Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds
Studying gene flow between different livestock breeds will benefit the discovery of genes related to production traits and provide insight into human historical breeding. Chinese pigs have played an indispensable role in the breeding of Western commercial pigs. However, the differences in the timing...
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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.2022.1070783/full |
| _version_ | 1797953907431833600 |
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| author | Yebo Peng Martijn FL Derks Martijn FL Derks Martien AM Groenen Yiqiang Zhao Mirte Bosse Mirte Bosse |
| author_facet | Yebo Peng Martijn FL Derks Martijn FL Derks Martien AM Groenen Yiqiang Zhao Mirte Bosse Mirte Bosse |
| author_sort | Yebo Peng |
| collection | DOAJ |
| description | Studying gene flow between different livestock breeds will benefit the discovery of genes related to production traits and provide insight into human historical breeding. Chinese pigs have played an indispensable role in the breeding of Western commercial pigs. However, the differences in the timing and volume of the contribution of pigs from different Chinese regions to Western pigs are not yet apparent. In this paper, we combine the whole-genome sequencing data of 592 pigs from different studies and illustrate patterns of gene flow from Chinese pigs into Western commercial pigs. We describe introgression patterns from four distinct Chinese indigenous groups into five Western commercial groups. There were considerable differences in the number and length of the putative introgressed segments from Chinese pig groups that contributed to Western commercial pig breeds. The contribution of pigs from different Chinese geographical locations to a given western commercial breed varied more than that from a specific Chinese pig group to different Western commercial breeds, implying admixture within Europe after introgression. Within different Western commercial lines from the same breed, the introgression patterns from a given Chinese pig group seemed highly conserved, suggesting that introgression of Chinese pigs into Western commercial pig breeds mainly occurred at an early stage of breed formation. Finally, based on analyses of introgression signals, allele frequencies, and selection footprints, we identified a ∼2.65 Mb Chinese-derived haplotype under selection in Duroc pigs (CHR14: 95.68–98.33 Mb). Functional and phenotypic studies demonstrate that this PRKG1 haplotype is related to backfat and loin depth in Duroc pigs. Overall, we demonstrate that the introgression history of domestic pigs is complex and that Western commercial pigs contain distinct traces of mixed ancestry, likely derived from various Chinese pig breeds. |
| first_indexed | 2024-04-10T23:10:28Z |
| format | Article |
| id | doaj.art-cce93d8c792a42a99b8b95f0048dfaa9 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-10T23:10:28Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-cce93d8c792a42a99b8b95f0048dfaa92023-01-13T06:17:55ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-01-011310.3389/fgene.2022.10707831070783Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breedsYebo Peng0Martijn FL Derks1Martijn FL Derks2Martien AM Groenen3Yiqiang Zhao4Mirte Bosse5Mirte Bosse6State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, ChinaAnimal Breeding and Genomics, Wageningen University & Research, Wageningen, NetherlandsTopigs Norsvin Research Center, Beuningen, NetherlandsAnimal Breeding and Genomics, Wageningen University & Research, Wageningen, NetherlandsState Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, ChinaAnimal Breeding and Genomics, Wageningen University & Research, Wageningen, NetherlandsAmsterdam Insitute of Life and Environment (A-Life), VU University Amsterdam, Amsterdam, NetherlandsStudying gene flow between different livestock breeds will benefit the discovery of genes related to production traits and provide insight into human historical breeding. Chinese pigs have played an indispensable role in the breeding of Western commercial pigs. However, the differences in the timing and volume of the contribution of pigs from different Chinese regions to Western pigs are not yet apparent. In this paper, we combine the whole-genome sequencing data of 592 pigs from different studies and illustrate patterns of gene flow from Chinese pigs into Western commercial pigs. We describe introgression patterns from four distinct Chinese indigenous groups into five Western commercial groups. There were considerable differences in the number and length of the putative introgressed segments from Chinese pig groups that contributed to Western commercial pig breeds. The contribution of pigs from different Chinese geographical locations to a given western commercial breed varied more than that from a specific Chinese pig group to different Western commercial breeds, implying admixture within Europe after introgression. Within different Western commercial lines from the same breed, the introgression patterns from a given Chinese pig group seemed highly conserved, suggesting that introgression of Chinese pigs into Western commercial pig breeds mainly occurred at an early stage of breed formation. Finally, based on analyses of introgression signals, allele frequencies, and selection footprints, we identified a ∼2.65 Mb Chinese-derived haplotype under selection in Duroc pigs (CHR14: 95.68–98.33 Mb). Functional and phenotypic studies demonstrate that this PRKG1 haplotype is related to backfat and loin depth in Duroc pigs. Overall, we demonstrate that the introgression history of domestic pigs is complex and that Western commercial pigs contain distinct traces of mixed ancestry, likely derived from various Chinese pig breeds.https://www.frontiersin.org/articles/10.3389/fgene.2022.1070783/fullintrogressionhybridizationselectioncommercial pigsgene flow |
| spellingShingle | Yebo Peng Martijn FL Derks Martijn FL Derks Martien AM Groenen Yiqiang Zhao Mirte Bosse Mirte Bosse Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds Frontiers in Genetics introgression hybridization selection commercial pigs gene flow |
| title | Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds |
| title_full | Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds |
| title_fullStr | Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds |
| title_full_unstemmed | Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds |
| title_short | Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds |
| title_sort | distinct traces of mixed ancestry in western commercial pig genomes following gene flow from chinese indigenous breeds |
| topic | introgression hybridization selection commercial pigs gene flow |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.1070783/full |
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