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Comprehensive inbred variation discovery in Bama pigs using de novo assemblies

Zhang, Li, Huang, Yuemeng, Si, Jinglei, Wu, Yanjun, Wang, Meng, Jiang, Qinyang, Guo, Yafen, Liang, Jing, Lan, Ganqiu
Gene 2018 v.679 pp. 81-89
animal models, gene expression regulation, gene ontology, genes, genetic variation, genome assembly, genomics, human diseases, inbreeding, metabolism, miniature swine, mutants, olfactory receptors, phenotype, phenotypic variation, quantitative polymerase chain reaction, reverse transcriptase polymerase chain reaction, single nucleotide polymorphism, swine
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.