CN108795947B - 一种翘嘴鳜il-6基因及其抗病snp标记的检测方法 - Google Patents
一种翘嘴鳜il-6基因及其抗病snp标记的检测方法 Download PDFInfo
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Abstract
本发明公开了一种翘嘴鳜IL‑6基因及其抗病SNP标记的检测方法。本发明克隆了翘嘴鳜IL‑6基因cDNA序列,如SEQ ID NO:1所示。在此基础上进一步克隆出含翘嘴鳜IL‑6基因内含子的IL‑6 gDNA序列,如SEQ ID NO:2所示。根据IL‑6 gDNA序列设计用于扩增抗病SNP位点的引物,扩增翘嘴鳜IL‑6基因获得扩增产物,并对扩增产物进行测序并找出与病毒疾病抗性相关的SNPs位点,根据DNA峰形图确定出SNP位点。本发明首次克隆到了翘嘴鳜IL‑6 cDNA全长序列、IL‑6 gDNA全长序列,为鱼类的抗病选育等工作提供研发基础;并且,本发明检测到了鳜鱼IL‑6基因与病毒疾病抗性相关的SNP位点,为翘嘴鳜的选育工作提供新思路,有利于推进翘嘴鳜的遗传育种进程,提高鳜鱼养殖经济效益。
Description
技术领域
本发明属于水产养殖、生物技术领域,尤其涉及一种翘嘴鳜IL-6基因及其抗病SNP标记的检测方法。
背景技术
翘嘴鳜(Siniperca chuatsi)作为我国具有重要经济价值的“名特优”鱼类,在我国的淡水养殖中占据重要地位,然而在近几年的大规模人工养殖条件下,翘嘴鳜的种质退化现象比较普遍,导致抗病能力逐渐下降,尤其是病毒性疾病日益猖獗,而且至今未有十分有效的防治方法,每年都造成严重的经济损失,严重制约了其养殖业的可持续发展。
现有鱼类选育技术是根据肉眼观察到的鱼类表观性状对鱼类进行选育,无法从与表观性状密切相关的基因差异角度对鱼类进行正确的选育,不仅无法开展早期选育、后代的性状难以保证,而且选育的盲目性大、费时费力。
开展与抗病相关基因的克隆,并利用SNP分子标记检测或筛选抗病的翘嘴鳜种质资源,进而选育出抗病种群,是提高翘嘴鳜对病毒性等疾病抗性的有效手段。其中,SNPs(signal nucleotide poly-morphisms),即单核苷酸多态性。基因片段上单个碱基发生转换、颠换、插入或缺失,会使得SNP表现出多态性,也会导致生物个体间的抗病性表型出现差异。
在抗病相关基因中,IL-6(白细胞介素-6,简称白介素6),是属于白细胞介素的一种细胞因子,能够促进参与免疫反应的各种细胞的增殖和分化,并且提高其功能,同时还会抑制细胞的凋亡。但目前有关鱼类IL-6基因克隆和功能的相关研究还很缺乏,这是由于鱼类和其他物种的IL-6基因序列的同源性很低,而且IL-6基因的转录和翻译过程在受到免疫刺激时会很不稳定,导致鱼类细胞因子的cDNA文库克隆成果较少。因此,克隆翘嘴鳜IL-6的cDNA全长序列、gDNA全长序列具有重要意义。
发明内容
本发明的目的在于提供一种翘嘴鳜抗病基因IL-6基因(白细胞介素-6,IL-6),旨在解决鱼类与其他物种IL-6基因的同源性很低,而有关鱼类IL-6基因缺乏的问题。
本发明的再一目的在于提供翘嘴鳜抗病SNP标记的检测方法,该方法以本发明所发现的翘嘴鳜IL-6基因为基础,利用单核苷酸多态性(SNP)与鱼类抗病表观性状相结合,以抗病或非抗病鱼类IL-6的SNP标记(或称突变位点)为依据,可精准选育出抗病鱼类种群,提高优种选育的工作效率,降低选育鱼类的发病率和死亡率,进而增加鱼类养殖的经济效益,这对于鱼类选育的技术进步具有非常重要的意义。
本发明是这样实现的,一种翘嘴鳜IL-6基因,该基因的cDNA序列如SEQ ID NO:1所示。
本发明进一步公开了基于上述翘嘴鳜IL-6基因的抗病SNP标记的检测方法,该方法包括以下步骤:
(1)根据含翘嘴鳜IL-6基因的内含子的IL-6 gDNA序列设计用于扩增抗病SNP位点的引物,扩增翘嘴鳜IL-6基因获得扩增产物;
(2)对扩增产物进行测序并找出与病毒疾病抗性相关的SNPs位点,根据DNA峰形图确定出SNP位点。
优选地,在步骤(1)中,所述IL-6 gDNA序列通过对翘嘴鳜IL-6基因设计特异性引物并扩增获得,该IL-6 gDNA序列的核苷酸序列如SEQ ID NO:2所示。
