Genomic Profiling of Antibody Repertoire in Rongchang Pigs Uncovers Conserved V(D)J Gene Usage and Breed-Specific...

Pigs are economically critical livestock andan optimal model for investigating the development and diversification of antibody repertoires. The Rongchang (RC) pig, a nationally protected indigenous breed in China, possesses unique genetic characteristics, yet genomic-level research on its antibody repertoire remains limited, as most porcine antibody studies have focused on Landrace pigs.

To decipher the genetic features of the antibody library in RC pigs, we used immunogenomic high-throughput sequencing to systematically analyze the antibody repertoires of five healthy purebred pig breeds, including two indigenous breeds (RC and BM) and three commercial breeds (Yorkshire, Duroc, and Landrace), with a focus on comparing conserved patterns and breed-specific differences in V(D)J gene utilization between Rongchang pigs and the other four breeds.

All five breeds exhibited a strong preference for a conserved subset of core IGHV genes. Notably, this study detected functional IGHJ3 expression (0.40.8%) in all examined breeds, contradicting the conventional view that only IGHJ5 is functional in porcine antibody repertoires. Among them, RC pigs showed the lowest IGHJ3 frequency. Furthermore, RC pigs ranked second in antibody repertoire diversity among the five breeds, implying abundant antigen-binding specificity, and exhibited the lowest CDR3 proportion, indicating breed-specific V(D)J recombination preferences.

These results clarify the conserved and breed-specific characteristics of RC pig antibody repertoires, establishing a basis for exploring the genetic regulation of V(D)J-mediated antibody repertoire changes under varied immune conditions. This work also provides genomic support for the rational utilization of RC pig genetic resources.