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

Abstract

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.

Copy number variation of amylase alpha 2B gene is associated with feed efficiency traits in Large White pigs

“…Similar events have been reported for increased copy numbers of the AMY2B gene in dogs (Axelsson et al 2013). However, no clear increase in the AMY gene has been detected in domesticated pigs (Paudel et al 2013;Pajic et al 2019;Yoshidomi et al 2021). It is believed that this is because wild boars are omnivorous; therefore, they do not require an increase in the number of copies of the amylase gene to adapt to starch-rich feed (Pajic et al 2019).…”

“…In Sscrofa11.1, there are seven loci, AMY2B, LOC100521789 (AMY2A), LOC110258046, LOC100153854, LOC110260364, LOC100522672 and LOC100153446, including those present in unplaced genomic scaffold contigs. It has been reported that CNVs of the AMY gene are present in pigs and wild boars (Paudel et al 2013;Pajic et al 2019;Yoshidomi et al 2021). However, unlike domesticated dogs, no clear difference was detected in the mean copy number of the AMY gene between pigs and wild boars (Paudel et al 2013;Pajic et al 2019;Yoshidomi et al 2021).…”

“…It has been reported that CNVs of the AMY gene are present in pigs and wild boars (Paudel et al 2013;Pajic et al 2019;Yoshidomi et al 2021). However, unlike domesticated dogs, no clear difference was detected in the mean copy number of the AMY gene between pigs and wild boars (Paudel et al 2013;Pajic et al 2019;Yoshidomi et al 2021). Based on these results, Pajic et al (2019) pointed out that pig domestication did not require any increased AMY gene copies for feed adaptation due to the omnivorous nature of wild boars.…”

“…At least three of the seven loci in the Sscrofa11.1 are probably pseudogenes because some of the exons are missing, and the predicted coding sequence cannot be translated as an amylase protein. In previous studies, the copy number of pig AMY genes was established for functional and pseudogenised loci (Paudel et al 2013;Pajic et al 2019;Yoshidomi et al 2021). Therefore, no association analysis between the CNVs of the AMY gene and the trait of pigs has been reported.…”