优选地,所述特异性引物为:
IL-6-1F:5’-CTCAGCATCAGCGGAAACTC-3’;
IL-6-1R:5’-TGCCCCTGTTGGCCATACTT-3’。
优选地,在步骤(1)中,所述翘嘴鳜IL-6基因通过cDNA末端快速扩增RACE技术克隆得到。
优选地,在步骤(1)中,所述扩增抗病SNP位点的引物为:
IL-6-L1F:5’-AACCCAAAGAGGCAGGTGAC-3’;
IL-6-L1R:5’-ACCATCCAATTTCCCTGAGGT-3’。
优选地,在步骤(2)中,通过DNAMAN软件对测序结果做多序列比对并找出疑似SNPs位点,根据Chromas软件查看DNA峰形图,判断是否为套峰以确定出SNP位点。
相比于现有技术的缺点和不足,本发明具有以下有益效果:
(1)本发明首先克隆到了翘嘴鳜IL-6 cDNA全长序列、IL-6 gDNA全长序列,为鱼类的抗病选育等工作提供研发基础;
(2)本发明检测到了鳜鱼IL-6基因与病毒疾病抗性相关的SNP位点,为翘嘴鳜的选育工作提供新思路,有利于推进翘嘴鳜的遗传育种进程,提高鳜鱼养殖经济效益。
附图说明
图1是翘嘴鳜IL-6基因各阶段扩增后的凝胶电泳结果;其中,图1(A)是翘嘴鳜IL-6基因cDNA 5’端RACE第二轮PCR琼脂糖凝胶电泳结果,泳道1为目的片段;图1(B)翘嘴鳜IL-6基因cDNA 3’端RACE第二轮PCR琼脂糖凝胶电泳结果,泳道1为目的片段;
图2是加入内含子所用的引物进行翘嘴鳜IL-6基因PCR扩增后的凝胶电泳结果;
图3是翘嘴鳜IL-6基因SNP位点检测PCR扩增后的凝胶电泳结果;
图4是翘嘴鳜头肾组织传染性脾肾坏死病毒(ISKNV)PCR检测结果;其中,泳道①DL500Mark电泳后得到的条带;泳道②③均为以ISKNV病毒感染组翘嘴鳜头肾组织匀浆液制备的模板PCR扩增、电泳得到单一明亮的ISKNV病毒核苷酸特异性条带(187bp);其它泳道为感染组翘嘴鳜头肾组织匀浆液制备的模板PCR扩增、电泳未见特异性条带;
图5是在22组翘嘴鳜样品的IL-6DNA反向互补序列进行比较后的结果截图;其中,有3个样品的碱基G突变为碱基A;
图6是基因测序仪器对翘嘴鳜样品的IL-6DNA测序时所生成的DNA峰形图,该图中翘嘴鳜样品的IL-6DNA未突变G纯合子;
图7是基因测序仪器对翘嘴鳜样品的IL-6DNA测序时所生成的DNA峰形图,该图中翘嘴鳜样品的IL-6DNA未突变G杂合子;
图8是基因测序仪器对翘嘴鳜样品的IL-6DNA测序时所生成的DNA峰形图,该图中翘嘴鳜样品的IL-6DNA突变为A纯合子。
具体实施方式
为了使本发明的目的、技术方案及优点更加清楚明白,以下结合附图及实施例,对本发明进行进一步详细说明。应当理解,此处所描述的具体实施例仅仅用以解释本发明,并不用于限定本发明。
一、翘嘴鳜IL-6 cDNA序列的克隆
1、翘嘴鳜IL-6 5’端序列的扩增
(1)cDNA第一链的合成、纯化及加尾
用SUPERSCRIPT II RT酶、引物GSP-IL-6-1对已提取的总RNA进行IL-6第一链cDNA的合成。使用RNase Mix对合成的cDNA进行去RNA处理。其中,反转录体系为:
70℃孵育10分钟,立刻置于冰上冷却1分钟,短暂离心收集液体,继续添加如下体系:
轻轻混匀后离心,42℃孵育1分钟,再添加1μl SUPERSCRIPTII RT,混匀后42℃孵育50分钟后,70℃孵育15分钟停止反应,离心后置于37℃,添加RNase mix 1μl,反应30分钟,对其进行纯化后,用TdT酶和dCTP对纯化后的cDNA末端加上poly(c)后,低温保存备用。
(2)cDNA 5’末端快速扩增
使用引物GSP-IL-6-2对已经加dC尾的cDNA进行PCR第一轮扩增,按如下顺序添加5’-RACE反应体系:
PCR反应程序为:94℃预变性2min,94℃变性30s,55℃重新分析退火30s,72℃延伸1min,30个循环,最后72℃终延伸7min。
使用引物GSP-IL-6-3和桥连通用扩增引物AUAP进行巢式PCR第二轮扩增,体系如下:
