Genetics; Animal Science and Zoology; General Medicine; Ecology, Evolution, Behavior and Systematics
Abstract :
[en] [en] 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.
Disciplines :
Animal production & animal husbandry Veterinary medicine & animal health Genetics & genetic processes
Author, co-author :
Naji, Maulana ; Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA)
Gualdrón Duarte, José Luis; Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Quartier Hôpital, Avenue de l'Hôpital, 11, 4000, Liege, Belgium ; Walloon Breeders Association (awe groupe), 5590, Ciney, Belgium
Forneris, Natalia ; Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA)
Druet, Tom ; Université de Liège - ULiège > GIGA > GIGA Medical Genomics - Unit of Animal Genomics ; Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA)
Language :
English
Title :
Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle.
Publication date :
2024
Journal title :
Genetics, Selection, Evolution
ISSN :
0999-193X
eISSN :
1297-9686
Publisher :
Springer Science and Business Media LLC, France
Volume :
56
Issue :
1
Pages :
10
Peer reviewed :
Peer Reviewed verified by ORBi
Tags :
CÉCI : Consortium des Équipements de Calcul Intensif
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