Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
College of Animal Science & Technology, Guangxi University, Nanning 530003, China.
Genes (Basel). 2023 Mar 5;14(3):655. doi: 10.3390/genes14030655.
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.
河南省位于中国中部，拥有丰富的国内猪种群；淮猪（HN）是三种河南本土品种之一，具有早熟、抗病力强和肉质好等优良性能。云南（YN）黑猪是一种典型的新培育品种，由 HN 猪和美国杜洛克猪杂交选育而成，具有生长速度快、肉质优良等重要性状的选择。然而，YN 黑猪和 HN 猪的基因组差异、选择特征和与重要经济性状相关的基因座仍未得到很好的理解。在这项研究中，基于对涵盖商业 DLY（杜洛克×长白×大白）猪、HN 猪和 YN 黑猪的 159 个样本的高密度 SNP 芯片分析，我们对三个品种的系统进化关系和遗传多样性进行了全面分析。此外，我们使用复合似然比检验（CLR）和 F 统计量（Fst）来鉴定与重要经济性状相关的特定选择特征和潜在候选基因。我们发现，在 YN-DLY 组中，基于遗传分化（Fst），有 147 个包含 90 个基因的选择区域（前 1%）。在 HN-DLY 组中，有 169 个包含 58 个基因的选择区域。在 YN-HN 组中，有 179 个包含 77 个基因的选择区域。此外，与 YN 黑猪的甘油三酯水平、木乃伊猪数量、血红蛋白和腰肌肉深度、HN 猪的窝产仔数和肌内脂肪含量以及 DLY 猪的肱骨长度、亚油酸含量和饲料转化率最重叠的 QTLs 数据库。值得注意的是，与 Fst 前 1%选择区域重叠的 14 个组织特异性启动子注释系统地证明了 YN 黑猪肌肉特异性和下丘脑特异性调节元件。综上所述，这些结果有助于准确了解杂交，从而有利于生产性能的评估，并在未来提高其他重要本土猪的基因组辅助育种水平。
