Sequenced-based GWAS for linear classification traits in Belgian Blue beef cattle reveals new coding variants in genes regulating body size in mammals.
Gualdrón Duarte, José Luis; Yuan, Can; Gori, Ann-Stephanet al.
2023 • In Genetics, Selection, Evolution, 55 (1), p. 83
Cattle/genetics; Body Size/genetics; Mammals/genetics; Quantitative Trait Loci; Body Size; Cattle; Genome-Wide Association Study; Genetics
Abstract :
[en] [en] BACKGROUND: Cohorts of individuals that have been genotyped and phenotyped for genomic selection programs offer the opportunity to better understand genetic variation associated with complex traits. Here, we performed an association study for traits related to body size and muscular development in intensively selected beef cattle. We leveraged multiple trait information to refine and interpret the significant associations.
RESULTS: After a multiple-step genotype imputation to the sequence-level for 14,762 Belgian Blue beef (BBB) cows, we performed a genome-wide association study (GWAS) for 11 traits related to muscular development and body size. The 37 identified genome-wide significant quantitative trait loci (QTL) could be condensed in 11 unique QTL regions based on their position. Evidence for pleiotropic effects was found in most of these regions (e.g., correlated association signals, overlap between credible sets (CS) of candidate variants). Thus, we applied a multiple-trait approach to combine information from different traits to refine the CS. In several QTL regions, we identified strong candidate genes known to be related to growth and height in other species such as LCORL-NCAPG or CCND2. For some of these genes, relevant candidate variants were identified in the CS, including three new missense variants in EZH2, PAPPA2 and ADAM12, possibly two additional coding variants in LCORL, and candidate regulatory variants linked to CCND2 and ARMC12. Strikingly, four other QTL regions associated with dimension or muscular development traits were related to five (recessive) deleterious coding variants previously identified.
CONCLUSIONS: Our study further supports that a set of common genes controls body size across mammalian species. In particular, we added new genes to the list of those associated with height in both humans and cattle. We also identified new strong candidate causal variants in some of these genes, strengthening the evidence of their causality. Several breed-specific recessive deleterious variants were identified in our QTL regions, probably as a result of the extreme selection for muscular development in BBB cattle.
Disciplines :
Animal production & animal husbandry Genetics & genetic processes Veterinary medicine & animal health
Author, co-author :
Gualdrón Duarte, José Luis; Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital, 1, Liège, 4000, Belgium. jlgualdron@awegroupe.be ; Walloon Breeders Association, Rue des Champs Elysées, 4, 5590, Ciney, Belgium. jlgualdron@awegroupe.be
Yuan, Can ; Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA) > Génomique animale
Gori, Ann-Stephan; Walloon Breeders Association, Rue des Champs Elysées, 4, 5590, Ciney, Belgium
Moreira, Gabriel C M; Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital, 1, Liège, 4000, Belgium
Takeda, Haruko ; Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA) > Génomique animale
Charlier, Carole ; Université de Liège - ULiège > GIGA > GIGA Medical Genomics
Georges, Michel ; Université de Liège - ULiège > GIGA > GIGA Medical Genomics - Unit of Animal Genomics
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 :
Sequenced-based GWAS for linear classification traits in Belgian Blue beef cattle reveals new coding variants in genes regulating body size in mammals.
Publication date :
28 November 2023
Journal title :
Genetics, Selection, Evolution
ISSN :
0999-193X
eISSN :
1297-9686
Publisher :
BioMed Central Ltd, France
Volume :
55
Issue :
1
Pages :
83
Peer reviewed :
Peer Reviewed verified by ORBi
Tags :
CÉCI : Consortium des Équipements de Calcul Intensif
This work was supported by the Service Public de Wallonie (WALInnov CAUSEL project). We used the supercomputing facilities of the “Consortium d’Equipements en Calcul Intensif en Fédération Wallonie-Bruxelles” (CECI), funded by the F.R.S.-FNRS.
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