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Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data
As a distinguished Chinese indigenous pig breed that exhibits disease resistance and high meat quality, the Anqing six-end-white (AQ) pig represents a valuable germplasm resource for improving the quality of the pig breeding industry. In this study, 24 AQ pigs that were distantly blood-related and 6...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9777694/ https://www.ncbi.nlm.nih.gov/pubmed/36553577 http://dx.doi.org/10.3390/genes13122310 |
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author | Chen, Yige Wu, Xudong Wang, Jinglin Hou, Yinhui Liu, Ying Wang, Bo Hu, Xiaojing Zheng, Xianrui Zhang, Xiaodong Ding, Yueyun Yin, Zongjun |
author_facet | Chen, Yige Wu, Xudong Wang, Jinglin Hou, Yinhui Liu, Ying Wang, Bo Hu, Xiaojing Zheng, Xianrui Zhang, Xiaodong Ding, Yueyun Yin, Zongjun |
author_sort | Chen, Yige |
collection | PubMed |
description | As a distinguished Chinese indigenous pig breed that exhibits disease resistance and high meat quality, the Anqing six-end-white (AQ) pig represents a valuable germplasm resource for improving the quality of the pig breeding industry. In this study, 24 AQ pigs that were distantly blood-related and 6 Asian Wild Boar (AWB) were selected for 10× deep-genome resequencing. The signatures of the selection were analyzed to explore the genetic basis of their germplasm characteristics and to identify excellent germplasm-related functional genes based on NGS data. A total of 49,289,052 SNPs and 6,186,123 indels were detected across the genome in 30 pigs. Most of the genetic variations were synonym mutations and existed in the intergenic region. We identified 275 selected regions (top 1%) harboring 85 genes by applying a crossover approach based on genetic differentiation (F(ST)) and polymorphism levels (π ratio). Some genes were found to be positively selected in AQ pigs’ breeding. The SMPD4 and DDX18 genes were involved in the immune response to pseudorabies virus (PRV) and porcine reproductive and respiratory syndrome virus (PRRSV). The BCL6 and P2RX6 genes were involved in biological regulation of immune T cells and phagocytes. The SLC7A4 and SPACA4 genes were related to reproductive performance. The MSTN and HIF1A genes were related to fat deposition and muscle development. Moreover, 138 overlapping regions were detected in selected regions and ROH islands of AQ pigs. Additionally, we found that the QTLs with the most overlapping regions were related to back fat thickness, meat color, pH value, fatty acid content, immune cells, parasitic immunity, and bacterial immunity. Based on functional enrichment analysis and QTLs mapping, we conducted further research on the molecular genetic basis of germplasm traits (disease resistance and excellent meat quality). These results are a reliable resource for conserving germplasm resources and exploiting molecular markers of AQ pigs. |
format | Online Article Text |
id | pubmed-9777694 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-97776942022-12-23 Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data Chen, Yige Wu, Xudong Wang, Jinglin Hou, Yinhui Liu, Ying Wang, Bo Hu, Xiaojing Zheng, Xianrui Zhang, Xiaodong Ding, Yueyun Yin, Zongjun Genes (Basel) Article As a distinguished Chinese indigenous pig breed that exhibits disease resistance and high meat quality, the Anqing six-end-white (AQ) pig represents a valuable germplasm resource for improving the quality of the pig breeding industry. In this study, 24 AQ pigs that were distantly blood-related and 6 Asian Wild Boar (AWB) were selected for 10× deep-genome resequencing. The signatures of the selection were analyzed to explore the genetic basis of their germplasm characteristics and to identify excellent germplasm-related functional genes based on NGS data. A total of 49,289,052 SNPs and 6,186,123 indels were detected across the genome in 30 pigs. Most of the genetic variations were synonym mutations and existed in the intergenic region. We identified 275 selected regions (top 1%) harboring 85 genes by applying a crossover approach based on genetic differentiation (F(ST)) and polymorphism levels (π ratio). Some genes were found to be positively selected in AQ pigs’ breeding. The SMPD4 and DDX18 genes were involved in the immune response to pseudorabies virus (PRV) and porcine reproductive and respiratory syndrome virus (PRRSV). The BCL6 and P2RX6 genes were involved in biological regulation of immune T cells and phagocytes. The SLC7A4 and SPACA4 genes were related to reproductive performance. The MSTN and HIF1A genes were related to fat deposition and muscle development. Moreover, 138 overlapping regions were detected in selected regions and ROH islands of AQ pigs. Additionally, we found that the QTLs with the most overlapping regions were related to back fat thickness, meat color, pH value, fatty acid content, immune cells, parasitic immunity, and bacterial immunity. Based on functional enrichment analysis and QTLs mapping, we conducted further research on the molecular genetic basis of germplasm traits (disease resistance and excellent meat quality). These results are a reliable resource for conserving germplasm resources and exploiting molecular markers of AQ pigs. MDPI 2022-12-08 /pmc/articles/PMC9777694/ /pubmed/36553577 http://dx.doi.org/10.3390/genes13122310 Text en © 2022 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 Chen, Yige Wu, Xudong Wang, Jinglin Hou, Yinhui Liu, Ying Wang, Bo Hu, Xiaojing Zheng, Xianrui Zhang, Xiaodong Ding, Yueyun Yin, Zongjun Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data |
title | Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data |
title_full | Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data |
title_fullStr | Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data |
title_full_unstemmed | Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data |
title_short | Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data |
title_sort | detection of selection signatures in anqing six-end-white pigs based on resequencing data |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9777694/ https://www.ncbi.nlm.nih.gov/pubmed/36553577 http://dx.doi.org/10.3390/genes13122310 |
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