SINE Insertion in the Pig Carbonic Anhydrase 5B (CA5B) Gene Is Associated with Changes in Gene Expression and Phenotypic Variation.

Transposons are genetic elements that are present in mammalian genomes and occupy a large proportion of the pig genome, with retrotransposons being the most abundant. In a previous study, it was found that a SINE retrotransposon was inserted in the 1 intron of the gene in pigs, and the present study aimed to investigate the SINE insertion polymorphism in this gene in different pig breeds. Polymerase chain reaction (PCR) was used to confirm the polymorphism in 11 pig breeds and wild boars), and it was found that there was moderate polymorphism information content in 9 of the breeds. Further investigation in cell experiments revealed that the 330 bp SINE insertion in the RIP- site promoted expression activity in the weak promoter region of this site. Additionally, an enhancer verification vector experiment showed that the 330 bp SINE sequence acted as an enhancer on the core promoter region upstream of the gene region. The expression of in adipose tissue (back fat and leaf fat) in individuals with the (SINE) genotype was significantly higher than those with (SINE) and (SINE) genotypes. The association analysis revealed that the (SINE) genotype was significantly associated with a higher back fat thickness than the (SINE) genotype. Moreover, it was observed that the insertion of SINE at the RIP- site carried ATTT repeats, and three types of (ATTT) repeats were identified among different individuals/breeds (i.e., (ATTT), (ATTT) and (ATTT)). Overall, the study provides insights into the genetic basis of adipose tissue development in pigs and highlights the role of a SINE insertion in the gene in this process.