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. 2022 Dec 8;13(12):2310.
doi: 10.3390/genes13122310.

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

Yige Chen  1 , Xudong Wu  2 , Jinglin Wang  1 , Yinhui Hou  1 , Ying Liu  1 , Bo Wang  1 , Xiaojing Hu  1 , Xianrui Zheng  1 , Xiaodong Zhang  1 , Yueyun Ding  1 , Zongjun Yin  1
Affiliations

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

Yige Chen et al. Genes (Basel). .

Abstract

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 (FST) 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.

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

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The functional annotation statistical map of genetic variation in Anqing six-end-white pigs (a) and Asian Wild Boar (b).
Figure 2
Figure 2
The statistical map of genetic variation locations of Anqing six-end-white pigs (a) and Asian Wild Boar (b).
Figure 3
Figure 3
Distribution of FST values among Anqing six-end-white pig autosomal chromosomes. Note: The red line represents the 0.01 level, and the blue line represents the 0.05 level. The different colors indicate that the SNPs are located on different chromosomes.
Figure 4
Figure 4
Distribution of π ratio among Anqing six-end-white pig autosomal chromosomes. Note: The red line represents the 0.01 level., and the blue line represents the 0.05 level. The different colors indicate that the SNPs are located on different chromosomes.
Figure 5
Figure 5
Selective sweeps regions identification of Anqing six-end-white pigs. Note: The final selection regions were based on two statistics. Points located to the right of the vertical dashed lines (corresponding to 1% right tails of the empirical π ratio distribution, where the π ratio was 3.21) and above the horizontal dashed line (1% above tail of the empirical FST distribution, where Fst was 0.46) were identified as selected regions for Anqing six-end-white pigs (red points).
Figure 6
Figure 6
GO enrichment analysis of genes in selected regions of Anqing six-end-white pigs.
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