Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs

South China indigenous pigs are famous for their superior meat quality and crude feed tolerance. Saba and Baoshan pigs without saddleback were located in the high-altitude area of Yunnan Province, while Tunchang and Ding’an pigs with saddleback were located in the low-altitude area of Hain...

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Main Authors:	Shuqi Diao, Shuwen Huang, Zitao Chen, Jinyan Teng, Yunlong Ma, Xiaolong Yuan, Zanmou Chen, Hao Zhang, Jiaqi Li, Zhe Zhang
Format:	Article
Language:	English
Published:	MDPI AG 2019-05-01
Series:	Genes
Subjects:	signatures of selection South China indigenous pigs SNP XP-EHH <i>F</i><sub>ST</sub>
Online Access:	https://www.mdpi.com/2073-4425/10/5/346

id	doaj-f1e9797a021348d0bc94670e9d064a2e
record_format	Article
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Shuqi Diao Shuwen Huang Zitao Chen Jinyan Teng Yunlong Ma Xiaolong Yuan Zanmou Chen Hao Zhang Jiaqi Li Zhe Zhang
spellingShingle	Shuqi Diao Shuwen Huang Zitao Chen Jinyan Teng Yunlong Ma Xiaolong Yuan Zanmou Chen Hao Zhang Jiaqi Li Zhe Zhang Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs Genes signatures of selection South China indigenous pigs SNP XP-EHH <i>F</i><sub>ST</sub>
author_facet	Shuqi Diao Shuwen Huang Zitao Chen Jinyan Teng Yunlong Ma Xiaolong Yuan Zanmou Chen Hao Zhang Jiaqi Li Zhe Zhang
author_sort	Shuqi Diao
title	Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs
title_short	Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs
title_full	Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs
title_fullStr	Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs
title_full_unstemmed	Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs
title_sort	genome-wide signatures of selection detection in three south china indigenous pigs
publisher	MDPI AG
series	Genes
issn	2073-4425
publishDate	2019-05-01
description	South China indigenous pigs are famous for their superior meat quality and crude feed tolerance. Saba and Baoshan pigs without saddleback were located in the high-altitude area of Yunnan Province, while Tunchang and Ding’an pigs with saddleback were located in the low-altitude area of Hainan Province. Although these pigs are different in appearance, the underlying genetic differences have not been investigated. In this study, based on the single-nucleotide polymorphism (SNP) genotypes of 124 samples, both the cross-population extended haplotype homozygosity (XP-EHH) and the fixation index (<i>F</i><sub>ST</sub>) statistic were used to identify potential signatures of selection in these pig breeds. We found nine potential signatures of selection detected simultaneously by two methods, annotated 22 genes in Hainan pigs, when Baoshan pigs were used as the reference group. In addition, eleven potential signatures of selection detected simultaneously by two methods, annotated 24 genes in Hainan pigs compared with Saba pigs. These candidate genes were most enriched in GO: 0048015~phosphatidylinositol-mediated signaling and ssc00604: Glycosphingolipid biosynthesis—ganglio series. These selection signatures were likely to overlap with quantitative trait loci associated with meat quality traits. Furthermore, one potential selection signature, which was associated with different coat color, was detected in Hainan pigs. These results contribute to a better understanding of the underlying genetic architecture of South China indigenous pigs.
topic	signatures of selection South China indigenous pigs SNP XP-EHH <i>F</i><sub>ST</sub>
url	https://www.mdpi.com/2073-4425/10/5/346
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spelling	doaj-f1e9797a021348d0bc94670e9d064a2e2020-11-25T00:14:41ZengMDPI AGGenes2073-44252019-05-0110534610.3390/genes10050346genes10050346Genome-Wide Signatures of Selection Detection in Three South China Indigenous PigsShuqi Diao0Shuwen Huang1Zitao Chen2Jinyan Teng3Yunlong Ma4Xiaolong Yuan5Zanmou Chen6Hao Zhang7Jiaqi Li8Zhe Zhang9Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, ChinaGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaSouth China indigenous pigs are famous for their superior meat quality and crude feed tolerance. Saba and Baoshan pigs without saddleback were located in the high-altitude area of Yunnan Province, while Tunchang and Ding’an pigs with saddleback were located in the low-altitude area of Hainan Province. Although these pigs are different in appearance, the underlying genetic differences have not been investigated. In this study, based on the single-nucleotide polymorphism (SNP) genotypes of 124 samples, both the cross-population extended haplotype homozygosity (XP-EHH) and the fixation index (<i>F</i><sub>ST</sub>) statistic were used to identify potential signatures of selection in these pig breeds. We found nine potential signatures of selection detected simultaneously by two methods, annotated 22 genes in Hainan pigs, when Baoshan pigs were used as the reference group. In addition, eleven potential signatures of selection detected simultaneously by two methods, annotated 24 genes in Hainan pigs compared with Saba pigs. These candidate genes were most enriched in GO: 0048015~phosphatidylinositol-mediated signaling and ssc00604: Glycosphingolipid biosynthesis—ganglio series. These selection signatures were likely to overlap with quantitative trait loci associated with meat quality traits. Furthermore, one potential selection signature, which was associated with different coat color, was detected in Hainan pigs. These results contribute to a better understanding of the underlying genetic architecture of South China indigenous pigs.https://www.mdpi.com/2073-4425/10/5/346signatures of selectionSouth China indigenous pigsSNPXP-EHH<i>F</i><sub>ST</sub>

Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs

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