Genome-Wide Selection Signal Analysis to Investigate Wide Genomic Heredity Divergence between Eurasian Wild Boar and Domestic Pig
As important livestock species, pigs provide essential meat resources for humans, so understanding the genetic evolution behind their domestic history could help with the genetic improvement of domestic pigs. This study aimed to investigate the evolution of convergence and divergence under selection...
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MDPI AG
2023-06-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/13/13/2158 |
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| author | Xinming Wu Haoyuan Zhang Haoyuan Long Dongjie Zhang Xiuqin Yang Di Liu Guangxin E |
| author_facet | Xinming Wu Haoyuan Zhang Haoyuan Long Dongjie Zhang Xiuqin Yang Di Liu Guangxin E |
| author_sort | Xinming Wu |
| collection | DOAJ |
| description | As important livestock species, pigs provide essential meat resources for humans, so understanding the genetic evolution behind their domestic history could help with the genetic improvement of domestic pigs. This study aimed to investigate the evolution of convergence and divergence under selection in European and Asian domestic pigs by using public genome-wide data. A total of 164 and 108 candidate genes (CDGs) were obtained from the Asian group (wild boar vs. domestic pig) and the European group (wild boar vs. domestic pig), respectively, by taking the top 5% of intersected windows of a pairwise fixation index (FST) and a cross population extended haplotype homozygosity test (XPEHH). GO and KEGG annotated results indicated that most CDGs were related to reproduction and immunity in the Asian group. Conversely, rich CDGs were enriched in muscle development and digestion in the European group. Eight CDGs were subjected to parallel selection of Eurasian domestic pigs from local wild boars during domestication. These CDGs were mainly involved in olfactory transduction, metabolic pathways, and progesterone-mediated oocyte maturation. Moreover, 36 and 18 haplotypes of <i>INPP5B</i> and <i>TRAK2</i> were identified in this study, respectively. In brief, this study did not only improve the understanding of the genetic evolution of domestication in pigs, but also provides valuable CDGs for future breeding and genetic improvement of pigs. |
| first_indexed | 2024-03-11T01:47:51Z |
| format | Article |
| id | doaj.art-2fe7dbdf8bd84708a9209cb43f7ceeed |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-11T01:47:51Z |
| publishDate | 2023-06-01 |
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| series | Animals |
| spelling | doaj.art-2fe7dbdf8bd84708a9209cb43f7ceeed2023-11-18T16:03:49ZengMDPI AGAnimals2076-26152023-06-011313215810.3390/ani13132158Genome-Wide Selection Signal Analysis to Investigate Wide Genomic Heredity Divergence between Eurasian Wild Boar and Domestic PigXinming Wu0Haoyuan Zhang1Haoyuan Long2Dongjie Zhang3Xiuqin Yang4Di Liu5Guangxin E6College of Animal Science and Technology, Southwest University, Chongqing 400716, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400716, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400716, ChinaInstitute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, ChinaCollege of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, ChinaInstitute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400716, ChinaAs important livestock species, pigs provide essential meat resources for humans, so understanding the genetic evolution behind their domestic history could help with the genetic improvement of domestic pigs. This study aimed to investigate the evolution of convergence and divergence under selection in European and Asian domestic pigs by using public genome-wide data. A total of 164 and 108 candidate genes (CDGs) were obtained from the Asian group (wild boar vs. domestic pig) and the European group (wild boar vs. domestic pig), respectively, by taking the top 5% of intersected windows of a pairwise fixation index (FST) and a cross population extended haplotype homozygosity test (XPEHH). GO and KEGG annotated results indicated that most CDGs were related to reproduction and immunity in the Asian group. Conversely, rich CDGs were enriched in muscle development and digestion in the European group. Eight CDGs were subjected to parallel selection of Eurasian domestic pigs from local wild boars during domestication. These CDGs were mainly involved in olfactory transduction, metabolic pathways, and progesterone-mediated oocyte maturation. Moreover, 36 and 18 haplotypes of <i>INPP5B</i> and <i>TRAK2</i> were identified in this study, respectively. In brief, this study did not only improve the understanding of the genetic evolution of domestication in pigs, but also provides valuable CDGs for future breeding and genetic improvement of pigs.https://www.mdpi.com/2076-2615/13/13/2158domesticationpigswild boarselection signal analysis |
| spellingShingle | Xinming Wu Haoyuan Zhang Haoyuan Long Dongjie Zhang Xiuqin Yang Di Liu Guangxin E Genome-Wide Selection Signal Analysis to Investigate Wide Genomic Heredity Divergence between Eurasian Wild Boar and Domestic Pig Animals domestication pigs wild boar selection signal analysis |
| title | Genome-Wide Selection Signal Analysis to Investigate Wide Genomic Heredity Divergence between Eurasian Wild Boar and Domestic Pig |
| title_full | Genome-Wide Selection Signal Analysis to Investigate Wide Genomic Heredity Divergence between Eurasian Wild Boar and Domestic Pig |
| title_fullStr | Genome-Wide Selection Signal Analysis to Investigate Wide Genomic Heredity Divergence between Eurasian Wild Boar and Domestic Pig |
| title_full_unstemmed | Genome-Wide Selection Signal Analysis to Investigate Wide Genomic Heredity Divergence between Eurasian Wild Boar and Domestic Pig |
| title_short | Genome-Wide Selection Signal Analysis to Investigate Wide Genomic Heredity Divergence between Eurasian Wild Boar and Domestic Pig |
| title_sort | genome wide selection signal analysis to investigate wide genomic heredity divergence between eurasian wild boar and domestic pig |
| topic | domestication pigs wild boar selection signal analysis |
| url | https://www.mdpi.com/2076-2615/13/13/2158 |
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