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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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References

Beja-Pereira, A, Alexandrino, P, Bessa, I, Carretero, Y, Dunner, S, Ferrand, N, Jordana, J, Laloe, D, Moazami-Goudarzi, K, Sánchez, A and Cañon, J 2003. Genetic characterization of Southwestern European Bovine breeds: a historical and biogeographical reassessment with a set of 16 microsatellites. Journal of Heredity 94, 243–250.CrossRefGoogle Scholar
Bellinge, RHS, Liberles, D, Iaschi, SP, O’Brien, P and Tay, GK 2005. Myostatin and its implications on animal breeding: a review. Animal Genetics 36, 1–6.CrossRefGoogle ScholarPubMed
Bennet, DC and Lamoreux, ML 2003. The color loci of mice – a genetic century. Pigment Cell Research 16, 333–344.CrossRefGoogle Scholar
Bongiorni, S, Mancini, G, Chillemi, G, Pariset, L and Valentini, A 2012. Identification of a short region on chromosome 6 affecting direct calving ease in Piedmontese cattle breed. PLoS One 7, 6–12.CrossRefGoogle Scholar
Bram, RJ, Valentine, V, Shaphiro, DN, Jenkins, NA, Gilbert, DJ and Copeland, NG 1996. The gene for calcium-modulating cyclophilin ligand (CAMLG) is located in human chromosome 5q23 and a syntenic region of mouse chromosome 13. Genomics 31, 257–260.CrossRefGoogle Scholar
Browning, SR and Browning, BL 2007. Rapid and accurate haplotype phasing and missing data inference for whole genome association studies by use of localized haplotype clustering. American Journal of Human Genetics 81, 1084–1097.CrossRefGoogle ScholarPubMed
Cañas-Álvarez, JJ, Gónzalez-Rodríguez, A, Martín-Collado, D, Avilés, C, Altarriba, J, Baro, JA, De la Fuente, LF, Diaz, C, Molina, A, Varona, L and Piedrafita, J 2014. Monitoring changes in the demographic and genealogical structure of the main Spanish local beef breeds. Journal of Animal Science 92, 4364–4374.CrossRefGoogle ScholarPubMed
Cañas-Álvarez, JJ, Gónzalez-Rodríguez, A, Munilla, S, Varona, L, Díaz, C, Baro, JA, Altarriba, J, Molina, A and Piedrafita, J 2015. Genetic diversity and divergence among Spanish beef cattle breeds assessed by a bovine high density SNP chip. Journal of Animal Science 93, 5164–5174.CrossRefGoogle ScholarPubMed
Cañas-Álvarez, JJ, Mouresan, EF, Varona, L, Díaz, C, Molina, A, Baro, JA, Altarriba, J, Carabaño, MJ, Casellas, J and Piedrafita, J 2016. Linkage disequilibrium, persistence of phase, and effective population size in Spanish local beef cattle breeds assessed through a high-density single nucleotide polymorphism chip. Journal of Animal Science 94, 2779–2788.CrossRefGoogle ScholarPubMed
Cargnello, M and Roux, PP 2012. Activation and function of the MAPKs and their substrates, the MAPK-activated protein kinases. Microbiology and Molecular Biology Reviews 76, 496–587.CrossRefGoogle Scholar
Chen, H, Shi, S, Acosta, L, Li, W, Lu, J, Bao, S, Chen, Z, Yang, Z, Schneider, MD, Chien, KR, Conway, SJ, Yoder, MC, Haneline, LS, Franco, D and Shou, W 2004. BMP-10 is essential for maintaining cardiac growth during murine cardiogenesis. Development 131, 2219–2231.CrossRefGoogle Scholar
Chen, J, Lai, F and Niswander, L 2012. The ubiquitin ligase mLin41 temporally promotes neural progenitor cells maintenance through FGF signaling. Genes and Development 26, 803–815.CrossRefGoogle ScholarPubMed
