Comprehensive inbred variation discovery in Bama pigs using de novo assemblies

Area of Science:

• Genomics
• Comparative genomics
• Animal models

Background:

• The Bama mini-pig (BM) is an inbred strain of the Bama Xiang pig (BX) and a valuable animal model for human disease research.
• Long-term inbreeding has led to distinct metabolic and olfactory characteristics between BM and BX strains, but genomic differences remain largely uncharacterized.

Purpose of the Study:

• To comprehensively analyze and compare the genomes of BX and BM pig strains.
• To identify genomic variations, including single nucleotide polymorphisms (SNPs), insertions and deletions (indels), structural variants (SVs), and copy number variants (CNVs), resulting from inbreeding.
• To investigate the differential gene expression of mutant genes and their association with observed phenotypic variations.

Main Methods:

• Whole-genome sequencing of the BX pig strain.
• Assembly-vs-assembly comparative genomic analysis against the BM pig reference genome.
• Identification and functional annotation of genetic variants (SNPs, indels, SVs, CNVs).
• Quantitative real-time PCR (qRT-PCR) to analyze differential gene expression.

Main Results:

• A draft genome assembly of the BX pig (2.56 Gb) was generated with N50 contig and scaffold lengths of approximately 11.87 kb and 99 kb, respectively.
• Extensive genetic variations were identified: 1,424,354 SNPs, 2,961,891 indels, 13,772 SVs, and 20,606 CNVs between BX and BM pigs.
• Genes such as ADGRE2, GPR143, and SHROOM2 showed higher expression in BX pigs, while olfactory receptor genes (olfactory receptor 52B4-like, olfactory receptor 10H1-like) exhibited lower expression in BX pigs compared to BM pigs.

Conclusions:

• The long inbreeding period has resulted in substantial genomic structural variations between the BX and BM pig strains.
• Differential expression of mutant genes, particularly those involved in metabolism and olfactory function, is significantly distinct between the two strains and likely contributes to their phenotypic differences.