Genome-wide assessment of the population structure and genetic diversity of four Portuguese native sheep breeds
As the effects of global warming become increasingly complex and difficult to manage, the conservation and sustainable use of locally adapted sheep breeds are gaining ground. Portuguese native sheep breeds are important reservoirs of genetic diversity, highly adapted to harsh environments and reared...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1109490/full |
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| author | Daniel Gaspar Daniel Gaspar Ana Usié Ana Usié Célia Leão Célia Leão Sílvia Guimarães Ana Elisabete Pires Ana Elisabete Pires Claudino Matos António Marcos Ramos António Marcos Ramos Catarina Ginja |
| author_facet | Daniel Gaspar Daniel Gaspar Ana Usié Ana Usié Célia Leão Célia Leão Sílvia Guimarães Ana Elisabete Pires Ana Elisabete Pires Claudino Matos António Marcos Ramos António Marcos Ramos Catarina Ginja |
| author_sort | Daniel Gaspar |
| collection | DOAJ |
| description | As the effects of global warming become increasingly complex and difficult to manage, the conservation and sustainable use of locally adapted sheep breeds are gaining ground. Portuguese native sheep breeds are important reservoirs of genetic diversity, highly adapted to harsh environments and reared in low input production systems. Genomic data that would describe the breeds in detail and accelerate the selection of more resilient animals to be able to cope with climatic challenges are still lacking. Here, we sequenced the genomes of 37 animals from four Portuguese native sheep breeds (Campaniça, Bordaleira Serra da Estrela, Merino Branco and Merino Preto) and 19 crossbred sheep to make inferences on their genomic diversity and population structure. Mean genomic diversities were very similar across these breeds (.30 ≤ Ho ≤ .34; .30 ≤ He ≤ .35; 1.7 × 10–3 ≤ π ≤ 3.1 × 10–3) and the levels of inbreeding were negligible (.005 ≤ FIS ≤ .038). The Principal Components, Bayesian clustering and Treemix analyses split the Portuguese breeds in two main groups which are consistent with historical records: one comprising Campaniça and Serra da Estrela together with other European and transboundary dairy breeds; and another of the well-differentiated multi-purpose Merino and Merino-related breeds. Runs of homozygosity analyses yielded 1,690 ROH segments covering an average of 2.27 Gb across the genome in all individuals. The overall genome covered by ROH segments varied from 27,75 Mb in Serra da Estrela to 61,29 Mb in Campaniça. The phylogenetic analysis of sheep mitogenomes grouped the Portuguese native breeds within sub-haplogroup B1a along with two animals of the Akkaraman breed from Turkey. This result provides additional support to a direct influence of Southwest Asian sheep in local breeds from the Iberian Peninsula. Our study is a first step pertaining to the genomic characterization of Portuguese sheep breeds and the results emphasize the potential of genomic data as a valid tool to guide conservation efforts in locally adapted sheep breeds. In addition, the genomic data we generated can be used to identify markers for breed assignment and traceability of certified breed-products. |
| first_indexed | 2024-04-10T23:11:23Z |
| format | Article |
| id | doaj.art-a6fe580280564eb4968e8fd6b5425ee4 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-10T23:11:23Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-a6fe580280564eb4968e8fd6b5425ee42023-01-13T05:28:56ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-01-011410.3389/fgene.2023.11094901109490Genome-wide assessment of the population structure and genetic diversity of four Portuguese native sheep breedsDaniel Gaspar0Daniel Gaspar1Ana Usié2Ana Usié3Célia Leão4Célia Leão5Sílvia Guimarães6Ana Elisabete Pires7Ana Elisabete Pires8Claudino Matos9António Marcos Ramos10António Marcos Ramos11Catarina Ginja12Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Beja, PortugalBIOPOIS/CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, PortugalCentro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Beja, PortugalMED—Mediterranean Institute for Agriculture, Environment and Development, Évora, PortugalCentro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Beja, PortugalMED—Mediterranean Institute for Agriculture, Environment and