Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle

Abstract

Background Cattle populations harbor generally high inbreeding levels that can lead to inbreeding depression (ID). Here, we study ID with different estimators of the inbreeding coefficient F, evaluate their sensitivity to used allele frequencies (founder versus sample allele frequencies), and compare effects from recent and ancient inbreeding. Methods We used data from 14,205 Belgian Blue beef cattle genotyped cows that were phenotyped for 11 linear classification traits. We computed estimators of F based on the pedigree information (FPED), on the correlation between uniting gametes (FUNI), on the genomic relationship matrix (FGRM), on excess homozygosity (FHET), or on homozygous-by-descent (HBD) segments (FHBD). Results FUNI and FGRM were sensitive to used allele frequencies, whereas FHET and FHBD were more robust. We detected significant ID for four traits related to height and length; FHBD and FUNI presenting the strongest associations. Then, we took advantage of the classification of HBD segments in different age-related classes (the length of an HBD segment being inversely related to the number of generations to the common ancestors) to determine that recent HBD classes (common ancestors present approximately up to 15 generations in the past) presented stronger ID than more ancient HBD classes. We performed additional analyses to check whether these observations could result from a lower level of variation in ancient HBD classes, or from a reduced precision to identify these shorter segments. Conclusions Overall, our results suggest that mutational load decreases with haplotype age, and that mating plans should consider mainly the levels of recent inbreeding.

Genomic prediction of individual inbreeding levels for the management of genetic diversity in populations with small effective size

“…In addition, these methods provide locus-specific estimates, which can be used to manage recessive alleles that cause genetic defects or have a large contribution to ID. They are also informative about the age of HBD segments (Kirin et al, 2010; Pemberton et al, 2012), thus allowing to estimate the recent inbreeding that is expected to be deleterious (Hinrichs et al, 2007; Szpiech et al, 2013; Stoffel et al, 2021; Naji et al, 2024) and therefore more relevant for management strategies. They are also more robust to the used allele frequencies (AF), that might introduce biases (Keller et al, 2011; Caballero et al, 2022; Naji et al, 2024).…”

“…They are also informative about the age of HBD segments (Kirin et al, 2010; Pemberton et al, 2012), thus allowing to estimate the recent inbreeding that is expected to be deleterious (Hinrichs et al, 2007; Szpiech et al, 2013; Stoffel et al, 2021; Naji et al, 2024) and therefore more relevant for management strategies. They are also more robust to the used allele frequencies (AF), that might introduce biases (Keller et al, 2011; Caballero et al, 2022; Naji et al, 2024). Finally, these estimators are more interpretable as they range between 0 and 1 as the pedigree-based estimators, and allow to define a base population comparable to the pedigree (Solé et al, 2017).…”