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CN105624298A - Method for detecting genetically modified components of rape - Google Patents

Method for detecting genetically modified components of rape Download PDF

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CN105624298A
CN105624298A CN201610061083.4A CN201610061083A CN105624298A CN 105624298 A CN105624298 A CN 105624298A CN 201610061083 A CN201610061083 A CN 201610061083A CN 105624298 A CN105624298 A CN 105624298A
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高利芬
彭海
张静
李丽丽
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Abstract

The invention discloses a method for detecting the genetically modified components of rape and belongs to the technical field of biology. The method includes: determining the genetically modified components, endogenous standard genes and exogenous standard genes; preparing multiple amplification primers; sampling and mixing to obtain a mixed sample; extracting the genome of the mixed sample, and adding the exogenous standard genes to obtain mixed nucleic acid; building a high-throughput sequencing library; performing high-throughput sequencing on the high-throughput sequencing library to obtain a sequencing fragment group; acquiring the number of the sequencing fragments of the genetically modified components in the to-be-detected sample, the numbers of the sequencing fragments of the endogenous standard genes in the to-be-detected sample and the sequencing fragments of the exogenous standard genes in the to-be-detected sample; judging whether the experiment is successful or not according to the number of the sequencing fragments of the exogenous standard genes, and calculating the content of the genetically modified components in the to-be-detected sample; judging whether the to-be-detected sample contains the genetically modified components or not according to the content of the genetically modified components. By the method, optional multiple genetically modified components in the to-be-detected sample can be quantitatively detected at the same time.

Description

一种油菜转基因成分的检测方法A detection method for genetically modified components of rapeseed

技术领域technical field

本发明涉及生物检测领域,特别涉及一种油菜转基因成分的检测方法。The invention relates to the field of biological detection, in particular to a method for detecting genetically modified components of rapeseed.

背景技术Background technique

油菜是我国主要作物,油菜转基因技术与产品均已成熟,需要对转基因油菜的推广进行监管,转基因成分检测是转基因监管的技术支撑。Rapeseed is the main crop in my country. Rapeseed transgenic technology and products have matured, and the promotion of genetically modified rapeseed needs to be supervised. The detection of genetically modified ingredients is the technical support for the supervision of genetically modified plants.

现有的转基因成分检测技术主要检测核酸或蛋白质,其中,基于核酸的检测方法主要流程为:提取待测样品中的核酸,利用PCR(PolymeraseChainReaction,聚合酶链反应)的方法扩增样品中的转基因成分,利用实时定量、琼脂糖电泳或芯片技术检测转基因成分是否存在。The existing genetically modified component detection technology mainly detects nucleic acid or protein. Among them, the main process of the nucleic acid-based detection method is: extract the nucleic acid in the sample to be tested, and use PCR (Polymerase Chain Reaction, polymerase chain reaction) method to amplify the transgene in the sample. Components, using real-time quantitative, agarose electrophoresis or chip technology to detect the presence of genetically modified components.

在实现本发明的过程中,发明人发现现有技术至少存在以下问题中的一种:In the process of realizing the present invention, the inventor found that the prior art has at least one of the following problems:

转基因成分多种多样,而现有技术一次只能检测其中一种或少数几种,因此,需要对可能的多种转基因成份逐一进行检测,才能确定为“非转基因”产品;一般检测的是共转化的转基因成分,而不是外源基因本身,因此,对于无标记转基因来说,采用现有的检测方法进行检测会失效;检测基本上是定性检测,但定量检测又有其现实需求,例如,相邻田块的转基因油菜品种的少量花粉被传到了非转基因品种上,在定性检测时,非转基因品种将被误判为转基因品种。There are many kinds of genetically modified ingredients, and the existing technology can only detect one or a few of them at a time. Therefore, it is necessary to test the possible multiple genetically modified ingredients one by one before they can be determined as "non-genetically modified" products; The transformed genetically modified components are not the exogenous gene itself. Therefore, for unmarked transgenes, the existing detection methods will be invalid; detection is basically qualitative detection, but quantitative detection has its practical needs, for example, A small amount of pollen from transgenic rapeseed varieties in adjacent fields has been transferred to non-transgenic varieties, and non-transgenic varieties will be misjudged as transgenic varieties during qualitative testing.

发明内容Contents of the invention

为了解决现有技术的问题,本发明实施例提供了一种油菜转基因成分的检测方法。所述技术方案如下:In order to solve the problems in the prior art, an embodiment of the present invention provides a method for detecting genetically modified components of rapeseed. Described technical scheme is as follows:

本发明实施例提供了一种油菜转基因成分的检测方法,所述方法包括:The embodiment of the present invention provides a method for detecting genetically modified components of rapeseed, the method comprising:

确定待测样品中需要检测的转基因成分、所述待测样品中的内源标准基因和所述待测样品的外源标准基因,所述待测样品为油菜植株或所述油菜植株的一部分;Determining the transgenic components to be detected in the sample to be tested, the endogenous standard gene in the sample to be tested and the exogenous standard gene in the sample to be tested, the sample to be tested is a rape plant or a part of the rape plant;

制备用于扩增所述转基因成分、所述内源标准基因和所述外源标准基因的测试区域的多重扩增引物;preparing multiplex amplification primers for amplifying the test regions of the transgenic component, the endogenous standard gene and the exogenous standard gene;

