Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs
Pudong White (PDW) pigs, historically originating from Shanghai, are the only Chinese indigenous pigs characterised by their completely white coats, with the exception of Rongchang pigs. However, there is limited information concerning their overall genetic structure or relationship with other breed...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-10-01
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| Series: | Animal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S175173112100197X |
| _version_ | 1818576740987961344 |
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| author | M. Huang H. Zhang Z.P. Wu X.P. Wang D.S. Li S.J. Liu S.M. Zheng L.J. Yang B.B. Liu G.X. Li Y.C. Jiang H. Chen J. Ren |
| author_facet | M. Huang H. Zhang Z.P. Wu X.P. Wang D.S. Li S.J. Liu S.M. Zheng L.J. Yang B.B. Liu G.X. Li Y.C. Jiang H. Chen J. Ren |
| author_sort | M. Huang |
| collection | DOAJ |
| description | Pudong White (PDW) pigs, historically originating from Shanghai, are the only Chinese indigenous pigs characterised by their completely white coats, with the exception of Rongchang pigs. However, there is limited information concerning their overall genetic structure or relationship with other breeds, especially the East Chinese (ECN) and European pigs. To uncover the genetic structure, selection signatures, and potential exotic introgression in PDW pigs, we sampled 15 PDW pigs using whole-genome sequencing (~20×). We then conducted in-depth population genetic analyses in 320 pigs from 27 global pig groups, namely, European wild boars, Chinese wild boars, and outgroup. Neighbour-joining tree and principal component analysis confirmed that PDW pigs belonged to the ecotype of ECN pigs. Both f3, D-statistics, and structure analysis showed that PDW pigs shared apparent alleles with Large White (LW) pigs. Three statistics, rIBD, a haplotype heat map and copy number variation, further indicated that PDW pigs shared apparent alleles with LW pigs at the KIT Proto-Oncogene, Receptor Tyrosine Kinase (KIT) and PARG-MARCHF8 loci, suggesting that the lineage of European pigs in PDW originated from LW pigs. After further detecting the KIT mutations in different pig breeds, PDW was confirmed to have the same duplication region 1, duplication region 2, and the splicing mutation on intron 17 of KIT as LW pigs that determine the white coat colour phenotype in European white pigs. We hypothesised that LW pigs were imported to China ∼110–160 years ago according to the admixture time estimate and then crossed with ECN pigs, resulting in the introgression of the KIT alleles that produce the white coat colour phenotype in the PDW pig breed. To our knowledge, this study presents the first thorough description of the genetic structure of PDW pigs via whole-genome resequencing data; moreover, the results provide a basis for the national project for the conservation of this unique Chinese local population. |
| first_indexed | 2024-12-16T06:18:50Z |
| format | Article |
| id | doaj.art-23fbc2f4607742c3b4814afbd208647d |
| institution | Directory Open Access Journal |
| issn | 1751-7311 |
| language | English |
| last_indexed | 2024-12-16T06:18:50Z |
| publishDate | 2021-10-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Animal |
| spelling | doaj.art-23fbc2f4607742c3b4814afbd208647d2022-12-21T22:41:11ZengElsevierAnimal1751-73112021-10-011510100354Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigsM. Huang0H. Zhang1Z.P. Wu2X.P. Wang3D.S. Li4S.J. Liu5S.M. Zheng6L.J. Yang7B.B. Liu8G.X. Li9Y.C. Jiang10H. Chen11J. Ren12College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, ChinaCollege of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, ChinaZhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, ChinaCollege of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, ChinaCollege of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, ChinaCollege of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, ChinaCollege of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, ChinaCollege of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, ChinaCollege of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, ChinaCollege of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, ChinaCollege of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, ChinaCollege of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi Province, China; Corresponding author.College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, ChinaPudong White (PDW) pigs, historically originating from Shanghai, are the only Chinese indigenous pigs characterised by their completely white coats, with the exception of Rongchang pigs. However, there is limited information concerning their overall genetic structure or relationship with other breeds, especially the East Chinese (ECN) and European pigs. To uncover the genetic structure, selection signatures, and potential exotic introgression in PDW pigs, we sampled 15 PDW pigs using whole-genome sequencing (~20×). We then conducted in-depth population genetic analyses in 320 pigs from 27 global pig groups, namely, European wild boars, Chinese wild boars, and outgroup. Neighbour-joining tree and principal component analysis confirmed that PDW pigs belonged to the ecotype of ECN pigs. Both f3, D-statistics, and structure analysis showed that PDW pigs shared apparent alleles with Large White (LW) pigs. Three statistics, rIBD, a haplotype heat map and copy number variation, further indicated that PDW pigs shared apparent alleles with LW pigs at the KIT Proto-Oncogene, Receptor Tyrosine Kinase (KIT) and PARG-MARCHF8 loci, suggesting that the lineage of European pigs in PDW originated from LW pigs. After further detecting the KIT mutations in different pig breeds, PDW was confirmed to have the same duplication region 1, duplication region 2, and the splicing mutation on intron 17 of KIT as LW pigs that determine the white coat colour phenotype in European white pigs. We hypothesised that LW pigs were imported to China ∼110–160 years ago according to the admixture time estimate and then crossed with ECN pigs, resulting in the introgression of the KIT alleles that produce the white coat colour phenotype in the PDW pig breed. To our knowledge, this study presents the first thorough description of the genetic structure of PDW pigs via whole-genome resequencing data; moreover, the results provide a basis for the national project for the conservation of this unique Chinese local population.http://www.sciencedirect.com/science/article/pii/S175173112100197XChinese indigenous pigsGenetic structureIntrogressionKITWhite coat colour |
| spellingShingle | M. Huang H. Zhang Z.P. Wu X.P. Wang D.S. Li S.J. Liu S.M. Zheng L.J. Yang B.B. Liu G.X. Li Y.C. Jiang H. Chen J. Ren Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs Animal Chinese indigenous pigs Genetic structure Introgression KIT White coat colour |
| title | Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs |
| title_full | Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs |
| title_fullStr | Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs |
| title_full_unstemmed | Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs |
| title_short | Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs |
| title_sort | whole genome resequencing reveals genetic structure and introgression in pudong white pigs |
| topic | Chinese indigenous pigs Genetic structure Introgression KIT White coat colour |
| url | http://www.sciencedirect.com/science/article/pii/S175173112100197X |
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