Population genetic structure analysis and identification of backfat thickness loci of Chinese synthetic Yunan pigs
Yunan is a crossed lean meat pig breed in China. Backfat thickness is the gold standard for carcass quality grading. However, over 14 years after breed registration, the backfat of Yunan thickened and the consistency of backfat thickness decreased. Meanwhile, no genetic study has been ever performed...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-11-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.1039838/full |
| _version_ | 1797985026524053504 |
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| author | Ruimin Qiao Menghao Zhang Ben Zhang Xinjian Li Xuelei Han Kejun Wang Xiuling Li Feng Yang Panyang Hu |
| author_facet | Ruimin Qiao Menghao Zhang Ben Zhang Xinjian Li Xuelei Han Kejun Wang Xiuling Li Feng Yang Panyang Hu |
| author_sort | Ruimin Qiao |
| collection | DOAJ |
| description | Yunan is a crossed lean meat pig breed in China. Backfat thickness is the gold standard for carcass quality grading. However, over 14 years after breed registration, the backfat of Yunan thickened and the consistency of backfat thickness decreased. Meanwhile, no genetic study has been ever performed on Yunan population. So, in this study we collected all the 120 nucleus individuals of Yunan and recorded six backfat traits of them, carried out population genetic structure analysis, selection signals analysis and genome-wide association study of Yunan pigs with the help of their founder population Duroc and Chinese native Huainan pigs, to determine the genomic loci on backfat of Yunan. Genetic diversity indexes suggested Yunan pigs had no inbreeding risk while population genetic structure showed they had few molecular pedigrees and were stratified. A total of 71 common selection signals affecting growth and fat deposition were detected by FST and XP-CLR methods. 34 significant loci associated with six backfat traits were detected, among which a 1.40 Mb region on SSC4 (20.03–21.43 Mb) were outstanding as the strong region underlying backfat. This region was common with the results of selection signature analysis, former reported QTLs for backfat and was common for different kinds of backfat traits at different development stage. ENPP2, EXT1 and SLC30A8 genes around were fat deposition related genes and were of Huainan pig’s origin, among which Type 2 diabetes related gene SLC30A8 was the most reasonable for being in a 193.21 Kb haplotype block of the 1.40 Mb region. Our results had application value for conservation, mating and breeding improvement of backfat thickness of Yunan pigs and provided evidence for a human function gene might be reproduced in pigs. |
| first_indexed | 2024-04-11T07:11:00Z |
| format | Article |
| id | doaj.art-3c6537feb321433f899729b3a903e0cc |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-11T07:11:00Z |
| publishDate | 2022-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-3c6537feb321433f899729b3a903e0cc2022-12-22T04:38:12ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-11-011310.3389/fgene.2022.10398381039838Population genetic structure analysis and identification of backfat thickness loci of Chinese synthetic Yunan pigsRuimin QiaoMenghao ZhangBen ZhangXinjian LiXuelei HanKejun WangXiuling LiFeng YangPanyang HuYunan is a crossed lean meat pig breed in China. Backfat thickness is the gold standard for carcass quality grading. However, over 14 years after breed registration, the backfat of Yunan thickened and the consistency of backfat thickness decreased. Meanwhile, no genetic study has been ever performed on Yunan population. So, in this study we collected all the 120 nucleus individuals of Yunan and recorded six backfat traits of them, carried out population genetic structure analysis, selection signals analysis and genome-wide association study of Yunan pigs with the help of their founder population Duroc and Chinese native Huainan pigs, to determine the genomic loci on backfat of Yunan. Genetic diversity indexes suggested Yunan pigs had no inbreeding risk while population genetic structure showed they had few molecular pedigrees and were stratified. A total of 71 common selection signals affecting growth and fat deposition were detected by FST and XP-CLR methods. 34 significant loci associated with six backfat traits were detected, among which a 1.40 Mb region on SSC4 (20.03–21.43 Mb) were outstanding as the strong region underlying backfat. This region was common with the results of selection signature analysis, former reported QTLs for backfat and was common for different kinds of backfat traits at different development stage. ENPP2, EXT1 and SLC30A8 genes around were fat deposition related genes and were of Huainan pig’s origin, among which Type 2 diabetes related gene SLC30A8 was the most reasonable for being in a 193.21 Kb haplotype block of the 1.40 Mb region. Our results had application value for conservation, mating and breeding improvement of backfat thickness of Yunan pigs and provided evidence for a human function gene might be reproduced in pigs.https://www.frontiersin.org/articles/10.3389/fgene.2022.1039838/fullsynthetic pig breedgenetic diversitypopulation structureselection signatureGWASbackfat thickness |
| spellingShingle | Ruimin Qiao Menghao Zhang Ben Zhang Xinjian Li Xuelei Han Kejun Wang Xiuling Li Feng Yang Panyang Hu Population genetic structure analysis and identification of backfat thickness loci of Chinese synthetic Yunan pigs Frontiers in Genetics synthetic pig breed genetic diversity population structure selection signature GWAS backfat thickness |
| title | Population genetic structure analysis and identification of backfat thickness loci of Chinese synthetic Yunan pigs |
| title_full | Population genetic structure analysis and identification of backfat thickness loci of Chinese synthetic Yunan pigs |
| title_fullStr | Population genetic structure analysis and identification of backfat thickness loci of Chinese synthetic Yunan pigs |
| title_full_unstemmed | Population genetic structure analysis and identification of backfat thickness loci of Chinese synthetic Yunan pigs |
| title_short | Population genetic structure analysis and identification of backfat thickness loci of Chinese synthetic Yunan pigs |
| title_sort | population genetic structure analysis and identification of backfat thickness loci of chinese synthetic yunan pigs |
| topic | synthetic pig breed genetic diversity population structure selection signature GWAS backfat thickness |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.1039838/full |
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