Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip
| Autor: | Marie-José Mercat, Christoph Zimmer, Anisa Ribani, I. Djurkin-Kušec, Danijel Karolyi, Luca Fontanesi, Radomir Savić, Giuseppina Schiavo, Jordi Estellé, Martin Škrlep, Čedomir Radović, María Muñoz, Marjeta Čandek-Potokar, Samuele Bovo, Valerio Joe Utzeri, Ana Isabel Fernández, Juliette Riquet, Maurizio Gallo, José Pedro Araújo, Vladimir Margeta, Cristina Óvilo, Riccardo Bozzi, Fabián García, Juan García-Casco, J.M. Martins, Rui Charneca, Raquel Quintanilla, Oreste Franci, Violeta Razmaite, Yolanda Núñez, J. Tibau |
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| Přispěvatelé: | Producció Animal, Genètica i Millora Animal, Departamento de Mejora Genética Animal, Instituto Nacional de Investigaciones Agronomicas, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Department of Agricultural and Food Sciences, University of Bologna, Kmetijski Institut Slovenije, Partenaires INRAE, Universidade de Évora, Institute of Agrifood Research and Technology (IRTA), University of Osijek, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Bäuerliche Erzeugergemeinschaft Schwäbisch Hall (BESH), Lithuanian University of health Sciences, Centro de Investigação de Montanha [Bragança, Portugal] (CIMO), Instituto Politécnico de Bragança, Faculty of Agriculture, Université nationale du Rwanda, Department of Animal Science, Faculty of Agriculture, University of Ghana, Associazione Nazionale Allevatori Suini, European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), Munoz M., Bozzi R., Garcia-Casco J., Nunez Y., Ribani A., Franci O., Garcia F., Skrlep M., Schiavo G., Bovo S., Utzeri V.J., Charneca R., Martins J.M., Quintanilla R., Tibau J., Margeta V., Djurkin-Kusec I., Mercat M.J., Riquet J., Estelle J., Zimmer C., Razmaite V., Araujo J.P., Radovic C., Savic R., Karolyi D., Gallo M., Candek-Potokar M., Fernandez A.I., Fontanesi L., Ovilo C., Óvilo, C., Università degli Studi di Firenze = University of Florence (UniFI), University of Bologna/Università di Bologna, Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT) |
| Jazyk: | portugalština |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Linkage disequilibrium pig breed genomic diversity SNP chip SNP chips Molecular biology Swine Population genetics [SDV]Life Sciences [q-bio] Sus scrofa lcsh:Medicine Breeding selection signatures Linkage Disequilibrium Effective population size local pig breeds lcsh:Science Oligonucleotide Array Sequence Analysis 2. Zero hunger education.field_of_study Principal Component Analysis Multidisciplinary Genome biology 04 agricultural and veterinary sciences Genomics Breed SNP genotyping Alentejana genomic diversity selection signatures local pig breeds SNPs Phenotype Animals Domestic Pigs SNPs Genotype Population SNP Polymorphism Single Nucleotide Article 03 medical and health sciences Genetic variation Animals Genetic resource [INFO]Computer Science [cs] education Animal breeding Population Density genomics local breeds diversity Genetic diversity [SDV.GEN]Life Sciences [q-bio]/Genetics Genomic diversity lcsh:R 0402 animal and dairy science Genetic Variation Phenotypic trait Selection signature biology.organism_classification 040201 dairy & animal science [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics 030104 developmental biology Genetics Population Evolutionary biology Local breeds lcsh:Q |
| Zdroj: | Scientific Reports IRTA Pubpro. Open Digital Archive Institut de Recerca i Tecnologia Agroalimentàries (IRTA) Scientific Reports, Nature Publishing Group, 2019, 9 (1), ⟨10.1038/s41598-019-49830-6⟩ Scientific Reports, Vol 9, Iss 1, Pp 1-14 (2019) Scientific Reports 1 (9), . (2019) Scientific Reports, 2019, 9 (1), ⟨10.1038/s41598-019-49830-6⟩ Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) Agência para a Sociedade do Conhecimento (UMIC)-FCT-Sociedade da Informação instacron:RCAAP Scientific Reports, London : Nature Publishing Group, 2019, vol. 9, no. 1, 13546, p. 1-14 |
| ISSN: | 2045-2322 |
| DOI: | 10.1038/s41598-019-49830-6⟩ |
| Popis: | Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions. |
| Databáze: | OpenAIRE |
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