title: Within- and across-breed genomic predictions and genomic relationships for Western Pyrenees dairy sheep breeds Latxa, Manech, and Basco-Béarnaise.
abstract: Genotypes, phenotypes and pedigrees of 6 breeds of dairy sheep (including subdivisions of Latxa, Manech, and Basco-Béarnaise) from the Spain and France Western Pyrenees were used to estimate genetic relationships across breeds (together with genotypes from the Lacaune dairy sheep) and to verify by forward cross-validation single-breed or multiple-breed genetic evaluations. The number of rams genotyped fluctuated between 100 and 1,300 but generally represented the 10 last cohorts of progeny-tested rams within each breed. Genetic relationships were assessed by principal components analysis of the genomic relationship matrices and also by the conservation of linkage disequilibrium patterns at given physical distances in the genome. Genomic and pedigree-based evaluations used daughter yield performances of all rams, although some of them were not genotyped. A pseudo-single step method was used in this case for genomic predictions. Results showed a clear structure in blond and black breeds for Manech and Latxa, reflecting historical exchanges, and isolation of Basco-Béarnaise and Lacaune. Relatedness between any 2 breeds was, however, lower than expected. Single-breed genomic predictions had accuracies comparable with other breeds of dairy sheep or small breeds of dairy cattle. They were more accurate than pedigree predictions for 5 out of 6 breeds, with absolute increases in accuracy ranging from 0.05 to 0.30 points. They were significantly better, as assessed by bootstrapping of candidates, for 2 of the breeds. Predictions using multiple populations only marginally increased the accuracy for a couple of breeds. Pooling populations does not increase the accuracy of genomic evaluations in dairy sheep; however, single-breed genomic predictions are more accurate, even for small breeds, and make the consideration of genomic schemes in dairy sheep interesting.
authors.affiliation: INRA, UR1388 GenPhySe, CS-52627, F-31326 Castanet-Tolosan, France. Electronic address: andres.legarra@toulouse.inra.fr.
authors.forename: A
authors.initials: A
authors.lastname: Legarra
authors.affiliation: INRA, UR1388 GenPhySe, CS-52627, F-31326 Castanet-Tolosan, France.
authors.forename: G
authors.initials: G
authors.lastname: Baloche
authors.affiliation: INRA, UR1388 GenPhySe, CS-52627, F-31326 Castanet-Tolosan, France.
authors.forename: F
authors.initials: F
authors.lastname: Barillet
authors.affiliation: Institut de l'Elevage, 149 rue de Bercy, F-75595 Paris, France.
authors.forename: J M
authors.initials: JM
authors.lastname: Astruc
authors.affiliation: CDEO, Route de Musculdy, Quartier Ahetzia, F-64130 Ordiarp, France.
authors.forename: C
authors.initials: C
authors.lastname: Soulas
authors.affiliation: CDEO, Route de Musculdy, Quartier Ahetzia, F-64130 Ordiarp, France.
authors.forename: X
authors.initials: X
authors.lastname: Aguerre
authors.affiliation: ARDIEKIN, Apdo 46, 01080 Vitoria-Gasteiz, Spain.
authors.forename: F
authors.initials: F
authors.lastname: Arrese
authors.affiliation: ARDIEKIN, Apdo 46, 01080 Vitoria-Gasteiz, Spain.
authors.forename: L
authors.initials: L
authors.lastname: Mintegi
authors.affiliation: ASLANA, c/Aintziburu, 31170 Iza, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Lasarte
authors.affiliation: INTIA SA, Avda. Serapio Huici 22, 31610 Villava, Spain.
authors.forename: F
authors.initials: F
authors.lastname: Maeztu
authors.affiliation: NEIKER-Tecnalia, Apdo 46, 01080 Vitoria-Gasteiz, Spain.
authors.forename: I
authors.initials: I
authors.lastname: Beltrán de Heredia
authors.affiliation: NEIKER-Tecnalia, Apdo 46, 01080 Vitoria-Gasteiz, Spain.
authors.forename: E
authors.initials: E
authors.lastname: Ugarte
mesh_terms: D000818:Animals; D001947:Breeding; D005260:Female; D005602:France; D016678:Genome; D023281:Genomics / Q000379:methods; D005838:Genotype; D015810:Linkage Disequilibrium / Q000235:genetics; D008297:Male; D010375:Pedigree; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D012756:Sheep / Q000235:genetics*; D013030:Spain
keywords: best linear unbiased predictor (BLUP); dairy sheep; genomic selection; linkage disequilibrium; principal component