Genomic Insights into Pig Domestication and Adaptation: An Integrated Approach Using Genome-Wide Selection Analysis and Multiple Public Datasets
As a global focus of animal husbandry, pigs provide essential meat resources for humans. Therefore, analyzing the genetic basis of adaptability, domestication, and artificial selection in pigs will contribute to further breeding. This study performed a genome-wide selection sweep analysis to identif...
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2024-11-01
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| author | Haoyuan Zhang Pengcheng Ruan He Cong Lu Xu Baigao Yang Tao Ren Dongjie Zhang Hongyue Chen Pengfei Hu Zhen Wang Hongmei Pan Xiuqin Yang Yanguo Han Yan Zeng Yongju Zhao Di Liu Simone Ceccobelli Guangxin E |
| author_facet | Haoyuan Zhang Pengcheng Ruan He Cong Lu Xu Baigao Yang Tao Ren Dongjie Zhang Hongyue Chen Pengfei Hu Zhen Wang Hongmei Pan Xiuqin Yang Yanguo Han Yan Zeng Yongju Zhao Di Liu Simone Ceccobelli Guangxin E |
| author_sort | Haoyuan Zhang |
| collection | DOAJ |
| description | As a global focus of animal husbandry, pigs provide essential meat resources for humans. Therefore, analyzing the genetic basis of adaptability, domestication, and artificial selection in pigs will contribute to further breeding. This study performed a genome-wide selection sweep analysis to identify candidate genes related to domestication and adaptive selection via data from 2413 public genotypes. Two complementary statistical analyses, <i>F<sub>ST</sub></i> (fixation index) and XP–EHH (cross–population extended haplotype homozygosity) were applied. The results revealed that numerous candidate genes were associated with high-altitude adaptability (e.g., <i>SIRPA</i>, <i>FRS2</i>, and <i>GRIN2B</i>) and habitat temperature adaptability (e.g., <i>MITF</i>, <i>PI3KC2A</i>, and <i>FRS2</i>). In addition, candidate genes related to the domestic genetic imprint of indigenous pigs (e.g., <i>TNR</i>, <i>NOCT</i>, and <i>SPATA5</i>) and strong artificial selection pressure in commercial breeds (e.g., <i>ITPR2</i>, <i>HSD17B12</i>, and <i>UGP2</i>) were identified in this study. Specifically, some MHC–related genes (e.g., <i>ZRTB12</i>, <i>TRIM26</i>, and <i>C7H6orf15</i>) were also under selection during domestication and artificial selection. Additionally, a phylogenetic comparative analysis revealed that the genetic divergence between populations does not fully follow the geographical distribution and management history in the major histocompatibility complex region/major histocompatibility complex II haplotypes, unlike that of the genome-wide genotypes. Furthermore, the higher heterozygosity and haplotype alleles of MHC reduce the differences between populations. Briefly, this study not only helps promote the relative theoretical understanding of environmental adaptive selection and domestication but also provides a theoretical reference for disease-resistant breeding in pigs. |
| format | Article |
| id | doaj-art-91362d3e4e284c8f92754da3be67d128 |
| institution | Kabale University |
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| language | English |
| publishDate | 2024-11-01 |
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| series | Animals |
| spelling | doaj-art-91362d3e4e284c8f92754da3be67d1282024-11-08T14:32:46ZengMDPI AGAnimals2076-26152024-11-011421315910.3390/ani14213159Genomic Insights into Pig Domestication and Adaptation: An Integrated Approach Using Genome-Wide Selection Analysis and Multiple Public DatasetsHaoyuan Zhang0Pengcheng Ruan1He Cong2Lu Xu3Baigao Yang4Tao Ren5Dongjie Zhang6Hongyue Chen7Pengfei Hu8Zhen Wang9Hongmei Pan10Xiuqin Yang11Yanguo Han12Yan Zeng13Yongju Zhao14Di Liu15Simone Ceccobelli16Guangxin E17College of Animal Science and Technology, Southwest University, Chongqing 400715, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400715, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400715, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400715, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400715, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400715, ChinaInstitute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, ChinaChongqing Animal Husbandry Technology Extension Station, Chongqing 401121, ChinaInstitute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130000, ChinaChongqing