樱桃谷鸭ATF4基因SNPs筛查及生物信息学分析

Single nucleotide polymorphism screening and bioinformatics analysis of ATF4 gene in Cherry Valley ducks

旨在在樱桃谷鸭群体中筛选出转录激活因子4(activating transcription factor 4,ATF4)基因突变个体,通过选育而培育具有优质蛋壳品质的优良家禽品种。以樱桃谷鸭为试验对象,构建DNA混合池,利用普通PCR分段扩增得到ATF 4基因序列,并筛查其单核苷酸多态性(single nucleotide polymorphism sites,SNPs),进行生物信息学分析。结果显示:樱桃谷鸭ATF4基因编码区全长1065 bp,可编码354个氨基酸,ATF 4基因编码的蛋白为不稳定的可溶性蛋白,不存在信号肽,有2个N-糖基化位点;ATF4基因CDS区共筛查到4个SNPs,分别是A^909G、G^636A、G^813A和T^867A,除T^867A是错义突变外,其他3个SNPs均为同义突变,4个SNPs均引起mRNA二级结构和自由能和基因频率的改变;蛋白质的二级结构和三级结构主要元件为α-螺旋、无规则卷曲和延伸链,T 867 A突变后蛋白质的二、三级结构均发生了变化,其中α-螺旋、延伸链和β-折叠含量均增加,无规则卷曲含量减少。以上研究表明,樱桃谷鸭ATF4基因具有丰富的多态性,为提高樱桃谷鸭蛋壳品质的分子标记辅助选择提供了理论基础。

To screen out the mutant individuals of activating transcription factor 4(ATF4)gene in Cherry Valley duck population and breed excellent poultry breeds with good egg shell quality,a DNA mixing pool was constructed with Cherry Valley duck as the test object.The ATF4 gene coding sequence was obtained by common PCR fragmentation amplification and screening.single nucleotide polymorphism sites(SNPs)and bioinformatics analysis were examined.The results showed that the coding region of ATF4 gene of Cherry Valley duck was 1065 bp in length,encoding 354 amino acids.The protein was unstable and soluble.There were no signal peptide but two N-glycosylation sites.Four SNPs were screened in the CDS region of ATF4 gene,namely A^909G,G^636A,G^813A and T^867A,except that T^867A was a missense mutation.All of them were synonymous mutations.Four SNPs caused changes in the secondary structure and free energy of RNA and gene frequency.The primary components of the secondary and tertiary structures of proteins were α-helix,random curl and extended chain.After T^867A mutation,the secondary and tertiary structures of proteins had all changed,and the contents of α-helix,extended chain and β-fold had all increased,while the contents of random curl had decreased.In conclusion,ATF4 gene of Cherry Valley duck had abundant polymorphism,which provided a theoretical basis for molecular marker-assisted selection to improve the egg shell quality of Cherry Valley duck.