Polymorphisms of AMY1A gene and their association with growth, carcass traits and feed intake efficiency in chickens

Investigations on the association between chicken traits and genetic variations can provide basic information to improve production performance in chickens. In our previous work, we genotyped 450 male chickens with a 600 K SNP array [1] and found that several SNPs in the genomic regions of the amylase alpha 1A (AMY1A) gene were significantly associated with feed intake efficiency and carcass traits. Given the lower accuracy of the SNP array, we performed direct sequencing with male and female chickens to further test chicken AMY1A polymorphisms and investigate their association with 17 traits in chickens. The results showed that 7 SNPs in the 5' flanking region, exon, intron and 3' UTR (3' untranslated region) of AMY1A, were significantly associated with daily gain (DG), average daily feed intake (ADFI), leg muscle weight (LMW) and abdominal fat (AF) (p < 0.05). Additionally, the haplotypes based on three SNPs, rs15910189, rs314354067 and rs316026696, showed significant associations with DG (p < 0.01), ADFI and AF (p < 0.05). To better understand the transcriptional regulation of AMY1A, we cloned its 5' flanking region and found that the SNPs rs316436216 and rs314213090 which might change the transcriptional regulator binding sites, were in the suppressor and enhancer regions, respectively. In addition, luciferase assays revealed that the SNP rs314613110 in the 3' UTR influenced the binding of the miRNA gga-miR-1764-3p. To validate whether there is any copy number variation in AMY1A in our population, we performed a genome-wide assessment of CNVs through whole-genome resequencing data. However, no CNV was found in AMY1A in our population, which is different from the increased copy number of AMY1A found in humans who consume a high-starch diet. Therefore, the present study provides substantial evidence for the association of AMY1A polymorphisms with growth traits and feed intake efficiency, which might contribute to chicken breeding programs.