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SNP genotypes reveal breed substructure, selection signatures and highly inbred regions in Piétrain pigs
The Piétrain pig originates from the Belgian village Piétrain some time between 1920 and 1950. Owing to its superior conformation, the Piétrain has spread worldwide since the 1960s. As initial population sizes were limited and close inbreeding was commonplace, the breed’s genetic diversity has been...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7003864/ https://www.ncbi.nlm.nih.gov/pubmed/31809557 http://dx.doi.org/10.1111/age.12888 |
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author | Gorssen, W. Meyermans, R. Buys, N. Janssens, S. |
author_facet | Gorssen, W. Meyermans, R. Buys, N. Janssens, S. |
author_sort | Gorssen, W. |
collection | PubMed |
description | The Piétrain pig originates from the Belgian village Piétrain some time between 1920 and 1950. Owing to its superior conformation, the Piétrain has spread worldwide since the 1960s. As initial population sizes were limited and close inbreeding was commonplace, the breed’s genetic diversity has been questioned. Therefore, this study examines Piétrain breed substructure, diversity and selection signatures using SNP data in comparison with Duroc, Landrace and Large White populations. Principal component analysis indicated three subpopulations, and F (ST) analysis showed that US Piétrains differ most from European Piétrains. Average inbreeding based on runs of homozygosity (ROH) segments larger than 4 Mb ranged between 16.7 and 20.9%. The highest chromosomal inbreeding levels were found on SSC8 (42.7%). ROH islands were found on SSC8, SSC15 and SSC18 in all Piétrain populations, but numerous population‐specific ROH islands were also detected. Moreover, a large ROH island on SSC8 (34–126 Mb) appears nearly fixed in all Piétrain populations, with a unique genotype. Chromosomal ROH patterns were similar between Piétrain populations. This study shows that Piétrain populations are genetically diverging, with at least three genetically distinct populations worldwide. Increasing genetic diversity in local Piétrain populations by introgression from other Piétrain populations seems to be only limited. Moreover, a unique 90 Mb region on SSC8 appeared largely fixed in the Piétrain breed, indicating that fixation was already present before the 1960s. We believe that strong selection and inbreeding during breed formation fixed these genomic regions in Piétrains. Finally, we hypothesize that independent coat color selection may have led to large ROH pattern similarities on SSC8 between unrelated pig breeds. |
format | Online Article Text |
id | pubmed-7003864 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-70038642020-02-11 SNP genotypes reveal breed substructure, selection signatures and highly inbred regions in Piétrain pigs Gorssen, W. Meyermans, R. Buys, N. Janssens, S. Anim Genet Articles The Piétrain pig originates from the Belgian village Piétrain some time between 1920 and 1950. Owing to its superior conformation, the Piétrain has spread worldwide since the 1960s. As initial population sizes were limited and close inbreeding was commonplace, the breed’s genetic diversity has been questioned. Therefore, this study examines Piétrain breed substructure, diversity and selection signatures using SNP data in comparison with Duroc, Landrace and Large White populations. Principal component analysis indicated three subpopulations, and F (ST) analysis showed that US Piétrains differ most from European Piétrains. Average inbreeding based on runs of homozygosity (ROH) segments larger than 4 Mb ranged between 16.7 and 20.9%. The highest chromosomal inbreeding levels were found on SSC8 (42.7%). ROH islands were found on SSC8, SSC15 and SSC18 in all Piétrain populations, but numerous population‐specific ROH islands were also detected. Moreover, a large ROH island on SSC8 (34–126 Mb) appears nearly fixed in all Piétrain populations, with a unique genotype. Chromosomal ROH patterns were similar between Piétrain populations. This study shows that Piétrain populations are genetically diverging, with at least three genetically distinct populations worldwide. Increasing genetic diversity in local Piétrain populations by introgression from other Piétrain populations seems to be only limited. Moreover, a unique 90 Mb region on SSC8 appeared largely fixed in the Piétrain breed, indicating that fixation was already present before the 1960s. We believe that strong selection and inbreeding during breed formation fixed these genomic regions in Piétrains. Finally, we hypothesize that independent coat color selection may have led to large ROH pattern similarities on SSC8 between unrelated pig breeds. John Wiley and Sons Inc. 2019-12-06 2020-02 /pmc/articles/PMC7003864/ /pubmed/31809557 http://dx.doi.org/10.1111/age.12888 Text en © 2019 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made. |
spellingShingle | Articles Gorssen, W. Meyermans, R. Buys, N. Janssens, S. SNP genotypes reveal breed substructure, selection signatures and highly inbred regions in Piétrain pigs |
title | SNP genotypes reveal breed substructure, selection signatures and highly inbred regions in Piétrain pigs |
title_full | SNP genotypes reveal breed substructure, selection signatures and highly inbred regions in Piétrain pigs |
title_fullStr | SNP genotypes reveal breed substructure, selection signatures and highly inbred regions in Piétrain pigs |
title_full_unstemmed | SNP genotypes reveal breed substructure, selection signatures and highly inbred regions in Piétrain pigs |
title_short | SNP genotypes reveal breed substructure, selection signatures and highly inbred regions in Piétrain pigs |
title_sort | snp genotypes reveal breed substructure, selection signatures and highly inbred regions in piétrain pigs |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7003864/ https://www.ncbi.nlm.nih.gov/pubmed/31809557 http://dx.doi.org/10.1111/age.12888 |
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