Trends in genetic diversity and the effect of inbreeding in American Angus Cattle under genomic selection

Authors: LOZADA-SOTO, EMMANUEL - North Carolina State University; MALTECCA, CHRISTIAN - North Carolina State University; LU, DUC - Angus Genetics, Inc; MILLER, STEPHEN - Angus Genetics, Inc; Cole, John; TIEZZI, FRANCESCO - North Carolina State University

Submitted to: Genetics Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/7/2021
Publication Date: 6/16/2021
Citation: Lozada-Soto, E.A., Maltecca, C., Lu, D., Miller, S., Cole, J.B., Tiezzi, F. 2021. Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection. Genetics Selection Evolution. 53:50. https://doi.org/10.1186/s12711-021-00644-z.
DOI: https://doi.org/10.1186/s12711-021-00644-z

Interpretive Summary: The adoption of genomic selection has resulted in increased rates of inbreeding, which correspond to a loss of genetic diversity. Such changes can have harmful effects on fitness, fertility, and performance traits. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain. Inbreeding that occurred a long time ago had much smaller effects on performance than inbreeding that happened recently, probably because harmful genetic variants have from old inbreeding have been purged from the population.

Technical Abstract: While the adoption of genomic evaluations in livestock has increased rates of genetic gain, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for high value traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus and quantify potential inbreeding depression effects using complete pedigrees and genomic information, as well as investigate the impact of recent and ancient inbreeding. We found the yearly rate of inbreeding accumulation to have remained similar in sires and decreased significantly in dams from before the implementation of genomic selection to now. Other measures, such as effective population size and effective number of chromosome segments, also show that genomic selection strategies have not been detrimental to genetic diversity in beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the effect of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding across most growth traits. In this study, we sought to quantify and understand the possible consequences of genomic selection on American Angus cattle’s genetic diversity. In both sires and dams, we generally found that genomic selection served to decrease generation intervals, decrease the rate of pedigree and genomic inbreeding accumulation, and increase or maintain the effective population size and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.