Animal Husbandry Technology Extension Station, Chongqing 401121, ChinaChongqing Academy of Animal Sciences, Chongqing 408599, ChinaCollege of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400715, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400715, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing 400715, ChinaInstitute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, ChinaDepartment of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, ItalyCollege of Animal Science and Technology, Southwest University, Chongqing 400715, ChinaAs a global focus of animal husbandry, pigs provide essential meat resources for humans. Therefore, analyzing the genetic basis of adaptability, domestication, and artificial selection in pigs will contribute to further breeding. This study performed a genome-wide selection sweep analysis to identify candidate genes related to domestication and adaptive selection via data from 2413 public genotypes. Two complementary statistical analyses, <i>F<sub>ST</sub></i> (fixation index) and XP–EHH (cross–population extended haplotype homozygosity) were applied. The results revealed that numerous candidate genes were associated with high-altitude adaptability (e.g., <i>SIRPA</i>, <i>FRS2</i>, and <i>GRIN2B</i>) and habitat temperature adaptability (e.g., <i>MITF</i>, <i>PI3KC2A</i>, and <i>FRS2</i>). In addition, candidate genes related to the domestic genetic imprint of indigenous pigs (e.g., <i>TNR</i>, <i>NOCT</i>, and <i>SPATA5</i>) and strong artificial selection pressure in commercial breeds (e.g., <i>ITPR2</i>, <i>HSD17B12</i>, and <i>UGP2</i>) were identified in this study. Specifically, some MHC–related genes (e.g., <i>ZRTB12</i>, <i>TRIM26</i>, and <i>C7H6orf15</i>) were also under selection during domestication and artificial selection. Additionally, a phylogenetic comparative analysis revealed that the genetic divergence between populations does not fully follow the geographical distribution and management history in the major histocompatibility complex region/major histocompatibility complex II haplotypes, unlike that of the genome-wide genotypes. Furthermore, the higher heterozygosity and haplotype alleles of MHC reduce the differences between populations. Briefly, this study not only helps promote the relative theoretical understanding of environmental adaptive selection and domestication but also provides a theoretical reference for disease-resistant breeding in pigs.https://www.mdpi.com/2076-2615/14/21/3159piggenome-wide selectionselection signaturemajor histocompatibility complexdisease-resistant breeding |
| spellingShingle | Haoyuan Zhang Pengcheng Ruan He Cong Lu Xu Baigao Yang Tao Ren Dongjie Zhang Hongyue Chen Pengfei Hu Zhen Wang Hongmei Pan Xiuqin Yang Yanguo Han Yan Zeng Yongju Zhao Di Liu Simone Ceccobelli Guangxin E Genomic Insights into Pig Domestication and Adaptation: An Integrated Approach Using Genome-Wide Selection Analysis and Multiple Public Datasets Animals pig genome-wide selection selection signature major histocompatibility complex disease-resistant breeding |
| title | Genomic Insights into Pig Domestication and Adaptation: An Integrated Approach Using Genome-Wide Selection Analysis and Multiple Public Datasets |
| title_full | Genomic Insights into Pig Domestication and Adaptation: An Integrated Approach Using Genome-Wide Selection Analysis and Multiple Public Datasets |
| title_fullStr | Genomic Insights into Pig Domestication and Adaptation: An Integrated Approach Using Genome-Wide Selection Analysis and Multiple Public Datasets |
| title_full_unstemmed | Genomic Insights into Pig Domestication and Adaptation: An Integrated Approach Using Genome-Wide Selection Analysis and Multiple Public Datasets |
| title_short | Genomic Insights into Pig Domestication and Adaptation: An Integrated Approach Using Genome-Wide Selection Analysis and Multiple Public Datasets |
| title_sort | genomic insights into pig domestication and adaptation an integrated approach using genome wide selection analysis and multiple public datasets |
| topic | pig genome-wide selection selection signature major histocompatibility complex disease-resistant breeding |
| url | https://www.mdpi.com/2076-2615/14/21/3159 |
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