PCR反应程序为:94℃预变性2min,94℃变性30s,59℃重新分析退火30s,72℃延伸1min,32个循环,最后72℃终延伸7min。
将第二轮PCR产物进行琼脂糖凝胶(1.2%)电泳,使用胶回收试剂盒(生工,上海)对目的条带进行切胶回收。回收纯化后的PCR产物,克隆到pMD18-T载体上(TaKaRa),挑取阳性克隆进行测序。
2、翘嘴鳜IL-6 3’端序列的扩增
(1)cDNA第一链的合成、纯化
用SUPERSCRIPT II RT酶、引物3’CDS primer A(SMARTerTMRACE cDNAAmplification Kit试剂盒,Clontech)对提取的总RNA进行逆转录,所用引物为3’CDSprimerA,其他成分与条件5’端扩增相同。
(2)cDNA末端快速扩增
使用引物GSP-IL-6-4和UPM,以之前合成的cDNA为模板进行PCR第一轮扩增,按如下顺序添加3’-RACE反应体系(反应程序同5’扩增程序):
将第一轮扩增的PCR产物稀释50倍,进行第二轮PCR扩增,除引物GSP-IL-6-5和UPM外,其他体系同第一轮扩增相同,反应程序同5’扩增程序。对第二轮PCR产物进行琼脂糖凝胶(1.2%)电泳,对目的条带切胶回收,如图1所示,将纯化后的产物克隆到pMD18-T载体上(TaKaRa),挑取阳性克隆进行测序,拼接得到的翘嘴鳜IL-6 cDNA完整系列,如SEQ ID NO:1所示,该翘嘴鳜IL-6 cDNA的编码氨基酸序列如SEQ ID NO:3所示。
表1 IL-6基因cDNA扩增所用引物的序列
3、翘嘴鳜IL-6 gDNA的获得
参照其他鱼类已知的IL-6 gDNA结构,对拼接得到的翘嘴鳜IL-6 cDNA完整片段设计特异性引物扩增IL-6基因的内含子(表2),设计扩增的片段要含有重叠区域,便于后续的序列拼接;以翘嘴鳜基因组DNA为模板,对该基因进行分片段PCR扩增,扩增程序为:94℃预变性5min,94℃变性30s,52℃退火30s,72℃延伸1min,30个循环,最后72℃终延伸10min。PCR产物用1.5%琼脂糖凝胶电泳检测,如图2所示,挑选单一条带切胶回收,采用T载体PCR产物克隆试剂盒(TAKARA)将其连入pUmc-T载体,10μL体系,4℃过夜。挑取阳性克隆,测序。采用人工比对和DNAMAN软件对所获得的序列进行拼接,得到翘嘴鳜IL-6 gDNA基因全长,如SEQ ID NO:2所示。
表2扩增IL-6基因内含子所用引物的序列
引物名称 | 引物序列(5’—3’) |
IL-6-1F | CTCAGCATCAGCGGAAACTC |
IL-6-1R | TGCCCCTGTTGGCCATACTT |
4、抗病SNP标记检测
(1)根据翘嘴鳜IL-6 gDNA的序列,设计引物(表3),PCR反应体系如表4所示。
表3扩增翘嘴鳜IL-6基因获得抗病SNP位点所用的引物序列
引物名称 | 引物序列(5’—3’) |
IL-6-L1F | AACCCAAAGAGGCAGGTGAC |
IL-6-L1R | ACCATCCAATTTCCCTGAGGT |
表4扩增翘嘴鳜IL-6基因获得抗病SNP位点所用的PCR反应体系
成分 | 体积(μl) |
模板DNA | 2 |
引物R(10μl) | 1 |
引物F(10μl) | 1 |
2×Easy Taq PCR Super Mix | 25 |
ddH<sub>2</sub>O | 21 |
合计 | 50 |
PCR扩增步骤:(1)94℃预变性5分钟;(2)94℃变性30秒;(3)52℃退火30秒;(4)72℃延伸1分钟,共30个循环;(5)72℃延伸10分钟;(6)4℃反应结束。
(2)PCR产物用1.5%琼脂糖凝胶电泳,获得PCR扩增产物,如图3所示,割胶后,立即测序。
(3)使用DNAMAN软件对测序结果做多序列比对,找出与病毒疾病抗性相关的SNPs位点,然后根据Chromas软件查看DNA峰形图,判断是否为套峰,从而确定出SNP位点。
二、基于翘嘴鳜IL-6基因的抗病SNP标记检测结果
