不同羽色鸡种ASIP基因SNP位点筛选及其生物信息学分析  

Screening of SNP locus and its bioinformatics analysis of ASIP gene in different chicken breeds with various feather colors

作　　者：简华锋 祖盘玉 李洪林 牟腾慧 龙广丽 饶永超 林家栋 李辉[1,2] 张福平 JIAN Hua-feng;ZU Pan-yu;LI Hong-lin;MOU Teng-hui;LONG Guang-li;RAO Yong-chao;LIN Jia-dong;LI Hui;ZHANG Fu-ping(College of Animal Science,Guizhou University/Key Laboratory of Animal Genetics,Breeding and Reproduction in the Plateau Mountainous Region,Ministry of Education/Key Laboratory of Animal Genetics,Breeding and Reproduction in Guizhou,Guiyang 550025,China;Institute of Poultry,Guizhou University,Guiyang 550025,China;Scientific Research Chicken Farm of Guizhou University,Guiyang 550025,China;Guizhou Agriculture Vocational College,Guiyang 551400,China)

机构地区：[1]贵州大学动物科学学院/高原山地动物遗传育种与繁殖教育部重点实验室/贵州省动物遗传育种与繁殖重点实验室,贵阳550025 [2]贵州大学家禽研究所,贵阳550025 [3]贵州大学科研鸡场,贵阳550025 [4]贵州农业职业学院,贵阳551400

出　　处：《南方农业学报》2020年第8期1823-1831,共9页Journal of Southern Agriculture

基　　金：贵州省科技计划项目(黔科合支撑〔2019〕2285号)。

摘　　要：【目的】揭示刺豚鼠信号蛋白基因(ASIP)SNP位点突变与不同鸡种羽色差异形成机制的关联性,筛选出与鸡种羽色相关的辅助育种分子标记。【方法】参考NCBI已公布的红色原鸡ASIP基因序列(登录号NC_006107.5),运用Primer Premier 5.0设计特异性引物,以罗曼蛋鸡、泰和乌骨鸡、兴义矮脚鸡白羽系、赤水乌骨鸡、贵州黄鸡和瑶山鸡为研究对象,通过DNA混合池及PCR直接测序法筛选不同羽色鸡种ASIP基因SNP位点;估算各SNP位点等位基因频率后,使用RNAfold、NetPhos 2.0、NetOGlyc 4.0、SOPMA和SWISS-MODEL等在线软件进行生物信息学分析,探究不同羽色鸡种ASIP基因SNP位点突变对基因mRNA二级结构、ASIP蛋白翻译后修饰位点及其二、三级结构的影响。【结果】从6个鸡种ASIP基因中检测到7个SNPs位点,分别为Exon-2-G17C、Exon-2-T168C、Exon-2-C3032T、Exon-2-T3203G、Exon-2-G3287A、Exon-2-G3313T和Exon-2-C3350T。其中,Exon-2-T3203G只出现在罗曼蛋鸡上,Exon-2-G3287A只出现在瑶山鸡上。Exon-2-T168C只出现在贵州黄鸡和兴义矮脚鸡白羽系且位于编码区,该位点突变导致编码氨基酸改变[苏氨酸(Thr)→甲硫氨酸(Met)],且能导致ASIP基因mRNA二级结构改变,最小自由能增加,稳定性降低。Exon-2-T168C位点突变还导致ASIP蛋白激酶磷酸化位点数量和位置发生改变,但糖基化位点未发生改变;Exon-2-T168C位点突变后ASIP蛋白二级结构中α-螺旋、β-转角和延伸链的占比增加,而无规则卷曲占比降低,且蛋白三级结构预测结果与二级结构预测结果一致。【结论】在贵州黄鸡和兴义矮脚鸡白羽系ASIP基因上检测到Exon-2-T168C位点,且该位点突变能引起ASIP基因m RNA二级结构、蛋白激酶磷酸化位点数量和位置及ASIP蛋白二、三级结构均发生改变,但并不是影响贵州黄鸡和兴义矮脚鸡白羽系羽色差异的内在机制。【Objective】In order to reveal the association between the agouti signal protein(ASIP)gene SNP mutation and the formation mechanism of the feather color difference in different chicken breeds,and screen out auxiliary breeding molecular markers related to the feather color of chicken breeds.【Method】According to the ASIP gene sequence of the red rock fowl(accession number NC_006107.5)published by NCBIand design specific primers by Primer Premier 5.0,Roman layer chicken,Taihe silky chicken,Xingyi bantam white feather line,Chishui black-bone chicken,Guizhou yellow chicken and Yaoshan chicken were chosen as research objects.The SNP locus of ASIP gene in different feather color chicken breeds were screened by DNA mixing pool and PCR direct sequencing method;RNAfold,NetPhos 2.0,NetOGlyc 4.0,SOPMA and SWISS-MODEL and other online software were used for bioinformatics analysis after estimating allele frequency of each SNP locus.Analyzing the effect of ASIP gene SNP site mutation in different feather color chickens on gene mRNA secondary structure,ASIP protein post-translational modification site and its secondary and tertiary structure.【Result】Seven SNPs were detected in ASIP gene from six chicken breeds,they were Exon-2-G17C,Exon-2-T168C,Exon-2-C3032T,Exon-2-T3203G,Exon-2-G3287A,Exon-2-G3313T and Exon-2-C3350T,respectively.Exon-2-T3203G only appeared in Roman layers,and Exon-2-G3287A only appeared in Yaoshan chicken.Exon-2-T168C only appeared in Guizhou yellow chicken and Xingyi bantam white feather line which was located in the coding region of ASIP gene.The mutation led to the change of coding amino acid site[threonine(Thr)→methionine(Met)],which caused the change of secondary structure of ASIP gene mRNA,increased minimum free energy and decreased stability.Exon-2-T168C site mutation also caused the change of number and location of ASIP protein kinase phosphorylation sites,but the glycosylation sites did not change.The secondary structure of ASIP protein such as the proportions ofα-helix,β-turn,and exten

关 键 词：鸡 羽色 刺豚鼠信号蛋白基因(ASIP) SNP位点 生物信息学 

分 类 号：S831.89[农业科学—畜牧学]