A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds
Abstract Background To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly av...
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| Format: | Article |
| Language: | deu |
| Published: |
BMC
2023-04-01
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| Series: | Genetics Selection Evolution |
| Online Access: | https://doi.org/10.1186/s12711-023-00797-z |
| _version_ | 1797850260863713280 |
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| author | Simone Ceccobelli Vincenzo Landi Gabriele Senczuk Salvatore Mastrangelo Maria Teresa Sardina Slim Ben-Jemaa Christian Persichilli Taki Karsli Valentin-Adrian Bâlteanu María Agustina Raschia Mario Andrés Poli Gabriel Ciappesoni Farai Catherine Muchadeyi Edgar Farai Dzomba Nokuthula Winfred Kunene Gesine Lühken Tatiana Evgenievna Deniskova Arsen Vladimirovich Dotsev Natalia Anatolievna Zinovieva Attila Zsolnai István Anton Szilvia Kusza Nuno Carolino Fátima Santos-Silva Aldona Kawęcka Marcin Świątek Roman Niżnikowski Marija Špehar Gabriel Anaya Antonio Granero Tiago Perloiro Pedro Cardoso Silverio Grande Beatriz López de los Santos Coralie Danchin-Burge Marina Pasquini Amparo Martínez Martínez Juan Vicente Delgado Bermejo Emiliano Lasagna Elena Ciani Francesca Maria Sarti Fabio Pilla |
| author_facet | Simone Ceccobelli Vincenzo Landi Gabriele Senczuk Salvatore Mastrangelo Maria Teresa Sardina Slim Ben-Jemaa Christian Persichilli Taki Karsli Valentin-Adrian Bâlteanu María Agustina Raschia Mario Andrés Poli Gabriel Ciappesoni Farai Catherine Muchadeyi Edgar Farai Dzomba Nokuthula Winfred Kunene Gesine Lühken Tatiana Evgenievna Deniskova Arsen Vladimirovich Dotsev Natalia Anatolievna Zinovieva Attila Zsolnai István Anton Szilvia Kusza Nuno Carolino Fátima Santos-Silva Aldona Kawęcka Marcin Świątek Roman Niżnikowski Marija Špehar Gabriel Anaya Antonio Granero Tiago Perloiro Pedro Cardoso Silverio Grande Beatriz López de los Santos Coralie Danchin-Burge Marina Pasquini Amparo Martínez Martínez Juan Vicente Delgado Bermejo Emiliano Lasagna Elena Ciani Francesca Maria Sarti Fabio Pilla |
| author_sort | Simone Ceccobelli |
| collection | DOAJ |
| description | Abstract Background To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations), XP-EHH (cross-population extended haplotype homozygosity), and runs of homozygosity (ROH) islands were applied to identify genomic variants with potential impact on the adaptability of Merino genetic type in two contrasting climate zones. Results The results indicate that a large part of the Merino’s genetic relatedness and admixture patterns are explained by their genetic background and/or geographic origin, followed by local admixture. Multi-dimensional scaling, Neighbor-Net, Admixture, and TREEMIX analyses consistently provided evidence of the role of Australian, Rambouillet and German strains in the extensive gene introgression into the other Merino and Merino-derived breeds. The close relationship between Iberian Merinos and other South-western European breeds is consistent with the Iberian origin of the Merino genetic type, with traces from previous contributions of other Mediterranean stocks. Using Rsb and XP-EHH approaches, signatures of selection were detected spanning four genomic regions located on Ovis aries chromosomes (OAR) 1, 6 and 16, whereas two genomic regions on OAR6, that partially overlapped with the previous ones, were highlighted by ROH islands. Overall, the three approaches identified 106 candidate genes putatively under selection. Among them, genes related to immune response were identified via the gene interaction network. In addition, several candidate genes were found, such as LEKR1, LCORL, GHR, RBPJ, BMPR1B, PPARGC1A, and PRKAA1, related to morphological, growth and reproductive traits, adaptive thermogenesis, and hypoxia responses. Conclusions To the best of our knowledge, this is the first comprehensive dataset that includes most of the Merino and Merino-derived sheep breeds raised in different regions of the world. The results provide an in-depth picture of the genetic makeup of the current Merino and Merino-derived breeds, highlighting the possible selection pressures associated with the combined effect of anthropic and environmental factors. The study underlines the importance of Merino genetic types as invaluable resources of possible adaptive diversity in the context of the occurring climate changes. |