Cohen-Zinder, M, Seroussi, E, Larkin, DM, Loor, JJ, Everts-van der Mind, A, Lee, JH, Drackley, JK, Band, MR, Hernández, AG, Shani, M, Lewin, HA, Weller, JI and Ron, M 2005. Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein Cattle. Genome Research 15, 936–944.CrossRefGoogle Scholar
Coppieters, F, Lefever, S, Leroy, BP and De Baere, E 2010. CEP290, a gene with many faces: mutation overview and presentation of CEP290base. Human Mutation 31, 1097–1108.CrossRefGoogle ScholarPubMed
De Boer, M, de Klein, A, Hossle, JP, Seger, R, Corbeel, L, Weening, RS and Roos, D 1992. Cytochrome b(588)-negative, autosomal recessive chronic granulomatous disease: two new mutations in the cytochrome b(588) light chain of the NADPH oxidase (p22-phox). American Journal of Human Genetics 51, 1127–1135.Google Scholar
Dorshorst, B, Henegar, C, Liao, X, Sällman-Almén, M, Rubin, CJ, Ito, S, Wakamatsu, K, Stothard, P, Van Doormaal, B, Plastow, G, Barsh, GS and Andersson, L 2015. Dominant red coat color in Holstein cattle is associated with a missense mutation in the Coatomer protein complex, Subunit Alpha (COPA) gene. PLoS One 10, e0128969.CrossRefGoogle ScholarPubMed
Dunner, S, Miranda, ME, Amigues, Y, Cañon, J, Georges, M, Hanset, R, Williams, J and Ménissier, F 2003. Haplotype diversity of the myostatin gene among beef cattle breeds. Genetics, Selection, Evolution 35, 103–118.CrossRefGoogle ScholarPubMed
Flicek, P, Amode, MR, Barrell, D, Beal, K, Billis, K, Brent, S, Carvalho-Silva, D, Clapham, P, Coates, G, Fitzgerald, S, Gil, L, García-Girón, C, Gordon, L, Hourlier, T, Hunt, S, Johnson, N, Juettemann, T, Kähäri, AK, Keenan, S, Kulesha, E, Martin, FJ, Maurel, T, McLaren, WM, Murphy, DN, Nag, R, Overduin, B, Pignatelli, M, Pritchard, B, Pritchard, E, Riat, HS, Ruffier, M, Sheppard, D, Taylor, K, Thormann, A, Trevanion, SJ, Vullo, A, Wilder, SP, Wilson, M, Zadissa, A, Aken, BL, Birney, E, Cunningham, F, Harrow, J, Herrero, J, Hubbard, TJ, Kinsella, R, Muffato, M, Parker, A, Spudich, G, Yates, A, Zerbino, DR and Searle, SM 2014. Ensembl 2014. Nucleic Acids Research 42, 749–755.CrossRefGoogle ScholarPubMed
Grobet, L, Martin, LJ, Poncelet, D, Pirottin, D, Brouwers, B, Riquet, J, Schoeberlein, A, Dunner, S, Ménissier, F, Massabanda, J, Fries, R and Hanset, RGM 1997. A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle. Nature Genetics 17, 71–74.CrossRefGoogle ScholarPubMed
Gutiérrez-Gil, B, Arranz, JJ and Wiener, P 2015. An interpretive review of selective sweep studies in Bos Taurus cattle populations: identification of unique and shared selection signals across breeds. Frontiers in Genetics 6, 167.Google ScholarPubMed
Karisa, BK, Thomson, J, Wang, Z, Stothard, P, Moore, SS and Plastow, GS 2013. Candidate genes and single nucleotide polymorphisms associated with variation in residual feed intake in beef cattle. Journal of Animal Science 91, 3502–3513.CrossRefGoogle ScholarPubMed
Kasprzyk, A 2011. BioMart: driving a paradigm change in biological data management. Database 2011, 1–3.CrossRefGoogle ScholarPubMed
Kemp, CM, Sensky, PL, Bardsley, RG, Buttery, PJ and Parr, T 2010. Tenderness: an enzymatic view. Meat Science 84, 248–256.CrossRefGoogle ScholarPubMed
Kemper, KE, Saxton, SJ, Bolormaa, S, Hayes, BJ and Goddard, ME 2014. Selection for complex traits leaves little or no classic signatures of selection. BMC Genomics 15, 246.CrossRefGoogle ScholarPubMed