Development, Évora, PortugalBIOPOIS/CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, PortugalBIOPOIS/CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, PortugalFaculdade de Medicina Veterinária, Universidade Lusófona, Lisboa, PortugalACOS—Agricultores do Sul, Beja, PortugalCentro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Beja, PortugalMED—Mediterranean Institute for Agriculture, Environment and Development, Évora, PortugalBIOPOIS/CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, PortugalAs the effects of global warming become increasingly complex and difficult to manage, the conservation and sustainable use of locally adapted sheep breeds are gaining ground. Portuguese native sheep breeds are important reservoirs of genetic diversity, highly adapted to harsh environments and reared in low input production systems. Genomic data that would describe the breeds in detail and accelerate the selection of more resilient animals to be able to cope with climatic challenges are still lacking. Here, we sequenced the genomes of 37 animals from four Portuguese native sheep breeds (Campaniça, Bordaleira Serra da Estrela, Merino Branco and Merino Preto) and 19 crossbred sheep to make inferences on their genomic diversity and population structure. Mean genomic diversities were very similar across these breeds (.30 ≤ Ho ≤ .34; .30 ≤ He ≤ .35; 1.7 × 10–3 ≤ π ≤ 3.1 × 10–3) and the levels of inbreeding were negligible (.005 ≤ FIS ≤ .038). The Principal Components, Bayesian clustering and Treemix analyses split the Portuguese breeds in two main groups which are consistent with historical records: one comprising Campaniça and Serra da Estrela together with other European and transboundary dairy breeds; and another of the well-differentiated multi-purpose Merino and Merino-related breeds. Runs of homozygosity analyses yielded 1,690 ROH segments covering an average of 2.27 Gb across the genome in all individuals. The overall genome covered by ROH segments varied from 27,75 Mb in Serra da Estrela to 61,29 Mb in Campaniça. The phylogenetic analysis of sheep mitogenomes grouped the Portuguese native breeds within sub-haplogroup B1a along with two animals of the Akkaraman breed from Turkey. This result provides additional support to a direct influence of Southwest Asian sheep in local breeds from the Iberian Peninsula. Our study is a first step pertaining to the genomic characterization of Portuguese sheep breeds and the results emphasize the potential of genomic data as a valid tool to guide conservation efforts in locally adapted sheep breeds. In addition, the genomic data we generated can be used to identify markers for breed assignment and traceability of certified breed-products.https://www.frontiersin.org/articles/10.3389/fgene.2023.1109490/fullOvis arieshigh-throughput sequencingpopulation structuregenomic diversitysingle nucleotide polymorphismnative breeds |
| spellingShingle | Daniel Gaspar Daniel Gaspar Ana Usié Ana Usié Célia Leão Célia Leão Sílvia Guimarães Ana Elisabete Pires Ana Elisabete Pires Claudino Matos António Marcos Ramos António Marcos Ramos Catarina Ginja Genome-wide assessment of the population structure and genetic diversity of four Portuguese native sheep breeds Frontiers in Genetics Ovis aries high-throughput sequencing population structure genomic diversity single nucleotide polymorphism native breeds |
| title | Genome-wide assessment of the population structure and genetic diversity of four Portuguese native sheep breeds |
| title_full | Genome-wide assessment of the population structure and genetic diversity of four Portuguese native sheep breeds |
| title_fullStr | Genome-wide assessment of the population structure and genetic diversity of four Portuguese native sheep breeds |
| title_full_unstemmed | Genome-wide assessment of the population structure and genetic diversity of four Portuguese native sheep breeds |
| title_short | Genome-wide assessment of the population structure and genetic diversity of four Portuguese native sheep breeds |
| title_sort | genome wide assessment of the population structure and genetic diversity of four portuguese native sheep breeds |
| topic | Ovis aries high-throughput sequencing population structure genomic diversity single nucleotide polymorphism native breeds |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1109490/full |
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