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Genomic differentiation between Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta and Rubia Gallega cattle breeds

Published online by Cambridge University Press:  08 March 2017

A. González-Rodríguez ,
S. Munilla ,
E. F. Mouresan ,
J. J. Cañas-Álvarez ,
J. A. Baro ,
A. Molina ,
C. Díaz ,
J. Altarriba ,
J. Piedrafita  and
L. Varona
A. González-Rodríguez
Affiliation:
Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013 Zaragoza, Spain
S. Munilla
Affiliation:
Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013 Zaragoza, Spain Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, 1417 CABA, Argentina
E. F. Mouresan
Affiliation:
Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013 Zaragoza, Spain
J. J. Cañas-Álvarez
Affiliation:
Departament de Ciència Animal i dels Aliments, Grup de Recerca en Remugants, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
J. A. Baro
Affiliation:
Departamento de Ciencias Agroforestales, Universidad de Valladolid, 34004-Palencia, Spain
A. Molina
Affiliation:
MERAGEM, Universidad de Córdoba, 14071 Córdoba, Spain
C. Díaz
Affiliation:
Departamento de Mejora Genética Animal, INIA, 28040-Madrid, Spain
J. Altarriba
Affiliation:
Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013 Zaragoza, Spain Instituto Agroalimentario de Aragón (IA2), 50013 Zaragoza, Spain
J. Piedrafita
Affiliation:
Departament de Ciència Animal i dels Aliments, Grup de Recerca en Remugants, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
L. Varona*
Affiliation:
Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013 Zaragoza, Spain Instituto Agroalimentario de Aragón (IA2), 50013 Zaragoza, Spain
*
†E-mail: lvarona@unizar.es
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Abstract

The Spanish local beef cattle breeds have most likely common origin followed by a process of differentiation. This particular historical evolution has most probably left detectable signatures in the genome. The objective of this study was to identify genomic regions associated with differentiation processes in seven Spanish autochthonous populations (Asturiana de los Valles (AV), Avileña-Negra Ibérica (ANI), Bruna dels Pirineus (BP), Morucha (Mo), Pirenaica (Pi), Retinta (Re) and Rubia Gallega (RG)). The BovineHD 777K BeadChip was used on 342 individuals (AV, n=50; ANI, n=48; BP, n=50; Mo, n=50; Pi, n=48; Re, n=48; RG, n=48) chosen to be as unrelated as possible. We calculated the fixation index (FST) and performed a Bayesian analysis named SelEstim. The output of both procedures was very similar, although the Bayesian analysis provided a richer inference and allowed us to calculate significance thresholds by generating a pseudo-observed data set from the estimated posterior distributions. We identified a very large number of genomic regions, but when a very restrictive significance threshold was applied these regions were reduced to only 10. Among them, four regions can be highlighted because they comprised a large number of single nucleotide polymorphisms and showed extremely high signals (Kullback–Leiber divergence (KLD)>6). They are located in BTA 2 (5 575 950 to 10 152 228 base pairs (bp)), BTA 5 (17 596 734 to 18 850 702 bp), BTA 6 (37 853 912 to 39 441 548 bp) and BTA 18 (13 345 515 to 15 243 838 bp) and harbor, among others, the MSTN (Myostatin), KIT-LG (KIT Ligand), LAP3 (leucine aminopeptidase 3), NAPCG (non-SMC condensing I complex, subunit G), LCORL (ligand dependent nuclear receptor corepressor-like) and MC1R (Melanocortin 1 receptor) genes. Knowledge on these genomic regions allows to identify potential targets of recent selection and helps to define potential candidate genes associated with traits of interest, such as coat color, muscle development, fertility, growth, carcass and immunological response.

Keywords

Bos taurusbeefselectiondifferentiationBayesian analysis
Type
Research Article
Information
animal , Volume 11 , Issue 10 , October 2017 , pp. 1667 - 1679
Copyright
© The Animal Consortium 2017 

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