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Consequences of Breed Formation on Patterns of Genomic Diversity and Differentiation: the Case of Highly Diverse Peripheral Iberian Cattle Rute R
da Fonseca et al. BMC Genomics (2019) 20:334 https://doi.org/10.1186/s12864-019-5685-2 RESEARCH ARTICLE Open Access Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle Rute R. da Fonseca1,2* , Irene Ureña3, Sandra Afonso3, Ana Elisabete Pires3,4, Emil Jørsboe2, Lounès Chikhi5,6 and Catarina Ginja3* Abstract Background: Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier admixture events in the observed diversity patterns. Results: We sequenced 48 genomes belonging to eight Iberian native breeds and found that the individual breeds are genetically very distinct with FST values ranging from 4 to 16% and have levels of nucleotide diversity similar or larger than those of their European counterparts, namely Jersey and Holstein. All eight breeds display significant gene flow or admixture from African taurine cattle and include mtDNA and Y-chromosome haplotypes from multiple origins. Furthermore, we detected a very low differentiation of chromosome X relative to autosomes within all analyzed taurine breeds, potentially reflecting male-biased gene flow. Conclusions: Our results show that an overall complex history of admixture resulted in unexpectedly high levels of genomic diversity for breeds with seemingly limited geographic ranges that are distantly located from the main domestication center for taurine cattle in the Near East. This is likely to result from a combination of trading traditions and breeding practices in Mediterranean countries. -
Supplementary Information
Supplementary information Supplementary Notes ......................................................................................................................... 2 Supplementary Tables ........................................................................................................................ 7 Supplementary Figures ..................................................................................................................... 13 References ........................................................................................................................................ 20 1 Supplementary notes Note S1. Brief description of the Iberian native cattle breeds sampled in our study The Barrosã cattle are one of the most emblematic of the Iberian Peninsula with their magnificent lyre‐shaped horns and short face. These cattle can be found grazing in the highlands of northwestern Portugal in a collectively managed herding system named ‘vezeira’. They are medium‐sized animals, with concave profile and brown‐blond coat colour. There is marked sexual dimorphism and the males are much darker particularly in the neck and have a characteristic dark ring around the eyes. The herdbook was established in 1985 and is managed by the breeders’ association AMIBA (http://www.amiba.pt). The certified protected designation of origin (PDO) meat ‘Carne Barrosã’ is highly valued due to the intramuscular fat content and large numbers of live Barrosã cattle were exported to England from Oporto in the mid‐19th century until 1920. The milk -
Meta-Analysis of Mitochondrial DNA Reveals Several Population
