Latitude-driven adaptive evolution of body length in diverse pig breeds across China.

Background: The geographical divergence of Chinese pigs led to various phenotypes through adaptive evolution. In particular, pigs from relatively low altitudes exhibit a positive correlation between body length and latitude. However, the molecular mechanisms underlying this relationship remain unclear. Identifying candidate genes associated with this body length variation is crucial for further understanding the genetic basis of adaptive traits in these Chinese pig breeds.

Results: We assembled a high-quality genome of the Neijiang pig as benchmark and analyse 297 Chinese domestic pigs and six Chinese wild boars distributed across different latitudes. Our study provides a comprehensive assessment of genetic diversity and population structure, revealing distinct genetic backgrounds of Chinese indigenous pigs from different regions. Most importantly, we observed a strong correlation between latitude and body length, and screened out the AFF4 gene through four calculation methods. Meanwhile, gene introgression and haplotype divergence of AFF4 among low-altitude pig breeds also proved that AFF4 may be one of the driver genes affecting the adaptive evolution of pig body length. Overexpression and knockdown experiments were performed in our study and confirmed the significantly impact of AFF4 on the osteogenic differentiation process.

Conclusions: These results enrich the pig genome pool, offer a comprehensive understanding of genetic architecture for Chinese pig breeds, and shed light on the correlation between latitude and body length of adaptive evolution of Chinese pigs.