load and increase fitness. Selection was applied to four beef cattle populations, three composites and purebred Angus. The composites beginning the selecting functional alleles (SFA) project were ¼ British (B) x ¾ Continental (C) breeds (MARC I), ½ B x ½ C (MARC II), and ¾ B x ¼ C (MARC III). Prior to 2016 breeding for 2017 calves, available bulls and females and were split between select and control lines within each population according to individual counts of LOF alleles. Subsequently, replacement heifers and bulls have been selected from within each line; select line calves with the lowest LOF counts were retained, as were random control line calves. Genotypes were initially obtained for LOF variants probed by the GGP-F250 assay. In 2020 and after, LOF genotypes were imputed from low-coverage WGS (~0.5X) with a reference panel of >900 individuals representing major dairy and beef breeds and crosses. Sires from the SFA populations were added to the imputation reference in 2022. Pedigree imputation with findhap was used to fill missing genotypes from the GGP-F250, as well as low probability calls from low-coverage WGS. Loss-of-function variants were identified using snpEff with the bovine assembly and Ensembl annotation that was current at the time. Allele frequencies across the SFA populations were determined, and the minor allele for each LOF variant was counted as the LOF allele. Genotypes were coded as 0, 1 or 2 copies of the LOF allele. Non-integer genotypes based on the imputed allele and allele frequency were assigned to partial genotypes imputed by findhap. The LOF count for each individual was the sum of their genotypes for each LOF variant. Within each composite, the difference between control and select mean LOF counts has tended to increase each year: 5.6±1.1 LOF per year for MARC I and IA, 6.4±1.1 for MARC II and 6.0±1.3 for MARC III. The difference between control and select LOF means for Angus, however, fluctuated around 18.6 without a clear trend for the difference to increase over time (0.3±1.3 LOF per year). Within each population, select and control lines had similar weaning rates and weaning weights. Further examination of these populations is needed to better understand selection for LOF and correlated responses that may occur in production traits. The USDA is an equal opportunity provider and employer.

Keywords: 2026

How to Cite:

Snelling, W., McDaneld, T., Bennett, G. & Kuehn, L., (2026) “Selecting functional alleles in purebred and composite beef cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2293458. doi: https://doi.org/10.31274/wcgalp.24313

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