College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China.
Gene. 2018 Dec 30;679:81-89. doi: 10.1016/j.gene.2018.08.051. Epub 2018 Sep 1.
The Bama mini-pig (BM pig) is an inbred strain of the Bama Xiang pig (BX pig) and an important animal model used for studying human diseases. The extremely long inbreeding period renders a clear distinction between the features of the BM and BX strains, such as in their metabolism and olfactory system. However, there is limited information about differences between BM and BX animals at the genomic level. In this study, we generated genome sequencing data and used the assembly-vs-assembly approach to evaluate the phenotypic variations caused by inbreeding in these strains. Moreover, we detected differential expression of mutant genes related to the phenotypes in BX and BM pigs. We sequenced the genome of the BX pig strain and performed a series of analyses to reveal the comprehensive inbred genetic variants between BX and BM pigs. Here, the 2.56-Gb draft genome assembly for the BX pig and an N50 contig length of approximately 11.87 kb is described, and an N50 scaffold length of approximately 99 kb and the variations in the BX pig genome were identified by comparison with the BM pig reference genome. There were 1,424,354 single nucleotide polymorphisms (SNPs), 2,961,891 insertions and deletions (indels), 13,772 structural variants (SVs), and 20,606 copy number variants (CNVs) identified in the BX genome. Functional annotation of SVs and CNVs showed that the genes (ADGRE2, GPR143, olfactory receptor 52B4-like, olfactory receptor 10H1-like and SHROOM2) with both SVs and CNVs were enriched in the most of all KEGG pathways and gene ontology (GO) terms of mutant genes. ADGRE2, GPR143 and SHROOM2 were both found to have significant higher expression levels in BX pigs than in BM pigs. In the contrary, the expressions of olfactory receptor 52B4-like and olfactory receptor 10H1-like were significant lower in BX pigs than in BM pigs. In conclusion, sequence analysis of the BX pig genome revealed that the genome structure of the two pig strains has considerable genomic variation that was caused by the long inbreeding period. Moreover, qRT-PCR analysis of the mutant genes displayed a significant distinction that may be associated with phenotypic differences between these pig strains.
巴马小型猪（BM 猪）是巴马香猪（BX 猪）的近交系，是研究人类疾病的重要动物模型。由于长期的近亲繁殖，BM 猪和 BX 猪在代谢和嗅觉系统等方面表现出明显的差异。然而，关于这两种猪在基因组水平上的差异信息有限。在这项研究中，我们生成了基因组测序数据，并使用组装对组装的方法来评估这些品系因近亲繁殖而导致的表型变化。此外，我们还检测到了与 BX 和 BM 猪表型相关的突变基因的差异表达。我们对 BX 猪品系进行了基因组测序，并进行了一系列分析，以揭示 BX 和 BM 猪之间综合的近亲遗传变异。在这里，我们描述了 BX 猪的 2.56-Gb 草图基因组组装，以及大约 11.87kb 的 N50 连续体长度，并通过与 BM 猪参考基因组的比较，确定了 BX 猪基因组的 N50 支架长度和变异情况。在 BX 基因组中发现了 1,424,354 个单核苷酸多态性（SNP）、2,961,891 个插入和缺失（indel）、13,772 个结构变异（SV）和 20,606 个拷贝数变异（CNV）。SV 和 CNV 的功能注释表明，具有 SV 和 CNV 的基因（ADGRE2、GPR143、嗅觉受体 52B4 样、嗅觉受体 10H1 样和 SHROOM2）在大多数所有的 KEGG 通路和基因本体（GO）术语中的突变基因中均有富集。ADGRE2、GPR143 和 SHROOM2 在 BX 猪中的表达均显著高于 BM 猪。相反，嗅觉受体 52B4 样和嗅觉受体 10H1 样在 BX 猪中的表达显著低于 BM 猪。总之，对 BX 猪基因组的序列分析表明，这两个猪种的基因组结构存在相当大的基因组变异，这是由于长期的近亲繁殖造成的。此外，对突变基因的 qRT-PCR 分析显示出显著的差异，这可能与这些猪种之间的表型差异有关。
