Introgression of pigs in Taihu Lake region possibly contributed to the improvement of fertility in Danish Large White pigs
Abstract Background Eurasian pigs have undergone lineage admixture throughout history. It has been confirmed that the genes of indigenous pig breeds in China have been introduced into Western commercial pigs, providing genetic materials for breeding Western pigs. Pigs in Taihu Lake region (TL), such...
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| Format: | Article |
| Language: | English |
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BMC
2023-12-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09860-x |
| _version_ | 1797398160884105216 |
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| author | Chenxi Liu Ruihua Huang Guosheng Su Liming Hou Wuduo Zhou Qian Liu Zijian Qiu Qingbo Zhao Pinghua Li |
| author_facet | Chenxi Liu Ruihua Huang Guosheng Su Liming Hou Wuduo Zhou Qian Liu Zijian Qiu Qingbo Zhao Pinghua Li |
| author_sort | Chenxi Liu |
| collection | DOAJ |
| description | Abstract Background Eurasian pigs have undergone lineage admixture throughout history. It has been confirmed that the genes of indigenous pig breeds in China have been introduced into Western commercial pigs, providing genetic materials for breeding Western pigs. Pigs in Taihu Lake region (TL), such as the Meishan pig and Erhualian pig, serve as typical representatives of indigenous pig breeds in China due to their high reproductive performances. These pigs have also been imported into European countries in 1970 and 1980 s. They have played a positive role in improving the reproductive performances in European commercial pigs such as French Large White pigs (FLW). However, it is currently unclear if the lineage of TL pigs have been introgressed into the Danish Large White pigs (DLW), which are also known for their high reproductive performances in European pigs. To systematically identify genomic regions in which TL pigs have introgressed into DLW pigs and their physiological functions, we collected the re-sequencing data from 304 Eurasian pigs, to identify shared haplotypes between DLW and TL pigs. Results The findings revealed the presence of introgressed genomic regions from TL pigs in the genome of DLW pigs indeed. The genes annotated within these regions were found to be mainly enriched in neurodevelopmental pathways. Furthermore, we found that the 115 kb region located in SSC16 exhibited highly shared haplotypes between TL and DLW pigs. The major haplotype of TL pigs in this region could significantly improve reproductive performances in various pig populations. Around this genomic region, NDUFS4 gene was highly expressed and showed differential expression in multiple reproductive tissues between extremely high and low farrowing Erhualian pigs. This suggested that NDUFS4 gene could be an important candidate causal gene responsible for affecting the reproductive performances of DLW pigs. Conclusions Our study has furthered our knowledge of the pattern of introgression from TL into DLW pigs and the potential effects on the fertility of DLW pigs. |
| first_indexed | 2024-03-09T01:21:42Z |
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| id | doaj.art-affd689966f5412ba51180de8677574f |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-09T01:21:42Z |
| publishDate | 2023-12-01 |
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| series | BMC Genomics |
| spelling | doaj.art-affd689966f5412ba51180de8677574f2023-12-10T12:08:46ZengBMCBMC Genomics1471-21642023-12-0124111410.1186/s12864-023-09860-xIntrogression of pigs in Taihu Lake region possibly contributed to the improvement of fertility in Danish Large White pigsChenxi Liu0Ruihua Huang1Guosheng Su2Liming Hou3Wuduo Zhou4Qian Liu5Zijian Qiu6Qingbo Zhao7Pinghua Li8Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural UniversityInstitute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural UniversityCenter for Quantitative Genetics and Genomics, Aarhus UniversityInstitute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural UniversityInstitute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural UniversityInstitute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural UniversityInstitute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural UniversityInstitute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural UniversityInstitute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural UniversityAbstract Background Eurasian pigs have undergone lineage admixture throughout history. It has been confirmed that the genes of indigenous pig breeds in China have been introduced into Western commercial pigs, providing genetic materials for breeding Western pigs. Pigs in Taihu Lake region (TL), such as the Meishan pig and Erhualian pig, serve as typical representatives of indigenous pig breeds in China due to their high reproductive performances. These pigs have also been imported into European countries in 1970 and 1980 s. They have played a positive role in improving the reproductive performances in European commercial pigs such as French Large White pigs (FLW). However, it is currently unclear if the lineage of TL pigs have been introgressed into the Danish Large White pigs (DLW), which are also known for their high reproductive performances in European pigs. To systematically identify genomic regions in which TL pigs have introgressed into DLW pigs and their physiological functions, we collected the re-sequencing data from 304 Eurasian pigs, to identify shared haplotypes between DLW and TL pigs. Results The findings revealed the presence of introgressed genomic regions from TL pigs in the genome of DLW pigs indeed. The genes annotated within these regions were found to be mainly enriched in neurodevelopmental pathways. Furthermore, we found that the 115 kb region located in SSC16 exhibited highly shared haplotypes between TL and DLW pigs. The major haplotype of TL pigs in this region could significantly improve reproductive performances in various pig populations. Around this genomic region, NDUFS4 gene was highly expressed and showed differential expression in multiple reproductive tissues between extremely high and low farrowing Erhualian pigs. This suggested that NDUFS4 gene could be an important candidate causal gene responsible for affecting the reproductive performances of DLW pigs. Conclusions Our study has furthered our knowledge of the pattern of introgression from TL into DLW pigs and the potential effects on the fertility of DLW pigs.https://doi.org/10.1186/s12864-023-09860-xTaihu Lake region pigsDanish Large White pigsIntrogressionFertilityNDUFS4 gene |
| spellingShingle | Chenxi Liu Ruihua Huang Guosheng Su Liming Hou Wuduo Zhou Qian Liu Zijian Qiu Qingbo Zhao Pinghua Li Introgression of pigs in Taihu Lake region possibly contributed to the improvement of fertility in Danish Large White pigs BMC Genomics Taihu Lake region pigs Danish Large White pigs Introgression Fertility NDUFS4 gene |
| title | Introgression of pigs in Taihu Lake region possibly contributed to the improvement of fertility in Danish Large White pigs |
| title_full | Introgression of pigs in Taihu Lake region possibly contributed to the improvement of fertility in Danish Large White pigs |
| title_fullStr | Introgression of pigs in Taihu Lake region possibly contributed to the improvement of fertility in Danish Large White pigs |
| title_full_unstemmed | Introgression of pigs in Taihu Lake region possibly contributed to the improvement of fertility in Danish Large White pigs |
| title_short | Introgression of pigs in Taihu Lake region possibly contributed to the improvement of fertility in Danish Large White pigs |
| title_sort | introgression of pigs in taihu lake region possibly contributed to the improvement of fertility in danish large white pigs |
| topic | Taihu Lake region pigs Danish Large White pigs Introgression Fertility NDUFS4 gene |
| url | https://doi.org/10.1186/s12864-023-09860-x |
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