摘要：

为检测汶上芦花鸡CDKN2A基因SNP位点,并对该基因进行生物信息学及其在皮肤组织中的表达规律分析。研究基于江苏省家禽科学研究所资源保护与评价课题组前期组装的汶上芦花鸡高质量染色体水平基因组,将其与鸡参考基因组(GRCg7b)比对获得CDKN2A基因SNP位点,采用MassARRAY核酸质谱技术对其进行多态性检测和基因分型;运用生物信息学软件预测CDKN2A基因调控序列,及其编码蛋白质理化性质和结构特征;采用转录组和实时荧光定量方法分析该基因在汶上芦花鸡不同时期皮肤组织中的表达情况。结果表明,汶上芦花鸡CDKN2A序列总长度为9.854 kb,CDS全长183 bp,共编码60个氨基酸,在该基因及其上下游1 kb序列范围内共发现41个SNP,其中4个为新发现的SNP,分别位于基因下游和内含子区,第1外显子上发现2个错义SNP:V9D和C10R,41个SNP中34个SNP在汶上芦花鸡群体中检出率在91%以上,但基本均为纯合突变型,无多态存在;汶上芦花鸡CDKN2A基因上游2 kb区域内预测到8个启动子和5个CpG岛,启动子区包含Sp1、MEB-1、YY1、C/EBPα和AP-2α等12种转录因子结合潜在位点,该基因编码蛋白分子质量为7.30 ku,理论等电点为12.82,为带正电荷的、不稳定亲水性蛋白,亚细胞定位主要在线粒体中,无信号肽区域和信号肽剪切位点,共存在8个潜在磷酸化位点,不存在糖基化位点,含有典型的TRP_2(瞬时受体电位离子通道Ⅱ)保守结构域,其二级和三级结构主要以α-螺旋和无规则卷曲为主,并与MDM2、NPM1、USP36蛋白存在相互作用;汶上芦花鸡1~35日龄CDKN2A基因在其背部皮肤中的表达呈上升趋势。

关键词: 汶上芦花鸡, CDKN2A, SNP变异位点, 生物信息学分析, 组织表达

Abstract:

This study aimed to detect the SNPs of CDKN2A gene in Wenshang Barred chicken,and perform the analysis of its bioinformatics and expressions in skin tissues.Based on the high quality chromosome-level genome of Wenshang Barred chicken assembled by the research group of Resource Conservation and Evaluation in Jiangsu Institute of Poultry Science,the sequences were blasted to chicken reference genome (GRCg7b) and the SNPs were acquired.These SNPs were detected and genotyped by MassARRAY nucleic acid mass spectrometry in the chicken population.Bioinformatics software was used to predict the regulatory sequence of CDKN2A gene.The physicochemical properties and structural characteristics of the encoded protein were analyzed.The expressions of this gene in the skin tissues of Wenshang Barred chicken at different periods were detected by transcriptome and Real-Time Fluorescence Quantitative PCR.The results showed that the total length of CDKN2A and its CDS were respectively 9.854 kb and 183 bp,encoding 60 amino acids.Forty-one SNPs were found in this gene and its upstream and downstream 1 kb,of which four SNPs were newly discovered loci.These four new SNPs were located in the downstream and the intron,respectively.The first exon had two SNPs,both of which were missense mutations:V9D and C10R.The detection rates of 34 SNPs among the 41 SNPs were all over 91% in the Wenshang Barred chicken population.These SNPs were almost homozygous mutants without polymorphism.Eight promoters and five CpG islands were predicted in the 2 kb upstream of CDKN2A in Wenshang Barred chicken.The promoter region contained a total of 12 transcription factor binding sites,including Sp1,MEB-1,YY1,C/EBPα,AP-2α.The protein encoded by this gene was a positively charged,unstable hydrophilic protein with a molecular mass of 7.30 ku and a theoretical isoelectric point of 12.82.The predictive subcellular localization of the protein was mainly in mitochondria.The protein had no signal peptide regions and signal peptide shear sites.It had eight potential phosphorylation sites and no glycosylation sites.The protein contained a typical TRP_2 (transient receptor potential ion channelⅡ) conserved domain and its secondary and tertiary structures were mainly α-helices and random coil.In addition,it had interactions with MDM2,NPM1,USP36 proteins.The expressions of CDKN2A gene in the back skins increased from 1 to 35 days old in Wenshang Barred chicken.

Key words: Wenshang Barred chicken, CDKN2A, SNP variations, Bioinformatics analysis, Tissue expression