Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information

Authors: SUMREDDEE, PATTARAPOL - University Of Georgia; Hay, El Hamidi; Toghiani, Sajjad; Roberts, Andrew; AGGREY, SAMMY - University Of Georgia; REKAYA, ROMDHANE - University Of Georgia

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/5/2021
Publication Date: 7/13/2021
Citation: Sumreddee, P., Hay, E.A., Toghiani, S., Roberts, A.J., Aggrey, S., Rekaya, R. 2021. Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information. Biomed Central (BMC) Genomics. 22.Article 538. https://doi.org/10.1186/s12864-021-07872-z.
DOI: https://doi.org/10.1186/s12864-021-07872-z

Interpretive Summary: Inbreeding is a major concern in the beef cattle industry. Inbreeding leads to a decrease in performance for several economically important traits. Thus, understanding the accumulation and impact of inbreeding is of paramount importance. In this study, a method was developed to discriminate between old and new inbreeding. Furthermore, the effects of old and new inbreeding on growth traits were evaluated. The results showed a superiority of the proposed method in discriminating between old and new inbreeding. The evaluation of the impact of inbreeding showed that new inbreeding was more harmful across all growth traits. However, both new and old inbreeding were found to be associated with decreased yearling weight and post weaning average daily gain.

Technical Abstract: Although inbreeding caused by the mating of animals related through a recent common ancestor is expected to have more pronounced effects on traits, estimating these effects requires a clear definition of recent (new) and ancient (old) inbreeding. Several methods have been proposed to classify inbreeding using pedigree and genomic data. Unfortunately, these methods are largely based on heuristic criteria such as the number of generations from a common ancestor or length of runs of homozygosity (ROH) segments. To mitigate these deficiencies, this study aimed to develop a method to classify pedigree and genomic inbreeding into recent and ancient classes based on a grid search algorithm driven by the hypothesis that new inbreeding tends to have a more pronounced effect on traits. The proposed method was tested using a cattle population characterized by a deep pedigree. Effects of recent and ancient inbreeding were assessed on four growth traits (birth, weaning and yearling weights and average daily gain). Thresholds to classify inbreeding into recent and ancient classes varied across traits and sources of information. Using pedigree information, inbreeding generated in the last 10 to 11 generations was considered as recent. When genomic information (ROH) was used, thresholds ranged between 4 to 7 generations, indicating the ability of ROH segments to better characterize the harmful effects of inbreeding in shorter periods of time. Using several model comparison criteria, the proposed approach was generally better than existing methods, particularly compared to pedigree-based approaches. Recent inbreeding seemed to be more harmful across the growth traits analyzed. However, both new and old inbreeding were found to be associated with decreased yearling weight and average daily gain. The proposed method provided a more objective quantitative approach for the classification of inbreeding. Selection may have played a role in limiting the impact of inbreeding in some traits through purging of deleterious alleles. Potential biases in the estimation of inbreeding effects may occur when new and old inbreeding are discriminated based on arbitrary thresholds. To minimize the impact of inbreeding, mating designs should take the different inbreeding origins into consideration.