An imputation-based genome-wide association study for growth and fatness traits in Sujiang pigs
Sujiang pigs are a synthetic breed derived from Jiangquhai, Fengjing, and Duroc pigs. In this study, we sequenced the genome of 62 pigs with a coverage depth of 10× to 20×, including 27 Sujiang and 35 founder breed pigs, and we collected 360 global pigs’ genome sequence data from public databases in...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-08-01
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| Series: | Animal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1751731122001446 |
| _version_ | 1817999090007408640 |
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| author | Pan Xu Desen Li Zhongping Wu Ligang Ni Jiaxing Liu Ying Tang Tongshun Yu Jun Ren Xuting Zhao Min Huang |
| author_facet | Pan Xu Desen Li Zhongping Wu Ligang Ni Jiaxing Liu Ying Tang Tongshun Yu Jun Ren Xuting Zhao Min Huang |
| author_sort | Pan Xu |
| collection | DOAJ |
| description | Sujiang pigs are a synthetic breed derived from Jiangquhai, Fengjing, and Duroc pigs. In this study, we sequenced the genome of 62 pigs with a coverage depth of 10× to 20×, including 27 Sujiang and 35 founder breed pigs, and we collected 360 global pigs’ genome sequence data from public databases including 39 Duroc pigs. We obtained a high-quality variant dataset of 365 Sujiang pigs by imputing the porcine 80 K single nucleotide polymorphism (SNP) Beadchip to the whole-genome scale with a total of 422 pigs as a reference panel. A dataset of 365 imputated Sujiang pigs was used to perform single-trait genome-wide association study (GWAS) and meta-analyses for growth and fatness traits. Single-trait GWAS identified 1 907, 18, and 14 SNPs surpassing the suggestively significant threshold for backfat thickness, chest circumference, and chest width, respectively. Meta-analyses identified 2 400 genome-wide significant SNPs and 520 suggestively significant SNPs for backfat thickness and chest circumference, and 719 genome-wide significant SNPs and 1 225 suggestively significant SNPs for all seven traits. According to the meta-analysis of backfat thickness and chest circumference, a remarkable region of 2.69 Mb on Sus scrofa chromosome 4 containing FAM110B, IMPAD1, LYN, MOS, PENK, PLAG1, SDR16C5 and XKR4 was identified as a candidate region. The haplotype heat map of the 2.69 Mb region verified that Sujiang pigs were derived from Duroc and Chinese indigenous pigs, especially Jiangquhai pigs. The Kruskal-Wallis test showed that haplotypes of the 2.69 Mb region significantly affected backfat thickness and chest circumference traits. We then focused on PLAG1, an important growth-related gene, and identified two synonymous SNPs with obvious differences among different breeds in the PLAG1 gene. We then performed genotyping of 365 Sujiang, 150 Duroc, 95 Jiangquhai, and 100 Fengjing pigs to confirm the above result and verified that the two variants significantly affected phenotypes of growth and fatness traits. Our findings not only provide insights into the genetic architecture of porcine growth and fatness traits but also provide potential markers for selective breeding of these traits in Sujiang pigs. |
| first_indexed | 2024-04-14T03:03:21Z |
| format | Article |
| id | doaj.art-15f65a00ed99437c9777967f689e7928 |
| institution | Directory Open Access Journal |
| issn | 1751-7311 |
| language | English |
| last_indexed | 2024-04-14T03:03:21Z |
| publishDate | 2022-08-01 |
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| record_format | Article |
| series | Animal |
