A Copy Number Variation Plays Another Major QTL Effect on Ear Size in Pigs

Ear size and type are important conformation characteristics of pig breeds. Several studies identified significant QTL for ear size on pig chromosome (SSC) 5. But its causative gene and mutation has not been characterized. We herein performed genome-wide association studies (GWAS) for ear size in five pig populations and evidenced the QTL on SSC5. By using haplotype-sharing and homozygosity mapping analysis, we refined the critical QTL region to a 138.05-kb interval. Only MSRB3 gene locates within this region. MSRB3 gene encodes a protein repair enzyme that catalyzes the reduction of methionine sulfoxide to methionine. Using genome resequencing data, we identified a 38.4-kb duplication covering the last two exons of MSRB3 gene. The duplication showed perfect concordance with the QTL genotypes of all 19 founder animals segregating in the White Duroc × Erhualian intercross. The duplication occurs at high frequencies in Chinese large-eared breeds, but has not been found in small and erect-eared breeds. Moreover, the duplication exhibits the extremely significant association with ear size in the tested pig populations and causes an increase of 13.84% ~ 33.35% in ear size. Western blot analysis found that the duplication significantly reduces the expression level of MSRB3 gene in ear tissue. Further experiments are being performed to confirm the causality of the duplication within MSRB3 gene for porcine ear size.