Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data

文献类型： 外文期刊

第一作者： Chen, Yige

作者： Chen, Yige;Wang, Jinglin;Hou, Yinhui;Liu, Ying;Wang, Bo;Hu, Xiaojing;Zheng, Xianrui;Zhang, Xiaodong;Ding, Yueyun;Yin, Zongjun;Wu, Xudong

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关键词： Anqing six-end-white pig; single nucleotide polymorphism; genetic diversity; positive selection; gene enrichment analyses

期刊名称：GENES （ 影响因子：4.141； 五年影响因子：4.474 ）

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年卷期： 2022 年 13 卷 12 期

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收录情况： SCI

摘要： 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 10x 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 (pi 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.

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