Table S1. Haplogroup distributions represented in Figure 1. N: number of sequences; J: banteng, Bali cattle (Bos javanicus ); G: yak (Bos grunniens ). Other haplogroup codes are as defined previously [1,2], but T combines T, T1’2’3’ and T5 [2] while the T1 count does not include T1a1c1 haplotypes. T1 corresponds to T1a defined by [2] (16050T, 16133C), but 16050C–16133C sequences in populations with a high T1 and a low T frequency were scored as T1 with a 16050C back mutation. Frequencies of I are only given if I1 and I2 have not been differentiated. Average haplogroup percentages were based on balanced representations of breeds. Country, Region Percentages per Haplogroup N Reference Breed(s) T T1 T1c1a1 T2 T3 T4 I1 I2 I J G Europe Russia 58 3.4 96.6 [3] Yaroslavl Istoben Kholmogory Pechora type Red Gorbatov Suksun Yurino Ukrain 18 16.7 72.2 11.1 [3] Ukrainian Whiteheaded Ukrainian Grey Estonia, Byelorussia 12 100 [3] Estonian native Byelorussia Red Finland 31 3.2 96.8 [3] Eastern Finncattle Northern Finncattle Western Finncattle Sweden 38 100.0 [3] Bohus Poll Fjall cattle Ringamala Cattle Swedish Mountain Cattle Swedish Red Polled Swedish Red-and-White Vane Cattle Norway 44 2.3 0.0 0.0 0.0 97.7 [1,4] Blacksided Trondheim Norwegian Telemark Westland Fjord Westland Red Polled Table S1. Cont. Country, Region Percentages per Haplogroup N Reference Breed(s) T T1 T1c1a1 T2 T3 T4 I1 I2 I J G Iceland 12 100.0 [1] Icelandic Denmark 32 100.0 [3] Danish Red (old type) Jutland breed Britain 108 4.2 1.2 94.6 [1,5,6] Angus Galloway Highland Kerry Hereford Jersey White Park Lowland Black-Pied 25 12.0 88.0 [1,4] Holstein-Friesian German Black-Pied C Europe 141 3.5 4.3 92.2 [1,4,7] Simmental Evolene Raetian Grey Swiss Brown Valdostana Pezzata Rossa Tarina Bruna Grey Alpine France 98 1.4 6.6 92.0 [1,4,8] Charolais Limousin Blonde d’Aquitaine Gascon 82.57 Northern Spain 25 4 13.4 [8,9] 1 Albera Alistana Asturia Montana Monchina Pirenaica Pallaresa Rubia Gallega Southern Spain 638 0.1 10.9 3.1 1.9 84.0 [5,8–11] Avileña Berrenda colorado Berrenda negro Cardena Andaluzia Table S1. -
Redalyc.Growth Hormone Alui Polymorphism Analysis in Eight
Archivos de Zootecnia ISSN: 0004-0592 [email protected] Universidad de Córdoba España Reis, C.; Navas, D.; Pereira, M.; Cravador, A. Growth hormone alui polymorphism analysis in eight portuguese bovine breeds. Archivos de Zootecnia, vol. 50, núm. 190, 2001, pp. 41-48 Universidad de Córdoba Córdoba, España Available in: http://www.redalyc.org/articulo.oa?id=49519007 How to cite Complete issue Scientific Information System More information about this article Network of Scientific Journals from Latin America, the Caribbean, Spain and Portugal Journal's homepage in redalyc.org Non-profit academic project, developed under the open access initiative GROWTH HORMONE ALUI POLYMORPHISM ANALYSIS IN EIGHT PORTUGUESE BOVINE BREEDS ANçLISIS DEL POLIMORFISMO ALUI DE LA HORMONA DE CRECIMENTO EN OCHO RAZAS BOVINAS PORTUGUESAS Reis, C.1, D. Navas2, M. Pereira3 and A. Cravador1 1Universidade do Algarve. UCTA. Campus de Gambelas. 8000-810 Faro. Portugal. E-mail: [email protected] / [email protected] 2Esta•‹o ZootŽcnica Nacional, Departamento de Bovinicultura. Fonte Boa. 2000-763 Vale de SantarŽm. Portugal. E-mail: [email protected] 3Esta•‹o ZootŽcnica Nacional. Departamento de Ovinicultura. Fonte Boa. 2000-763 Vale de SantarŽm. Portugal. E-mail: [email protected] ADDITIONAL KEYWORDS PALABRAS CLAVE ADICIONALES Somatotropin. Polymorphism. Meat production. Somatotropina. Polimorfismo. Producci—n de car- PCR-RFLP. ne. PCR-RFLP. SUMMARY RESUMEN A total of 195 bulls of eight Portuguese beef Un total de 195 bovinos pertenecientes a cattle breeds (Alentejana, Arouquesa, Barros‹, ocho razas productoras de carne portuguesas Maronesa, Marinhoa, Mertolenga, Mirandesa (Alentejana, Arouquesa, Barros‹, Maronesa, and Preta) were genotyped for the GH AluI Marinhoa, Mertolenga, Mirandesa y Preta) fue- polymorphism by the polymerase chain reaction ron genotipados utilizando PCR-RFLP para el and restriction length polymorphism (PCR- polimorfismo CH AluI. -
