Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms
Wallachian and Sumava sheep are autochthonous breeds that have undergone a significant bottleneck effect and subsequent restoration efforts. The first objective of this study was to evaluate the degree of genetic variability of both breeds and, therefore, the current management of the breeding. The...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Animal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1751731122002476 |
| _version_ | 1828054125635436544 |
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| author | Karolína Machová Héctor Marina Juan Jose Arranz Rocío Pelayo Jana Rychtářová Michal Milerski Luboš Vostrý Aroa Suárez-Vega |
| author_facet | Karolína Machová Héctor Marina Juan Jose Arranz Rocío Pelayo Jana Rychtářová Michal Milerski Luboš Vostrý Aroa Suárez-Vega |
| author_sort | Karolína Machová |
| collection | DOAJ |
| description | Wallachian and Sumava sheep are autochthonous breeds that have undergone a significant bottleneck effect and subsequent restoration efforts. The first objective of this study was to evaluate the degree of genetic variability of both breeds and, therefore, the current management of the breeding. The second was to determine whether these two breeds still retain their genetic uniqueness in relation to each other and other breeds, despite regenerative interventions. Our data consisted of 48 individuals of Sumava and 37 individuals of Wallachian sheep. The comparison data contained 25 other breeds (primarily European) from the HapMap dataset generated by the International Sheep Genomics Consortium. When comparing all 27 breeds, the Czech breeds clustered with 15 other breeds and formed a single branch with them according to Nei's distances. At the same time, however, the clusters of both breeds were integral and easily distinguishable from the others when displayed with principal component analysis (PCA). Population substructure analysis did not show any common genetic ancestry of the Czech national breeds and breeds used for regeneration or, eventually, breeds whose ancestral population was used for regeneration. The average values of FST were higher in Wallachian sheep (FST = 0.14) than in Sumava sheep (FST = 0.08). The linkage disequilibrium (LD) extension per autosome was higher in Wallachian than in Sumava sheep. Consequently, the Ne estimates five generations ago were 68 for Sumava versus 34 for Wallachian sheep. Both native Czech breeds exhibit a wide range of inbreeding based on the excess of homozygosity (FHOM) among individuals, from −0.04 to 0.16 in Sumava and from −0.13 to 0.12 in Wallachian. Average inbreeding based on runs of homozygosity was 0.21 in Sumava and 0.27 in Wallachian. Most detected runs of homozygosity (ROH) were less than 5 Mb long for both breeds. ROH segments longer than 15 Mb were absent in Wallachian sheep. Concerning putative selection signatures, a total of 471 candidate genes in Wallachian sheep within 11 hotspots and 653 genes within 13 hotspots in Sumava sheep were identified. Czech breeds appear to be well differentiated from each other and other European breeds. Their genetic diversity is low, especially in the case of the Wallachian breed. Sumava is not so threatened by low diversity but has a larger share of the non-native gene pool. |
| first_indexed | 2024-04-10T20:17:53Z |
| format | Article |
| id | doaj.art-88c18274e5f94ffb9c3a431a4d12936c |
| institution | Directory Open Access Journal |
| issn | 1751-7311 |
| language | English |
| last_indexed | 2024-04-10T20:17:53Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Animal |
| spelling | doaj.art-88c18274e5f94ffb9c3a431a4d12936c2023-01-26T04:44:48ZengElsevierAnimal1751-73112023-01-01171100690Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphismsKarolína Machová0Héctor Marina1Juan Jose Arranz2Rocío Pelayo3Jana Rychtářová4Michal Milerski5Luboš Vostrý6Aroa Suárez-Vega7Department of Genetics and Breeding, Czech University of Life Sciences (CZU), Prague, Czech Republic, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, 165 00 Praha, Suchdol, Czech Republic; Corresponding author.Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, SpainDepartment of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, SpainDepartment of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, SpainInstitute of Animal Science, Prague, Czech republic, Přátelství 815, 104 00 Praha, Uhříněves, Czech RepublicInstitute of Animal Science, Prague, Czech republic, Přátelství 815, 104 00 Praha, Uhříněves, Czech RepublicDepartment of Genetics and Breeding, Czech University of Life Sciences (CZU), Prague, Czech Republic, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, 165 00 Praha, Suchdol, Czech RepublicDepartment of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, SpainWallachian and Sumava sheep are autochthonous breeds that have undergone a significant bottleneck effect and subsequent restoration efforts. The first objective of this study was to evaluate the degree of genetic variability of both breeds and, therefore, the current management of the breeding. The second was to determine whether these two breeds still retain their genetic uniqueness in relation to each other and other breeds, despite regenerative interventions. Our data consisted of 48 individuals of Sumava and 37 individuals of Wallachian sheep. The comparison data contained 25 other breeds (primarily European) from the HapMap dataset generated by the International Sheep Genomics Consortium. When comparing all 27 breeds, the Czech breeds clustered with 15 other breeds and formed a single branch with them according to Nei's distances. At the same time, however, the clusters of both breeds were integral and easily distinguishable from the others when displayed with principal component analysis (PCA). Population substructure analysis did not show any common genetic ancestry of the Czech national breeds and breeds used for regeneration or, eventually, breeds whose ancestral population was used for regeneration. The average values of FST were higher in Wallachian sheep (FST = 0.14) than in Sumava sheep (FST = 0.08). The linkage disequilibrium (LD) extension per autosome was higher in Wallachian than in Sumava sheep. Consequently, the Ne estimates five generations ago were 68 for Sumava versus 34 for Wallachian sheep. Both native Czech breeds exhibit a wide range of inbreeding based on the excess of homozygosity (FHOM) among individuals, from −0.04 to 0.16 in Sumava and from −0.13 to 0.12 in Wallachian. Average inbreeding based on runs of homozygosity was 0.21 in Sumava and 0.27 in Wallachian. Most detected runs of homozygosity (ROH) were less than 5 Mb long for both breeds. ROH segments longer than 15 Mb were absent in Wallachian sheep. Concerning putative selection signatures, a total of 471 candidate genes in Wallachian sheep within 11 hotspots and 653 genes within 13 hotspots in Sumava sheep were identified. Czech breeds appear to be well differentiated from each other and other European breeds. Their genetic diversity is low, especially in the case of the Wallachian breed. Sumava is not so threatened by low diversity but has a larger share of the non-native gene pool.http://www.sciencedirect.com/science/article/pii/S1751731122002476Domestic sheepGenetic variabilityInbreedingIndigenous breedsPopulation structure |
| spellingShingle | Karolína Machová Héctor Marina Juan Jose Arranz Rocío Pelayo Jana Rychtářová Michal Milerski Luboš Vostrý Aroa Suárez-Vega Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms Animal Domestic sheep Genetic variability Inbreeding Indigenous breeds Population structure |
| title | Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms |
| title_full | Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms |
| title_fullStr | Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms |
| title_full_unstemmed | Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms |
| title_short | Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms |
| title_sort | genetic diversity of two native sheep breeds by genome wide analysis of single nucleotide polymorphisms |
| topic | Domestic sheep Genetic variability Inbreeding Indigenous breeds Population structure |
| url | http://www.sciencedirect.com/science/article/pii/S1751731122002476 |
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