Detection of copy number variation of alpha amylase genes in domestic pigs (Sus scrofa domesticus) and wild boars (Sus scrofa)

Copy numbers of alpha amylase genes (AMY), which encode starch-digesting enzymes, are markedly increased in modern humans and domesticated dogs as an adaptive evolutionary mechanism in response to increased consumption of starch-rich foods acquired either by farming or domestication. In this study, we surveyed total AMY gene copy numbers in 150 domestic pigs (50 pigs of Berkshire breed, 50 of Landrace breed, and 50 of Large White breed) and 51 wild boars (30 Sus scrofa leucomystax and 21 S. s. riukiuanus) to identify whether the gene copy number has changed during the domestication of pigs. The relative copy number of AMY genes was measured using a quantitative polymerase chain reaction (qPCR) and it varied from 2.7 to 10.8 per haploid genome among individuals. However, in the four remaining populations, excluding S. s. riukiuanus, the average copy number was approximately six, and no significant differences were observed between the three selected pig breeds and S. s. leucomystax wild boar. Conversely, S. s. riukiuanus had an average of 7.2 copies. The results indicating six AMY copies per haploid genome were consistent with the porcine genome reference sequence (Sscrofa11.1). These results suggest that there has been no significant increase in the AMY gene copy number during the domestication process of pigs.