Caracterização Morfológica Da População Bovina Jarmelista
DGV Direcção Geral de Veterinária CARACTERIZAÇÃO MORFOLÓGICA DA POPULAÇÃO BOVINA JARMELISTA Fevereiro 2006 A POPULAÇÃO BOVINA JARMELISTA CARACTERIZAÇÃO MORFOLÓGICA DA POPULAÇÃO BOVINA JARMELISTA Protocolo de colaboração: Junho de 2004 Instituições Participantes Direcção Geral de Veterinária (DGV) Direcção Regional de Agricultura da Beira Interior (DRABI) Instituto Nacional de Investigação Agrária e das Pescas / Estação Zootécnica Nacional / Estação Nacional de Melhoramento de Plantas (INIA/EZN/) Associação de Criadores de Ruminantes do Concelho da Guarda (ACRIGUARDA) Equipa técnica: Maria de Fátima Sobral (DGV) Carmen Roberto (INIA/EZN) Dolores Navas (INIA/ ENMP) José Manuel Nunes (ACRIGUARDA) Paulo Poço (ACRIGUARDA) Sabina Mónica Duarte (ACRIGUARDA) i A POPULAÇÃO BOVINA JARMELISTA RESUMO DOS TRABALHOS DESENVOLVIDOS Foi efectuada a inventariação e identificação da população bovina Jarmelista através da identificação dos criadores e explorações, determinação do tamanho da população, distribuição etária, proporção entre sexos e recolha da informação disponível sobre a origem e genealogia do efectivo. Foi analisada a diversidade morfológica de trinta e nove fêmeas Mirandesas e de todos os animais identificados como Jarmelistas num total de vinte e quatro fêmeas e dois machos. Para a caracterização morfológica foram utilizados 185 caracteres morfológicos para as fêmeas e 170 caracteres para os machos recorrendo aos métodos de análise de dados/taxonomia numérica. Os resultados obtidos neste estudo, foram analisados em conjunto com resultados anteriormente obtidos para cinco raças bovinas autóctones de fêmeas da região Sul de Portugal - Algarvia (AG), Alentejana (AL), Garvonesa (GA), Mertolenga (ME), Preta (PR) - e doze raças autóctones de machos: Algarvia, Alentejana, Arouquesa (AR), Barrosã (BA), Cachena (CA), Garvonesa, Marinhoa (MA), Maronesa (MO), Mertolenga, Minhota (MN), Mirandesa (MI) e Preta. -
RSI December 2012 Volume IV Number 2
2 H.A.R.S. - RSI J – ΚΠΕ - R ICR – ZRW Editorial Board 2011 – 2012 The Board of the HELLENIC Regional Science Inquiry Journal PROFESSOR PANAGIOTIS LIARGOVAS Department of Economics ASSOCIATION OF REGIONAL University of Peloponnese, Greece SCIENTISTS H.A.R.S. 2011-2012 Managing Editor PROFESSOR THEODORE PELAGIDIS PROFESSOR MARIA GIAOUTZI [H.A.R.S. is a Think Tank of groups of people with Department of Maritime Studies Department of Rural and Surveying Engineering, National multidisciplinary work in the fields of Regional Science, University of Piraeus, Greece Technical which occurs with the selfless contribution of University of Athens, Greece participants who offer their work to the global scientific PROFESSOR EFSTATHIOS TSACHALIDIS community] Department of Forestry and Environmental Hon. Managing Editor Management Democritus University of Thrace, President and Chair, Journals Management Greece PROFESSOR PETER NIJKAMP Committee (RSI J – ΚΠΕ - R ICR – ZRW) Free University Faculty of Economics and Business PROFESSOR MOH’D AHMAD AL-NIMR Administration, Department of Spatial Economics Mechanical Engineering Department Dr Christos Ladias Amsterdam, the Netherlands Jordan University of Science and Technology, Irbid – Jordan Legal Committee Editors PROFESSOR IOANNIS MAZIS Lukas Apostolidis, Associate Professor Dimitrios PROFESSOR IOANNIS MOURMOURIS Department of Turkish and Modern Asian Studies Panagiotopoulos, Assistant Professor Panagiotis Department of International Economic Relations and National and Kapodistrian Kribas, Dr Leandros Lefakis, -
