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ARS Home » Plains Area » Miles City, Montana » Livestock and Range Research Laboratory » Research » Publications at this Location » Publication #388143
Research Project: Alleviating Rate Limiting Factors that Compromise Beef Production Efficiency

Location: Livestock and Range Research Laboratory

Title: Inbreeding calculated with runs of homozygosity suggests chromosome-specific inbreeding depression regions in Line 1 Hereford

Author
item PILON, BETHANY - Cornell University
item HINTERNEDER, KELLY - Lincoln Memorial University
item Hay, El Hamidi
item FRAGOMENI, BRENO - University Of Connecticut

Submitted to: Animals
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/25/2021
Publication Date: 10/30/2021
Citation: Pilon, B., Hinterneder, K., Hay, E.A., Fragomeni, B. 2021. Inbreeding calculated with runs of homozygosity suggests chromosome-specific inbreeding depression regions in Line 1 Hereford. Animals. 11(11). Article 3105. https://doi.org/10.3390/ani11113105.
DOI: https://doi.org/10.3390/ani11113105

Interpretive Summary: With the increasing use of genomic selection in beef cattle and other livestock species, inbreeding is becoming a concern. The accumulation of inbreeding negatively impacts the performance of animals. Thus, understanding the mechanisms and impact of inbreeding is of great interest to the beef cattle industry and animal agriculture in general. In this study, a closed Hereford population was used to detect regions in the genome associated with inbreeding. Moreover, inbreeding estimates were used to predict average daily gain. The results showed a small prediction accuracy of average daily gain and revealed several regions in the genome with significant association with inbreeding. This suggests that inbreeding should be evaluated per individual regions of the genome. Moreover, mating schemes to avoid inbreeding depression should focus on specific homozygous regions with negative effects. Finally, using homozygous regions in the genome as an added information may increase prediction of the genetic merit of animals.

Technical Abstract: The goal of this study was to evaluate inbreeding in a closed beef cattle population and the accuracy of predicting phenotypes using inbreeding information. Effects of inbreeding on average daily gain phenotype in the line 1 Hereford cattle population were assessed in this study. Genomic data was used to calculate inbreeding based on runs of homozygosity (ROH), and pedigree information was used to calculate the probability of an allele being identical by descent. Prediction ability of phenotypes using inbreeding coefficients calculated based on pedigree information and runs of homozygosity over the whole genome was close to 0, even with a significant inbreeding coefficient. On the other hand, including only ROH from chromosomes with higher predicting ability further increased accuracy of prediction. The accuracy of predicting ability, inbreeding depression, and its magnitude on chromosome specific ROHs varied widely across the genome. The results of this study suggest that inbreeding should be evaluated per individual regions of the genome. Moreover, mating schemes to avoid inbreeding depression should focus on specific ROH with negative effects. Finally, using ROH as an added information may increase prediction of the genetic merit of animals in a genomic selection program.