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

Abstract

Background Although inbreeding caused by the mating of animals related through a recent common ancestor is expected to have more harmful effects on phenotypes than ancient inbreeding (old inbreeding), 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 assumption that new inbreeding tends to have a more pronounced detrimental effect on traits. The proposed method was tested using a cattle population characterized by a deep pedigree. Results 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 were trait-specific and 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 four to seven generations, indicating, in part, the ability of ROH segments to characterize the harmful effects of inbreeding in shorter periods of time. Nevertheless, using the proposed classification method, the discrimination between new and old inbreeding was less robust when ROH segments were used compared to pedigree. Using several model comparison criteria, the proposed approach was generally better than existing methods. Recent inbreeding appeared 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. Conclusions The proposed method provided a more objective quantitative approach for the classification of inbreeding. The proposed method detected a clear divergence in the effects of old and recent inbreeding using pedigree data and it was superior to existing methods for all analyzed traits. Using ROH data, the discrimination between old and recent inbreeding was less clear and the proposed method was superior to existing approaches for two out of the four analyzed traits. Deleterious effects of recent inbreeding were detected sooner (fewer generations) using genomic information than pedigree. Difference in the results using genomic and pedigree information could be due to the dissimilarity in the number of generations to a common ancestor. Additionally, the uncertainty associated with the identification of ROH segments and associated inbreeding could have an effect on the results. 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.

Genomic inbreeding coefficients using imputed genotypes: Assessing different estimators in Holstein-Friesian dairy cows

“…(2) HBD (Druet and Gautier, 2017) or age-based HBD (Solé et al, 2017). Various implementations of these methods have been proposed based on arbitrary thresholds (Doekes et al, 2019), clustering approaches (Pemberton et al, 2012), hidden Markov models, and grid search algorithms (Sumreddee et al, 2021). The general objective though remains the same, that is to find a way to distinguish recent from old inbreeding or HBD from non-HBD DNA segments.…”

Inbreeding depression and the probability of racing in the Thoroughbred horse

“…The proportion of the genome covered by ROH affects production traits in livestock populations [ 12 , 13 ]. Generally, shorter ROH reflect distant inbreeding resulting from a common ancestor many generations back in the pedigree, whereas long ROH reflect a more recent common ancestor [ 14 ]. Mutations in long ROH are expected to be more harmful (deleterious) than those in short ROH since there have been fewer generations for purging to occur.…”

Inbreeding depression on growth and prolificacy traits in two lines of rabbit

“…Accordingly, AHC and Fa.B may provide a better representation of the evidence of purging than Fa.K because the last parameter represents the probability that any allele in an individual is currently IBD and has been IBD in previous generations at least once which could be considered somehow like a mix of recent and old inbreeding. However, in the partition of the inbreeding approach, as a consequence of varied mating systems, pedigree depths, and generation intervals, the number of generations that determined new inbreeding do not allow fair and straight comparisons between studies (Sumreddee et al, 2021). The same happens in the comparison of results of our two lines for a specific trait which is not Despite this lack of a common base for comparisons, the effectiveness of the purging process may explain some of the heterogeneity in inbreeding depression across studies (Sumreddee et al, 2021).…”