Consequences of Breed Formation on Patterns of Genomic Diversity and Differentiation: the Case of Highly Diverse Peripheral Iberian Cattle Rute R
da Fonseca et al. BMC Genomics (2019) 20:334 https://doi.org/10.1186/s12864-019-5685-2 RESEARCHARTICLE Open Access Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle Rute R. da Fonseca1,2* , Irene Ureña3, Sandra Afonso3, Ana Elisabete Pires3,4, Emil Jørsboe2, Lounès Chikhi5,6 and Catarina Ginja3* Abstract Background: Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier admixture events in the observed diversity patterns. Results: We sequenced 48 genomes belonging to eight Iberian native breeds and found that the individual breeds are genetically very distinct with FST values ranging from 4 to 16% and have levels of nucleotide diversity similar or larger than those of their European counterparts, namely Jersey and Holstein. All eight breeds display significant gene flow or admixture from African taurine cattle and include mtDNA and Y-chromosome haplotypes from multiple origins. Furthermore, we detected a very low differentiation of chromosome X relative to autosomes within all analyzed taurine breeds, potentially reflecting male-biased gene flow. Conclusions: Our results show that an overall complex history of admixture resulted in unexpectedly high levels of genomic diversity for breeds with seemingly limited geographic ranges that are distantly located from the main domestication center for taurine cattle in the Near East. This is likely to result from a combination of trading traditions and breeding practices in Mediterranean countries. -
Contraste Leiteiro Nos Pequenos Ruminantes
Ações de Conservação e Melhoramento dos RGAn em Portugal Nuno Carolino [email protected] XXXVII Reunião de Primavera da SPPF “Pastagens, Forragens e Raças Autóctones” N.Carolino Serpa, 29 e 30 de abril de 2016 1/ 27 PORTUGAL Área Territorial: 91 000 km2 Habitantes: 10 341 974 PIB: 179 409 Milh € http://www.pordata.pt/Portugal 51 Raças Autóctones (bovinos, ovinos, caprinos, suínos, galinhas e equídeos) + 11 Raças Autóctones de Cães N.Carolino 2/ 45 Biodiversidade dos Países Mediterrâneos Uma das 25 regiões do mundo com a categoria de “hotspots” de la biodiversidade Cincotta et al., 2000. Nature 404, 990-992 (27 April 2000) N.Carolino 3/ 45 51 Iberos Celtas Celtiberos Lusitanos Fenícios Clima Gregos Cartagineses Romanos Solos Alanos Vândalos Estrutura fundiária Suevos visigodos Aspetos culturais e Tradições Muçulmanos Localização geográfica N.Carolino 4/ 45 Acontecimentos Relevantes / Programas Nacionais 1990 1991 Convenção para a Diversidade Biológica 1992 NOVAGRI (CBD – Convenção do Rio) 1993 1994 1995 1996 1997 PAMAF 1998 1999 2000 2001 2002 2003 AGRO 1º Relatório Mundial sobre o Estado dos RGAn 2004 Relatório Nacional sobre o Estado dos RGAn 2005 2006 Plano Global de Ação para os RGAn da FAO 2007 Declaração de Interlaken 2008 2009 2010 PRODER 2011 2012 Plano Nacional para os Recursos Genéticos 2013 Animais 2014 2015 ↓ 2020 N.Carolino 5/ 45 Ações de Conservação e Melhoramento nas Raças Autóctones Década de 90 ...................................... A defesa e melhoramento do património genético animal é uma prioridade ! (NOVAGRI, PAMAF, AGRO, PRODER, PDR2020) Transferência de funções para as Ass. de Criadores . Gestão dos LG/RZ e dos Programas de Conservação/Melhoramento Programas de Conservação \Melhoramento aprovados pelos Serv. -