| first_indexed | 2024-04-09T18:57:31Z |
| format | Article |
| id | doaj.art-ce8e19978e144454af0f21fd16ce3e1d |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-04-09T18:57:31Z |
| publishDate | 2023-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-ce8e19978e144454af0f21fd16ce3e1d2023-04-09T11:06:16ZdeuBMCGenetics Selection Evolution1297-96862023-04-0155111810.1186/s12711-023-00797-zA comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breedsSimone Ceccobelli0Vincenzo Landi1Gabriele Senczuk2Salvatore Mastrangelo3Maria Teresa Sardina4Slim Ben-Jemaa5Christian Persichilli6Taki Karsli7Valentin-Adrian Bâlteanu8María Agustina Raschia9Mario Andrés Poli10Gabriel Ciappesoni11Farai Catherine Muchadeyi12Edgar Farai Dzomba13Nokuthula Winfred Kunene14Gesine Lühken15Tatiana Evgenievna Deniskova16Arsen Vladimirovich Dotsev17Natalia Anatolievna Zinovieva18Attila Zsolnai19István Anton20Szilvia Kusza21Nuno Carolino22Fátima Santos-Silva23Aldona Kawęcka24Marcin Świątek25Roman Niżnikowski26Marija Špehar27Gabriel Anaya28Antonio Granero29Tiago Perloiro30Pedro Cardoso31Silverio Grande32Beatriz López de los Santos33Coralie Danchin-Burge34Marina Pasquini35Amparo Martínez Martínez36Juan Vicente Delgado Bermejo37Emiliano Lasagna38Elena Ciani39Francesca Maria Sarti40Fabio Pilla41Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheDepartment of Veterinary Medicine, University of Bari ‘‘Aldo Moro”Department of Agricultural, Environmental and Food Sciences, University of MoliseDepartment of Agricultural, Food and Forest Sciences, University of PalermoDepartment of Agricultural, Food and Forest Sciences, University of PalermoLaboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de CarthageDepartment of Agricultural, Environmental and Food Sciences, University of MoliseDepartment of Animal Science, Faculty of Agriculture, Eskisehir Osmangazi UniversityLaboratory of Genomics, Biodiversity, Animal Breeding and Molecular Pathology, Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine of Cluj-NapocaInstituto de Genética “Ewald A. Favret”, Instituto Nacional de Tecnología Agropecuaria, CICVyA-CNIAInstituto de Genética “Ewald A. Favret”, Instituto Nacional de Tecnología Agropecuaria, CICVyA-CNIAInstituto Nacional de Investigación AgropecuariaAgricultural Research Council - Biotechnology PlatformDiscipline of Genetics, School of Life Sciences, University of KwaZulu-NatalDepartment of Agriculture, University of ZululandInstitute of Animal Breeding and Genetics, Justus Liebig UniversityL.K. Ernst Federal Research Center for Animal HusbandryL.K. Ernst Federal Research Center for Animal HusbandryL.K. Ernst Federal Research Center for Animal HusbandryDepartment of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life SciencesDepartment of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life SciencesCentre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of DebrecenInstituto Nacional de Investigação Agrária e VeterináriaInstituto Nacional de Investigação Agrária e VeterináriaDepartment of Sheep and Goat Breeding, National Research Institute of Animal ProductionDepartment of Animal Breeding, Institute of Animal Sciences, Warsaw University of Life Sciences-SGGWDepartment of Animal Breeding, Institute of Animal Sciences, Warsaw University of Life Sciences-SGGWCroatian Agency for Agriculture and FoodMERAGEM Group, Department of Genetics, University of CórdobaAsociación Nacional de Criadores de Ganado Merino (ACME)Associação Nacional de Criadores de Ovinos da Raça Merina (ANCORME)Associação de Produtores Agropecuários (OVIBEIRA)Associazione Nazionale della Pastorizia (ASSONAPA)Departamento de Investigación y Desarrollo, EA GROUP SCInstitut de l’ElevageDepartment of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheDepartamento de Genética, Universidad de CórdobaDepartamento de Genética, Universidad de CórdobaDepartment