同一群体的翘嘴鳜均按照同样的饲养条件进行养殖,在养殖两个月左右后,从养殖的群体中随机挑选100尾,进行攻毒试验,各组每尾鱼通过腹腔注射传染性脾肾坏死病毒(ISKNV)(也称虹彩病毒)10×TCID50ISKNV,连续观察10天,观察到其发病症状与自然环境下感染ISKNV发病症状相同,发病鱼在水面游动缓慢甚至直接漂浮于水面,体表无破损,体色偏白,鱼鳃呈现缺血状的发白,解剖发现:腹腔有较多腹水,肝脏、胃壁、肠壁充血,肠道内有黄色积液;抗病鱼异常。PCR检测发病翘嘴鳜头肾的为ISKNV阳性,表明其死亡原因是由于感染ISKNV所致。
选取其中的未发病鱼9尾,发病鱼3尾(标记为E05、H07、A07),分别剪下鱼的少量尾鳍并放入无水乙醇中在4℃下进行低温保存。按上述实施例中记载的抗病SNP标记检测方法,获得PCR扩增产物,如图4所示,割胶后,测序,用DNAMAN软件进行多序列比对,在233bp处找到与病毒疾病抗性相关的SNP位点,如图5所示。
用Chromas软件查看上述序列中疑似突变的碱基在233bp的峰形图,如图6、图7、图8所示,在互相对应的碱基G和A处,峰均单一明显无杂峰,由此得出,在233bp处,碱基确实发生了突变,由G转换为A,即G233A。又因为这个突变发生在DNA反向互补序列上,所以,在原DNA序列中,SNP位点为C1744T,位于外显子上。碱基发生变异的3个样品(E05、H07、A07)均是易感病毒的翘嘴鳜。因此,易感病毒的翘嘴鳜IL-6基因的SNP是在1744bp处碱基发生了由C转换为T的突变。通过此方法可鉴别抗病毒的翘嘴鳜与易感病毒的翘嘴鳜。
以上所述仅为本发明的较佳实施例而已,并不用以限制本发明,凡在本发明的精神和原则之内所作的任何修改、等同替换和改进等,均应包含在本发明的保护范围之内。
序列表
<110> 苏州大学
<120> 一种翘嘴鳜IL-6基因、克隆及其抗病SNP标记的检测方法
<130> PA181852F
<141> 2018-06-29
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tgccctataa actcaacgcg tacctgctct ctgcagtgat gctggcagct ccgctgcagt 180
gcgctcccgg agctccagct gaatacgcgc ccaccgacag cccggcaggt gactcctcag 240
gtgaggagga ggaggaggag aggccctctg aactactgag cgtctccaag gagttggagt 300
tgatccttgg cgcaaccaaa cgccacaggg aggagtttga agatgaattc caaactgagg 360
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ccaacttcag caaggaggct tgtctccaca ggttggccca tgggctgcct atttacagag 480
ttcttctcaa gtatgtggag aaggagtgcc ccagcagccg gatcccctca gaggccagat 540
tctacggagg cctcctgatc agtcagatca aagaaaagat gaagaaccct gaacaggtca 600
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gcaaaagagc tattaaaaaa agggagttca gagcaagtat ggccaacagg ggcatggcac 780
ctgttacttt ctattaccaa aagttaaaaa tatgaaggta ttaaaaatca cttattacgt 840
aatacctcag ggaaattgga tggtgttaaa agtacatgtt ctgagtacac caactgtact 900
gttggtatag tgggtctatc aatctatgac tgtgtaaatc ttacagacct caaggcttga 960
accaaccact attacacaac ttatttaacc tatttatgct tagtgaaaag tgatatttat 1020