Extensive Beef Cattle Production in Portugal: the Added Value of Indigenous Breeds in the Beef Market Rodrigues, A.M., Pinto De Andrade, L
Extensive beef cattle production in Portugal: the added value of indigenous breeds in the beef market Rodrigues, A.M., Pinto de Andrade, L. & Várzea Rodrigues, J. Escola Superior Agrária de Castelo Branco, Quinta da Srª de Mércules, 6000 Castelo Branco, Portugal Summary Beef production in less-favoured areas in Portugal is usually extensive, and along with forestry and agriculture is one of the main sources of income and employment. It has also an important role both in a social and environmental context. Portugal is not self-sufficient in beef pro- duction, though the BSE crisis has severely hit beef sales, and it is difficult to envisage consumption making a full recovery in the short to medium term. However, it is possible to see an emergent market for beef produced by Portuguese indigenous breeds from extensive production systems. Beef from indigenous breeds is considered to be a high quality product by producers and consumers, mainly because of the superior taste and structure of the meat resulting from the production methods: differences within breeds, slow growth rate and type of vegetation con- sumed. This product differentiation has allowed the enlargement of small niche markets and has led to an increase in the value of meat with a Protected Designation of Origin (PDO). The specificity of a product linked with a PDO has a fundamental role in the establishment of the strategies for agricultural enterprises and in rural development. Since Portuguese agriculture cannot compete on quantity or production cost with other competitors, differentiation and quality seem to be the alternatives that may stimulate rural activities in LFAs and create a regional added value able to contribute to sustainable development. -
6 H Portugal Presentation..Ppt [Mode De Compatibilité]
Meeting of the ERFP WG "Ex situ 19/06/2019 conservation" Portuguese Animal Germplasm Bank animal genetic resources Rosa Lino Neto Pereira Unit of Biotechnology and Genetic Resources Estação Zootécnica Nacional, Santarém Portugal [email protected] ERFP the Ex situ Working Group - Madrid 2019 May Portugal has a rich and diverse animal genetic heritage with 62 autochthonous Burro de Miranda breeds Bisaro Several of the Pedrês domestic animal Garrano 62 Preta de Montesinho autochthonous Serra da Estrela breeds of Portugal Jarmelista Malhado de Alcobaça are currently in an Barbado da Terceira endangered status Churra do Campo Garvonesa Barrocal Algarvio Madrid, May 22nd 2019 1 Meeting of the ERFP WG "Ex situ 19/06/2019 conservation" North Portuguese Animal Center Germplasm Bank South ERFP the Ex situ Working Group - Madrid 2019 May Semen Cattle Sheep Goats Alentejana Bordaleira ED Algarvia Algarvia Minho Bravia Embryos Arouquesa Campaniça Charnequeira Barrosã Churra Algarvia Preta de Breed N♀ Total Brava Churra Badana Montesinho Ch Galega 6 20 Cachena Churra do Campo Serpentina Mirandesa Garvonesa Churra do Minho Serrana (3 Jarmelista Chur G Mirandesa ecotipos) Mer Prta 29 161 Marinhoa ChuG Brangançana 6 breeds, 59 Algarvia 7 41 Maronesa Merina Branca animais, 12588 Serpentina 14 93 Mertolenga Merina da Beira doses Minhota Baixa Bravia 2 10 Mirandesa Merina Preta Serrana 4 41 Preta Mondegueira Alentejana 10 51 Ramo Grande Saloia Pigs and Brava Serra da Estrela Mertolenga 2 9 horses Ovarian tissue 15 breeds, 235 14 breeds, 92 1 breed each animals, 175 834 animals, 12842 Algarvia 3 6 ov doses dosesadapt Horta et al. -
