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

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 (F_PED), on the correlation between uniting gametes (F_UNI), on the genomic relationship matrix (F_GRM), on excess homozygosity (F_HET), or on homozygous-by-descent (HBD) segments (F_HBD).

Results: F_UNI and F_GRM were sensitive to used allele frequencies, whereas F_HET and F_HBD were more robust. We detected significant ID for four traits related to height and length; F_HBD and F_UNI 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.