Keyse, SM 2008. Dual-specificity MAP kinase phosphatases (MKPs) and cancer. Cancer and Metastasis Reviews 27, 253–261.CrossRefGoogle ScholarPubMed
Levy, C and Fisher, DE 2011. Dual roles of lineage restricted transcription factors: the case of MIFT in melanocytes. Transcription 2, 19–22.CrossRefGoogle Scholar
Lin, JY and Fisher, DE 2007. Melanocyte biology and skin pigmentation. Nature 445, 843–850.CrossRefGoogle ScholarPubMed
Maltecca, C, Weigel, K, Khatib, H, Cowan, M and Bagnato, A 2009. Whole-genome scan for quantitative trait loci associated with birth weight, gestation length and passive immune transfer in a Holstein×Jersey crossbred population. Animal Genetics 40, 27–34.CrossRefGoogle Scholar
Mastroberardino, L, Spindler, B, Pfeiffer, R, Skelly, PJ, Loffing, J, Shoemaker, CB and Verrey, F 2008. Amino-acid transport by heterodimers of 4F2hc/CD98 and members of a permease family. Nature 17, 288–291.Google Scholar
Panwar, D, Rawal, L, Sehgal, N and Ali, S 2015. Cross Talk between KGF and KITLG proteins implicated with ovarian folliculogenesis in Buffalo Bubalus bubalis . PLoS One 17, e0127993.CrossRefGoogle Scholar
Pauchs, H, Wang, X, Jung, S, Krogmeier, D, Edel, C, Emmerling, R, Götz, KU and Fries, R 2012. Identification of QTL for UV-protective eye area pigmentation in cattle by progeny phenotyping and genome-wide association analysis. PLoS One 7, e36346.Google Scholar
Picardo, M and Cardinali, G 2011. The genetic determination of skin pigmentation: KITLG and KITLG7c-Kit Pathway as key players in the onset of human familiar pigmentary diseases. Journal of Investigative Dermatology 131, 1182–1185.CrossRefGoogle Scholar
Piedrafita, J, Quintanilla, R, Sañudo, C, Olleta, JL, Campo, MM, Panea, B, Renand, G, Turin, F, Jabet, S, Osoro, K, Olivan, MC, Noval, G, García, P, García, MD, Oliver, MA, Gispert, M, Serra, X, Espejo, M, García, S, López, M and Izquierdo, M 2003. Carcass quality of 10 beef cattle breeds of the Southwest of Europe in their typical production systems. Livestock Production Science 82, 1–13.CrossRefGoogle Scholar
Pryce, JE, Hayes, BJ, Bolormaa, S and Goddard, ME 2011. Polymorphic regions affecting human height also control stature in cattle. Genetics 187, 981–984.CrossRefGoogle ScholarPubMed
Purcell, S, Neale, B, Todd-Brown, K, Thomas, L, Ferreira, MA, Bender, D, Maller, J, Sklar, P, de Bakker, PIW, Daly, MJ and Scham, PC 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics 81, 559–575.CrossRefGoogle ScholarPubMed
Qanbari, S and Simianer, H 2014. Mapping signatures of positive selection in the genome of livestock. Livestock Science 116, 133–143.CrossRefGoogle Scholar
Ritchie, JW and Taylor, PM 2001. Role of the System L permease LAT1 in amino acid and iodothyronine transport in placenta. Biochemical Journal 15, 719–725.CrossRefGoogle Scholar
Ron, M, Kliger, D, Feldmesser, E, Seroussi, E, Ezra, E and Weller, JL 2001. Multiple quantitative trait locus analysis of bovine chromosome 6 in the Israeli Holstein population by a daughter design. Genetics 159, 727–735.CrossRefGoogle ScholarPubMed
Rothammer, S, Seichter, D, Förster, M and Medugorac, I 2013. A genome-wide scan for signatures of differential artificial selection in ten cattle breeds. BMC Genomics 14, 908.CrossRefGoogle ScholarPubMed
