College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China.
Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China.
Genes (Basel). 2022 Dec 8;13(12):2310. doi: 10.3390/genes13122310.
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) and polymorphism levels (π ratio). Some genes were found to be positively selected in AQ pigs' breeding. The and genes were involved in the immune response to pseudorabies virus (PRV) and porcine reproductive and respiratory syndrome virus (PRRSV). The and genes were involved in biological regulation of immune T cells and phagocytes. The and genes were related to reproductive performance. The and 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.
作为一种具有抗病力和高品质肉质的著名中国本土猪种，安庆六白猪是提高猪养殖产业质量的宝贵种质资源。在这项研究中，选择了 24 头血缘较远的安庆六白猪和 6 头亚洲野猪进行 10×深度基因组重测序。分析选择的特征，以探讨其种质特征的遗传基础，并基于 NGS 数据识别优秀的种质相关功能基因。在 30 头猪的基因组中总共检测到 49,289,052 个 SNP 和 6,186,123 个 indel。大多数遗传变异是同义突变，存在于基因间区。我们应用基于遗传分化（F）和多态性水平（π比值）的交叉方法，确定了 275 个含有 85 个基因的选择区域（前 1%）。在 AQ 猪的选育过程中发现了一些基因受到正选择。和基因参与对伪狂犬病病毒（PRV）和猪繁殖与呼吸综合征病毒（PRRSV）的免疫反应。和基因参与免疫 T 细胞和吞噬细胞的生物调节。和基因与繁殖性能有关。和基因与脂肪沉积和肌肉发育有关。此外，在 AQ 猪的选择区域和 ROH 岛上检测到 138 个重叠区域。此外，我们发现具有最多重叠区域的 QTL 与背脂厚度、肉质颜色、pH 值、脂肪酸含量、免疫细胞、寄生免疫和细菌免疫有关。基于功能富集分析和 QTL 映射，我们对种质特性（抗病性和优良肉质）的分子遗传基础进行了进一步研究。这些结果为安庆六白猪的种质资源保护和分子标记开发提供了可靠的资源。