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taacccaaag aggcaggtga ctcctcagga caggtgactc ctcagggcag gtgactcctc 60
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cctcttttgt tgttcattca gtcattcatg ctttacgtcc ccgcacagac gcgtacctgc 240
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cgcccaccga cagcccggca ggtgactcct caggtgagga ggaggaggag gagaggccct 360
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tgtttctttc atcatttccc cttatcagtt tgaagatgaa ttccaaactg aggtgaaata 600
tgactttctg aggcactaca cagtctcctc acttccagca agctgccctt actccaactt 660
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tggtggggtt catttgagca ctgacagtga ttttctttcc tctctccagg aggcttgtct 780
ccacaggttg gcccatgggc tgcctattta cagagttctt ctcaagtatg tggagaagga 840
gtgccccagc agccggatcc cctcagaggc cagattctac ggaggcctcc tgatcagtca 900
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gaagtagcac aaaatggaaa tacccaagca aagtacctca aaactgtact taagctcagt 1380
acttgagtaa tgtacttact tacattccac cactggttat agctcagtta ttagattccc 1440
tacttataat ttcttttgcg tttaatttct gttgcgtaaa tgtctgattt tgtcttctat 1500
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ggtcacggca ctcaccagca gccaggagaa taagctgctg aaggacctcg acaaccccga 1680
cactttccac agaaagatga cggcacacag catcctgcgc cagctccact acttccttgt 1740
cgacggcaaa agagctatta aaaaaaggga gttcagagca agtatggcca acaggggcat 1800
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Gln Leu His Tyr Phe Leu Val Asp Gly Lys Arg Ala Ile Lys Lys Arg
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aaagggagtt cagagcaagt atggc 25
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Claims (1)
1.一种与病毒抗性相关的SNP标记在制备用于选育抗病毒翘嘴鳜试剂中的用途,其特征在于,所述SNP标记位于翘嘴鳜的核苷酸序列如SEQ ID NO:2所示的gDNA序列的第1744bp处,其中,易感病毒翘嘴鳜的所述1744bp处碱基为T,抗病毒翘嘴鳜的所述1744bp处的碱基为C;所述病毒为传染性脾肾坏死病毒。
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