Saatchi, M, Schnabel, RD, Taylor, JF and Garrick, DJ 2014. Large-effect pleiotropic or closely linked QTL segregate within and across ten US cattle breeds. BMC Genomics 15, 442.CrossRefGoogle ScholarPubMed
Seguchi, O, Takashima, S, Yamazaki, S, Asakura, M, Asano, Y, Shintani, Y, Wakeno, M, Minamino, T, Kondo, H, Furukawa, H, Nakamuru, K, Naito, A, Takahashi, T, Ohtsuka, T, Kawakami, K, Isomura, T, Kitamura, S, Tomoike, H, Mochizuki, N and Kitakaze, M 2007. A cardiac myosin light chain kinase regulates sarcomere assembly in the vertebrate heart. The Journal of Clinical Investigation 117, 2812–2824.CrossRefGoogle ScholarPubMed
Seitz, JJ, Schmutz, SM, Thue, TD and Buchanan, FC 1999. A missense mutation in the bovine MGF gene is associated with the roan phenotype in Belgian Blue and Shorthorn cattle. Mammalian Genome 10, 710–712.CrossRefGoogle ScholarPubMed
Serra, X, Guerrero, L, Guàrdia, MD, Gil, M, Sañudo, C, Panea, B, Campo, MM, Olleta, JL, García-Cachan, MD, Piedrafita, J and Oliver, MA 2008. Eating quality of young bulls from three Spanish beef breed-production systems and its relationships with chemical and instrumental meat quality. Meat Science 79, 98–104.CrossRefGoogle ScholarPubMed
Snelling, WM, Allan, MF, Keele, JW, Kuehn, LA, McDaneld, T, Smith, TPL, Sonstegard, TS, Thallman, RM and Bennett, GL 2010. Genome-wide association study of growth in crossbred beef cattle. Journal of Animal Science 88, 837–848.CrossRefGoogle ScholarPubMed
Stella, A, Ajmone-Marsan, P, Lazzari, B and Boettcher, P 2010. Identification of selection signatures in cattle breeds selected for dairy production. Genetics 185, 1451–1461.CrossRefGoogle ScholarPubMed
Sumimoto, H 2008. Structure, regulation and evolution of Nox-family NADPH oxidases that produce reactive oxygen species. The FEBS Journal 13, 3249–3277.CrossRefGoogle Scholar
Van de Wetering, M, Oostewegel, M, Dooijes, D and Clevers, H 1991. Identification and cloning of TCF-1, a T lymphocyte specific transcription factor containing a sequence-specific HMG box. EMBO Journal 10, 123–132.CrossRefGoogle Scholar
Verrey, F 2003. System L: heteromeric exchangers of large, neutral amino acids involved in directional transport. Pflugers Arch 445, 529–533.CrossRefGoogle ScholarPubMed
Vitalis, R, Gautier, M, Dawson, KJ and Beaumont, M 2014. Detecting and measuring selection from gene frequency data. Genetics 196, 799–817.CrossRefGoogle ScholarPubMed
Weikard, R, Widmann, P, Buitkamp, J, Emmerling, R and Kuehn, C 2012. Revisiting the quantitative trait loci for milk production traits on BTA6. Animal Genetics 43, 318–323.CrossRefGoogle ScholarPubMed
Werth, LA, Hawkins, GA, Eggen, A, Petit, E, Elduque, C, Kreigesmann, B and Bishop, MD 1996. Rapid communication: melanocyte stimulating hormone receptor (MC1R) maps to bovine chromosome 18. Journal of Animal Science 74, 262.CrossRefGoogle ScholarPubMed
Wiener, P and Gutiérrez-Gil, B 2009. Assessment of selection mapping near the myostatin gene (GDF-8) in cattle. Animal Genetics 40, 598–608.CrossRefGoogle ScholarPubMed
Wright, S 1951. The genetical structure of populations. Annals of Eugenics 15, 323–354.CrossRefGoogle ScholarPubMed
Zhao, F, McParland, S, Kearney, F, Du, L and Berry, DP 2015. Detection of selection signatures in dairy and beef cattle using high-density genomic information. Genetics, Selection, Evolution 47, 49.CrossRefGoogle ScholarPubMed