cDNA cloning and polymorphism of the porcine carbonic anhydrase III (CA3) gene

Carbonic anhydrase III (CA3) is a member of a multigene family that encode carbonic anhydrase, isozymes. In this study, a complete coding sequence of the pig CA3 gene which encodes a 260 amino-acid protein as determined. The amino acid comparison showed high sequence similarities with previously identified human (86.5%) CA3 gene and mouse (91.5%) Car3 genes. The partial genomic DNA sequences were also investigated. The length of intron 1 as 727 bp. Comparative sequencing of three pig breeds revealed that there was a T -> C substitution at position 363 within intron 1. The substitution was situated within a NeoI recognition site and was developed as a PCR-restriction fragment length polymorphism (RFLP) marker for further use in population variation investigations and association analysis. Two alleles (A and B) were identified, and 617 bp fragments were observed for the AA genotype and 236 bp and 381 bp fragments for the BB genotype, The polymorphism of CA3 as detected in 8 pig breeds, Allele AA was predominant in the Western pig breeds. In addition, association studies of the CA3 polymorphism with carcass traits in 140 Yorkshire x Meishan F-2 offspring showed that the NcoI PCR-RFLP genotype may be associated with variation in several carcass traits of interest for pig breeding. Allele B was associated with increases in lean meat percentage, loin eye height and loin eye area. Statistically significant association with backfat thickness was also founds pigs with the AB genotype had much less backfat thickness than AA or BB genotypes.