| spelling | doaj.art-15f65a00ed99437c9777967f689e79282022-12-22T02:15:50ZengElsevierAnimal1751-73112022-08-01168100591An imputation-based genome-wide association study for growth and fatness traits in Sujiang pigsPan Xu0Desen Li1Zhongping Wu2Ligang Ni3Jiaxing Liu4Ying Tang5Tongshun Yu6Jun Ren7Xuting Zhao8Min Huang9School of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, PR ChinaCollege of Animal Science, South China Agricultural University, Guangzhou, PR ChinaZhongkai University of Agriculture and Engineering, Guangzhou, PR ChinaSchool of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, PR ChinaSchool of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, PR ChinaSchool of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, PR ChinaSchool of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, PR ChinaCollege of Animal Science, South China Agricultural University, Guangzhou, PR ChinaSchool of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, PR ChinaCollege of Animal Science, South China Agricultural University, Guangzhou, PR China; Corresponding author at: College of Animal Science, South China Agricultural University, 510642 Guangzhou, PR China.Sujiang pigs are a synthetic breed derived from Jiangquhai, Fengjing, and Duroc pigs. In this study, we sequenced the genome of 62 pigs with a coverage depth of 10× to 20×, including 27 Sujiang and 35 founder breed pigs, and we collected 360 global pigs’ genome sequence data from public databases including 39 Duroc pigs. We obtained a high-quality variant dataset of 365 Sujiang pigs by imputing the porcine 80 K single nucleotide polymorphism (SNP) Beadchip to the whole-genome scale with a total of 422 pigs as a reference panel. A dataset of 365 imputated Sujiang pigs was used to perform single-trait genome-wide association study (GWAS) and meta-analyses for growth and fatness traits. Single-trait GWAS identified 1 907, 18, and 14 SNPs surpassing the suggestively significant threshold for backfat thickness, chest circumference, and chest width, respectively. Meta-analyses identified 2 400 genome-wide significant SNPs and 520 suggestively significant SNPs for backfat thickness and chest circumference, and 719 genome-wide significant SNPs and 1 225 suggestively significant SNPs for all seven traits. According to the meta-analysis of backfat thickness and chest circumference, a remarkable region of 2.69 Mb on Sus scrofa chromosome 4 containing FAM110B, IMPAD1, LYN, MOS, PENK, PLAG1, SDR16C5 and XKR4 was identified as a candidate region. The haplotype heat map of the 2.69 Mb region verified that Sujiang pigs were derived from Duroc and Chinese indigenous pigs, especially Jiangquhai pigs. The Kruskal-Wallis test showed that haplotypes of the 2.69 Mb region significantly affected backfat thickness and chest circumference traits. We then focused on PLAG1, an important growth-related gene, and identified two synonymous SNPs with obvious differences among different breeds in the PLAG1 gene. We then performed genotyping of 365 Sujiang, 150 Duroc, 95 Jiangquhai, and 100 Fengjing pigs to confirm the above result and verified that the two variants significantly affected phenotypes of growth and fatness traits. Our findings not only provide insights into the genetic architecture of porcine growth and fatness traits but also provide potential markers for selective breeding of these traits in Sujiang pigs.http://www.sciencedirect.com/science/article/pii/S1751731122001446Backfat thicknessChest circumferenceHaplotypePLAG1Synthetic pig |
| spellingShingle | Pan Xu Desen Li Zhongping Wu Ligang Ni Jiaxing Liu Ying Tang Tongshun Yu Jun Ren Xuting Zhao Min Huang An imputation-based genome-wide association study for growth and fatness traits in Sujiang pigs Animal Backfat thickness Chest circumference Haplotype PLAG1 Synthetic pig |
| title | An imputation-based genome-wide association study for growth and fatness traits in Sujiang pigs |
| title_full | An imputation-based genome-wide association study for growth and fatness traits in Sujiang pigs |
| title_fullStr | An imputation-based genome-wide association study for growth and fatness traits in Sujiang pigs |
| title_full_unstemmed | An imputation-based genome-wide association study for growth and fatness traits in Sujiang pigs |
| title_short | An imputation-based genome-wide association study for growth and fatness traits in Sujiang pigs |
| title_sort | imputation based genome wide association study for growth and fatness traits in sujiang pigs |
| topic | Backfat thickness Chest circumference Haplotype PLAG1 Synthetic pig |
| url | http://www.sciencedirect.com/science/article/pii/S1751731122001446 |
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