Genetic Diversity, Structure, and Breed Relationships in Iberian Cattle I
Genetic diversity, structure, and breed relationships in Iberian cattle I. Martín-Burriel, C. Rodellar, J. Cañón, O. Cortés, S. Dunner, V. Landi, A. Martínez-Martínez, L. T. Gama, C. Ginja, M. C. T. Penedo, A. Sanz, P. Zaragoza and J. V. Delgado J ANIM SCI 2011, 89:893-906. doi: 10.2527/jas.2010-3338 The online version of this article, along with updated information and services, is located on the World Wide Web at: http://jas.fass.org/content/89/4/893 www.asas.org Downloaded from jas.fass.org by James Rohl on January 3, 2012 Genetic diversity, structure, and breed relationships in Iberian cattle1 I. Martín-Burriel,*2 C. Rodellar,* J. Cañón,† O. Cortés,† S. Dunner,† V. Landi,‡ A. Martínez-Martínez,‡ L. T. Gama,§ C. Ginja,§# M. C. T. Penedo,# A. Sanz,* P. Zaragoza,* and J. V. Delgado‡ *Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain; †Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; ‡Departamento de Genética, Universidad de Córdoba, Campus Rabanales C-5, 14071 Córdoba, Spain; §L-INIA, Instituto Nacional dos Recursos Biológicos, 2005-048 Vale de Santarém, Portugal; and #University of California, Veterinary Genetics Laboratory, One Shields Avenue, Davis 95616 ABSTRACT: In Iberia there are 51 officially recog- de Lide), 3 breeds (Berrenda en Negro, Negra An- nized cattle breeds of which 15 are found in Portu- daluza, and Mertolenga) were divided in 2 independent gal and 38 in Spain. We present here a comprehensive clusters each, and 2 breeds were considered admixed analysis of the genetic diversity and structure of Ibe- (Asturiana de los Valles and Berrenda en Colorado). -
Origins and Genetic Diversity of New World Creole Cattle: Inferences from Mitochondrial and Y Chromosome Polymorphisms
doi:10.1111/j.1365-2052.2009.01976.x Origins and genetic diversity of New World Creole cattle: inferences from mitochondrial and Y chromosome polymorphisms C. Ginja*, M. C. T. Penedo†, L. Melucci‡, J. Quiroz§, O. R. Martı´nez Lo´ pez¶, M. A. Revidatti**, A. Martı´nez-Martı´nez††, J. V. Delgado‡‡ and L. T. Gama§§ *Veterinary Genetics Laboratory, University of California, One Shields Avenue, Davis, CA 95616, USA; Instituto Superior de Agronomia, Lisboa, Portugal; Departamento de Gene´ tica e Melhoramento Animal, Instituto Nacional dos Recursos Biolo´ gicos, Fonte Boa, 2005-048 Vale de Santare´ m, Portugal. †Veterinary Genetics Laboratory, University of California, One Shields Avenue, Davis, CA 95616, USA. ‡Facultad Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina; Estacio´ n Experimental Agropecuaria Balcarce, Instituto Nacional de Tecnologı´a Agropecuaria, Balcarce, Argentina. §Instituto Nacional de Investigaciones Forestales, Agrı´colas y Pecuarias, Me´ xico. ¶Departamento de Produccio´ n Animal, Facultad de Ciencias Agrarias, Universidad Nacional de Asuncio´ n, San Lorenzo, Paraguay; PDIZ, Universidade Federal Rural de Pernambuco, Pernambuco, Brazil. **Universidad Nacional del Nordeste, Corrientes, Argentina. ††Departamento de Gene´ tica, Universidad de Co´ rdoba, Campus Rabanales C-5 14071, Co´ rdoba, Spain. ‡‡Departamento de Gene´ tica, Universidad de Co´ rdoba, Campus Rabanales C-5 14071, Co´ rdoba, Spain. §§Departamento de Gene´ tica e Melhoramento Animal, Instituto Nacional dos Recursos Biolo´ gicos, Fonte Boa, 2005-048 Vale de Santare´ m, Portugal Summary The ancestry of New World cattle was investigated through the analysis of mitochondrial and Y chromosome variation in Creoles from Argentina, Brazil, Mexico, Paraguay and the United States of America.