of Agricultural, Food and Environmental Sciences, University of PerugiaDepartment of Bioscience, Biotechnology and Biopharmaceutics, University of Bari “Aldo Moro”Department of Agricultural, Food and Environmental Sciences, University of PerugiaDepartment of Agricultural, Environmental and Food Sciences, University of MoliseAbstract Background To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations), XP-EHH (cross-population extended haplotype homozygosity), and runs of homozygosity (ROH) islands were applied to identify genomic variants with potential impact on the adaptability of Merino genetic type in two contrasting climate zones. Results The results indicate that a large part of the Merino’s genetic relatedness and admixture patterns are explained by their genetic background and/or geographic origin, followed by local admixture. Multi-dimensional scaling, Neighbor-Net, Admixture, and TREEMIX analyses consistently provided evidence of the role of Australian, Rambouillet and German strains in the extensive gene introgression into the other Merino and Merino-derived breeds. The close relationship between Iberian Merinos and other South-western European breeds is consistent with the Iberian origin of the Merino genetic type, with traces from previous contributions of other Mediterranean stocks. Using Rsb and XP-EHH approaches, signatures of selection were detected spanning four genomic regions located on Ovis aries chromosomes (OAR) 1, 6 and 16, whereas two genomic regions on OAR6, that partially overlapped with the previous ones, were highlighted by ROH islands. Overall, the three approaches identified 106 candidate genes putatively under selection. Among them, genes related to immune response were identified via the gene interaction network. In addition, several candidate genes were found, such as LEKR1, LCORL, GHR, RBPJ, BMPR1B, PPARGC1A, and PRKAA1, related to morphological, growth and reproductive traits, adaptive thermogenesis, and hypoxia responses. Conclusions To the best of our knowledge, this is the first comprehensive dataset that includes most of the Merino and Merino-derived sheep breeds raised in different regions of the world. The results provide an in-depth picture of the genetic makeup of the current Merino and Merino-derived breeds, highlighting the possible selection pressures associated with the combined effect of anthropic and environmental factors. The study underlines the importance of Merino genetic types as invaluable resources of possible adaptive diversity in the context of the occurring climate changes.https://doi.org/10.1186/s12711-023-00797-z |
| spellingShingle | Simone Ceccobelli Vincenzo Landi Gabriele Senczuk Salvatore Mastrangelo Maria Teresa Sardina Slim Ben-Jemaa Christian Persichilli Taki Karsli Valentin-Adrian Bâlteanu María Agustina Raschia Mario Andrés Poli Gabriel Ciappesoni Farai Catherine Muchadeyi Edgar Farai Dzomba Nokuthula Winfred Kunene Gesine Lühken Tatiana Evgenievna Deniskova Arsen Vladimirovich Dotsev Natalia Anatolievna Zinovieva Attila Zsolnai István Anton Szilvia Kusza Nuno Carolino Fátima Santos-Silva Aldona Kawęcka Marcin Świątek Roman Niżnikowski Marija Špehar Gabriel Anaya Antonio Granero Tiago Perloiro Pedro Cardoso Silverio Grande Beatriz López de los Santos Coralie Danchin-Burge Marina Pasquini Amparo Martínez Martínez Juan Vicente Delgado Bermejo Emiliano Lasagna Elena Ciani Francesca Maria Sarti Fabio Pilla A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds Genetics Selection Evolution |
| title | A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds |
| title_full | A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds |
| title_fullStr | A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds |
| title_full_unstemmed | A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds |
| title_short | A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds |
| title_sort | comprehensive analysis of the genetic diversity and environmental adaptability in worldwide merino and merino derived sheep breeds |
| url | https://doi.org/10.1186/s12711-023-00797-z |
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