The vast genetic diversity between Asian and European pig breeds harbors valuable insights into genome variation and adaptation. In this study, we newly assembled three Asian local pig breeds (Bamei, Juema, Hanjiang Black) and one European commercial pig breed (Large White) using PacBio HiFi and HIC technology and the contig N50 achieved 65.54-81.24Mb. Combining public pig genomes, we used 27 pig genomes constructed the largest pig graph pan-genome and genotyped 598 whole genome sequence pig accessions to study the structure variation and adaptation.
- Construction of the Largest Pig Graph Pan-Genome: We assembled four new pig genomes, expanding the existing dataset to 27 pig genomes. This unprecedented resource, the largest pig graph pan-genome to date, facilitates comprehensive analysis of structural variation and non-reference sequences.
- Accurate Structural Variant Detection: By employing our graph pan-genome, we achieve significantly enhanced structural variant (SV) detection compared to conventional methods like Manta. This improved accuracy rivals that of SNP and Indel variant calling.
- Deciphering Environmental Adaptation: We explored the role of SV in environmental adaptation, identifying a suite of candidate genes associated with tolerance to temperature, altitude, ultraviolet radiation, and soil conditions. These findings provide novel insights into the evolutionary mechanisms underlying pig adaptation to diverse environments.
- Unveiling a Key Meat Quality Candidate gene: Through SV and pangenome analysis, we uncover BTF3 as a potential regulator of meat quality. Molecular biological studies further elucidate the role of BTF3 in regulating meat quality traits, demonstrating the translational potential of our findings.
Our research offers a comprehensive and in-depth exploration of the genomic landscape of pigs, shedding light on the genetic basis of adaptation and agronomic characteristics. The construction of the largest pig graph pan-genome and the development of improved SV detection methods provide invaluable resources for future research in pig genomics.
If you have any questions in the process and article, please feel free to contact me (lidong9866(@)nwsuaf.edu.cn).
Dong Li, Yulong Wang, Tiantian Yuan, Minghao Cao, Yulin He, Lin Zhang, Xiang Li et al. 2024. “Pangenome and genome variations analysis of pigs unveil genomic facets for its adaptation and agronomic characteristics.” iMeta 3. e257. https://doi.org/10.1002/imt2.257.