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Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs
Henan Province is located in central China and rich in domestic pig populations; Huainan (HN) pigs are one of three Henan indigenous breeds with great performance, including early maturation, strong disease resistance and high meat quality. Yunan (YN) black pigs are a typical, newly cultivated breed...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10048629/ https://www.ncbi.nlm.nih.gov/pubmed/36980926 http://dx.doi.org/10.3390/genes14030655 |
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author | Han, Yachun Tan, Tao Li, Zixin Ma, Zheng Lan, Ganqiu Liang, Jing Li, Kui Bai, Lijing |
author_facet | Han, Yachun Tan, Tao Li, Zixin Ma, Zheng Lan, Ganqiu Liang, Jing Li, Kui Bai, Lijing |
author_sort | Han, Yachun |
collection | PubMed |
description | Henan Province is located in central China and rich in domestic pig populations; Huainan (HN) pigs are one of three Henan indigenous breeds with great performance, including early maturation, strong disease resistance and high meat quality. Yunan (YN) black pigs are a typical, newly cultivated breed, synthesized between HN pigs and American Duroc, and are subjected to selection for important traits, such as fast growth and excellent meat quality. However, the genomic differences, selection signatures and loci associated with important economic traits in YN black pigs and HN pigs are still not well understood. In this study, based on high-density SNP chip analysis of 159 samples covering commercial DLY (Duroc × Landrace × Large White) pigs, HN pigs and YN black pigs, we performed a comprehensive analysis of phylogenetic relationships and genetic diversity among the three breeds. Furthermore, we used composite likelihood ratio tests (CLR) and F-statistics (Fst) to identify specific signatures of selection associated with important economic traits and potential candidate genes. We found 147 selected regions (top 1%) harboring 90 genes based on genetic differentiation (Fst) in the YN-DLY group. In the HN-DLY group, 169 selected regions harbored 58 genes. In the YN-HN group, 179 selected regions harbored 77 genes. In addition, the QTLs database with the most overlapping regions was associated with triglyceride level, number of mummified pigs, hemoglobin and loin muscle depth for YN black pigs, litter size and intramuscular fat content for HN pigs, and humerus length, linolenic acid content and feed conversion ratio mainly in DLY pigs. Of note, overlapping 14 tissue-specific promoters’ annotation with the top Fst 1% selective regions systematically demonstrated the muscle-specific and hypothalamus-specific regulatory elements in YN black pigs. Taken together, these results contribute to an accurate knowledge of crossbreeding, thus benefitting the evaluation of production performance and improving the genome-assisted breeding of other important indigenous pig in the future. |
format | Online Article Text |
id | pubmed-10048629 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-100486292023-03-29 Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs Han, Yachun Tan, Tao Li, Zixin Ma, Zheng Lan, Ganqiu Liang, Jing Li, Kui Bai, Lijing Genes (Basel) Article Henan Province is located in central China and rich in domestic pig populations; Huainan (HN) pigs are one of three Henan indigenous breeds with great performance, including early maturation, strong disease resistance and high meat quality. Yunan (YN) black pigs are a typical, newly cultivated breed, synthesized between HN pigs and American Duroc, and are subjected to selection for important traits, such as fast growth and excellent meat quality. However, the genomic differences, selection signatures and loci associated with important economic traits in YN black pigs and HN pigs are still not well understood. In this study, based on high-density SNP chip analysis of 159 samples covering commercial DLY (Duroc × Landrace × Large White) pigs, HN pigs and YN black pigs, we performed a comprehensive analysis of phylogenetic relationships and genetic diversity among the three breeds. Furthermore, we used composite likelihood ratio tests (CLR) and F-statistics (Fst) to identify specific signatures of selection associated with important economic traits and potential candidate genes. We found 147 selected regions (top 1%) harboring 90 genes based on genetic differentiation (Fst) in the YN-DLY group. In the HN-DLY group, 169 selected regions harbored 58 genes. In the YN-HN group, 179 selected regions harbored 77 genes. In addition, the QTLs database with the most overlapping regions was associated with triglyceride level, number of mummified pigs, hemoglobin and loin muscle depth for YN black pigs, litter size and intramuscular fat content for HN pigs, and humerus length, linolenic acid content and feed conversion ratio mainly in DLY pigs. Of note, overlapping 14 tissue-specific promoters’ annotation with the top Fst 1% selective regions systematically demonstrated the muscle-specific and hypothalamus-specific regulatory elements in YN black pigs. Taken together, these results contribute to an accurate knowledge of crossbreeding, thus benefitting the evaluation of production performance and improving the genome-assisted breeding of other important indigenous pig in the future. MDPI 2023-03-05 /pmc/articles/PMC10048629/ /pubmed/36980926 http://dx.doi.org/10.3390/genes14030655 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Han, Yachun Tan, Tao Li, Zixin Ma, Zheng Lan, Ganqiu Liang, Jing Li, Kui Bai, Lijing Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs |
title | Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs |
title_full | Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs |
title_fullStr | Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs |
title_full_unstemmed | Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs |
title_short | Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs |
title_sort | identification of selection signatures and loci associated with important economic traits in yunan black and huainan pigs |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10048629/ https://www.ncbi.nlm.nih.gov/pubmed/36980926 http://dx.doi.org/10.3390/genes14030655 |
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