Genetic insights into large and small body size variation in Diqing Tibetan pigs: A comparative genomic analysis

In Diqing Prefecture, we identified two Tibetan pig groups that exhibit a significant difference in body size at six months of age, with the large-bodied pigs weighing 55.00 kg and the small-bodied pigs weighing 28.00 kg. To elucidate the genetic distance and relatedness between these two groups, we employed whole-genome resequencing and constructed a genomic dataset containing 247 pigs, including 60 newly sequenced individuals and 187 publicly available samples. We first assessed their phylogenetic relationships through population genetic differentiation analyses, and further explored their genome-wide differences using methods such as nucleotide diversity (θπ), integrated haplotype score (iHS), allele frequency difference (ΔAF), and genome-wide association analysis (GWAS). The results showed that both groups belong to the Diqing Tibetan pig population, and they can be classified as large-bodied and small-bodied Diqing Tibetan pigs, respectively. Combined analyses of selective sweep signals and GWAS revealed that the genomic regions with significant divergence between the two groups mainly contain genes involved in skeletal development, muscle growth, energy metabolism, and endocrine regulation. This study is the first to demonstrate, at the genomic level, that the Diqing Tibetan pig population contains distinct large- and small-bodied types. Although both belong to the same breed, their marked difference in body size leads to substantial variation in meat production capacity. Future studies may employ multi-omics approaches-including transcriptomics, proteomics, and metabolomics-using the two types as comparative models under the same genetic background to systematically identify key genes, proteins, and metabolites that influence meat production performance. The findings of this study not only provide valuable material for further elucidating the mechanisms underlying skeletal and muscle development, but also establish a foundation for breeding Diqing Tibetan pigs with improved meat production traits.