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.

研究鸡的性状与遗传变异之间的关系可以为提高鸡的生产性能提供基本信息。在我们之前的工作中，我们用 600 K SNP 阵列 [1] 对 450 只雄性鸡进行了基因分型，发现淀粉酶 α 1A ( AMY1A ) 基因的基因组区域中的几个 SNP 与采食效率和胴体性状显着相关。鉴于 SNP 阵列的准确性较低，我们对雄性和雌性鸡进行了直接测序，以进一步测试鸡AMY1A多态性并研究它们与鸡的 17 个性状的关联。结果表明，AMY1A的5'侧翼区、外显子、内含子和3' UTR（3'非翻译区）有7个SNP, 与日增重 (DG)、平均日采食量 (ADFI)、腿部肌肉重量 (LMW) 和腹部脂肪 (AF) 显着相关 ( p  < 0.05)。此外，基于 rs15910189、rs314354067 和 rs316026696 这三个 SNP 的单倍型与 DG ( p  < 0.01)、ADFI 和 AF ( p  < 0.05) 有显着相关性。为了更好地了解AMY1A 的转录调控，我们克隆了它的 5' 侧翼区域，发现可能改变转录调节子结合位点的 SNP rs316436216 和 rs314213090 分别位于抑制子和增强子区域。此外，荧光素酶测定显示 3' UTR 中的 SNP rs314613110 影响 miRNA gga-miR-1764-3p 的结合。为了验证我们人群中AMY1A是否存在任何拷贝数变异，我们通过全基因组重测序数据对 CNV 进行了全基因组评估。然而，在我们的人群中，在AMY1A中没有发现 CNV ，这与在食用高淀粉饮食的人中发现的AMY1A拷贝数增加不同。因此，本研究提供了大量证据证明具有生长性状和采食效率的AMY1A多态性可能有助于鸡育种计划。