Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK.
The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). We combined this dataset with Spanish ovine data previously reported by the International Sheep Genomics Consortium (N = 229). Multidimensional scaling and Admixture analyses revealed that Canaria de Pelo and, to a lesser extent, Roja Mallorquina, Latxa and Churra are clearly differentiated populations, while the remaining seven breeds (Ojalada, Castellana, Gallega, Xisqueta, Ripollesa, Rasa Aragonesa and Segureña) share a similar genetic background. Performance of a genome scan with BayeScan and hapFLK allowed us identifying three genomic regions that are consistently detected with both methods i.e. Oar3 (150-154 Mb), Oar6 (4-49 Mb) and Oar13 (68-74 Mb). Neighbor-joining trees based on polymorphisms mapping to these three selective sweeps did not show a clustering of breeds according to their predominant productive specialization (except the local tree based on Oar13 SNPs). Such cryptic signatures of selection have been also found in the bovine genome, posing a considerable challenge to understand the biological consequences of artificial selection.
Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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Manunza
Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.|CAPES Foundation, Ministry of Education of Brazil, Brasilia D. F., Zip Code 70.040-020, Brazil.
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Cardoso
Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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Noce
Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain.
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Martínez
Unitat de Races Autòctones, Servei de Millora Agrària i Pesquera (SEMILLA), Son Ferriol 07198, Spain.
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Pons
Departamento de Ingeniería, Producción y Economía Agrarias, Universidad de La Laguna, 38071 La Laguna, Tenerife, Spain.
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Bermejo
Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain.
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Landi
Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.|Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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Sànchez
Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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Jordana
Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain.
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Delgado
Federación de Razas Autóctonas de Galicia (BOAGA), Pazo de Fontefiz, 32152 Coles. Ourense, Spain.
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Adán
Instituto Canario de Investigaciones Agrarias, La Laguna 38108, Tenerife, Spain.
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Capote
Departament de Biologia, Universitat de Girona, Girona 17071, Spain.
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Vidal
Neiker-Tecnalia, Campus Agroalimentario de Arkaute, apdo 46 E-01080 Vitoria-Gazteiz (Araba), Spain.
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Ugarte
Departamento de Producción Animal, Universidad de León, León 24071, Spain.
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Arranz
Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unidad de Tecnología en Producción Animal, Avda. Montañana, 930, 50059 Zaragoza, Spain.
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Calvo
Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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Casellas
Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.|Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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Amills
D000818:Animals; D016000:Cluster Analysis; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D060005:Genotyping Techniques; D012641:Selection, Genetic; D012756:Sheep / Q000145:classification* / Q000235:genetics*; D013030:Spain