对所述待测样品进行抽样并混合,得到混合样品;Sampling and mixing the samples to be tested to obtain a mixed sample;

提取所述混合样品的基因组;extracting the genome of the mixed sample;

向所述混合样品的基因组中加入所述外源标准基因,得到混合核酸;adding the exogenous standard gene to the genome of the mixed sample to obtain a mixed nucleic acid;

利用所述多重扩增引物对所述混合核酸进行扩增,得到扩增产物,利用所述扩增产物构建高通量测序文库;Using the multiple amplification primers to amplify the mixed nucleic acid to obtain an amplification product, using the amplification product to construct a high-throughput sequencing library;

对所述高通量测序文库进行高通量测序,得到测序片段组;performing high-throughput sequencing on the high-throughput sequencing library to obtain a sequencing fragment set;

分析所述测序片段组,获得所述待测样品中所述转基因成分的测序片段的数量、所述内源标准基因的测序片段的数量和所述外源标准基因的测序片段的数量;analyzing the sequenced fragment group to obtain the number of sequenced fragments of the transgenic component, the number of sequenced fragments of the endogenous standard gene and the number of sequenced fragments of the exogenous standard gene in the sample to be tested;

根据所述外源标准基因的测序片段的数量,判断实验是否成功;According to the number of sequencing fragments of the exogenous standard gene, judge whether the experiment is successful;

若所述实验成功,则计算所述待测样品种中所述转基因成分的含量;If the experiment is successful, then calculate the content of the genetically modified component in the sample species to be tested;

根据所述转基因成分的含量判断所述待测样品中是否含有转基因成分。According to the content of the genetically modified component, it is judged whether the sample to be tested contains the genetically modified component.

具体地,所述转基因成分为外源功能基因、抗性标记基因、启动子、终止子和外源插入旁侧序列中的至少一种。Specifically, the transgene component is at least one of an exogenous functional gene, a resistance marker gene, a promoter, a terminator, and an exogenous insertion flanking sequence.

具体地,所述内源标准基因为所述待测样品的基因组中的单拷贝基因。Specifically, the endogenous standard gene is a single-copy gene in the genome of the sample to be tested.

具体地,所述外源标准基因不存在于所有生物中。Specifically, the exogenous standard gene is not present in all organisms.

具体地,所述判断实验是否成功的方法为:当所述外源标准基因的测序片段的数量和所述内源标准基因的测序片段的数量均≥α1时,则实验成功;当所述外源标准基因的测序片段的数量或所述内源标准基因的测序片段的数量<α1时,则实验失败;其中,α1为判定阈值。Specifically, the method for judging whether the experiment is successful is: when the number of sequenced fragments of the exogenous standard gene and the number of sequenced fragments of the endogenous standard gene are both ≥ α1, the experiment is successful; When the number of sequenced fragments of the source standard gene or the number of sequenced fragments of the endogenous standard gene < α1, the experiment fails; where α1 is the threshold for determination.

具体地,所述判定所述待测样品是否含有转基因成分的方法为:当需要检测的任意一种所述转基因成分的含量≥α2时,判定所述待测样品含有转基因成分;当所有所述转基因成分的含量<α2时,判定所述待测样品不含有转基因成分;其中,α2为判定阈值。Specifically, the method for determining whether the sample to be tested contains genetically modified components is: when the content of any one of the genetically modified components to be detected is greater than or equal to α2, it is determined that the sample to be tested contains genetically modified components; When the content of the genetically modified component is <α2, it is determined that the sample to be tested does not contain the genetically modified component; wherein, α2 is the judgment threshold.

具体地,计算所述待测样品种中所述转基因成分的含量的方法为:第m种所述转基因成分的含量的计算公式为其中,i为所述第m种转基因成分的第i个测试区域,n1为所述第m种转基因成分的所述测试区域的个数,bi为所述第m种转基因成分的第i个所述测试区域的所述测序片段的数量,k为第k种所述内源标准基因,n3为所述内源标准基因的个数,j为第k种所述内源标准基因的第j个测试区域,n2为所述第k种内源标准基因的所述测试区域的个数,aj为所述第k种内源标准基因的第j种所述测试区域的所述测序片段的数量;N为所有所述内源标准基因的所述测试区域的总数。Specifically, the method for calculating the content of the genetically modified component in the sample species to be tested is: the calculation formula for the content of the mth genetically modified component is: Wherein, i is the i-th test area of the m-th transgenic component, n1 is the number of the test areas of the m-th transgenic component, and bi is the i-th test area of the m-th transgenic component. The number of the sequenced fragments in the test area, k is the kth endogenous standard gene, n3 is the number of the endogenous standard gene, and j is the jth of the kth endogenous standard gene Test area, n2 is the number of the test area of the kth endogenous standard gene, aj is the number of the sequencing fragments of the jth test area of the kth endogenous standard gene; N is the total number of said test regions for all said endogenous standard genes.

具体地,所述外源标准基因的质量与所述混合样品的基因组的总质量的比例大于1/100000。Specifically, the ratio of the mass of the exogenous standard gene to the total mass of the genome of the mixed sample is greater than 1/100000.

本发明实施例提供的技术方案带来的有益效果是:本发明提供的检测方法可以在不同待测样品、不同检测的目标基因间通用,可以一次性检测任意多种需要检测的转基因成分,从而判定待测样品是否含有转基因成分,该方法可以实现定量检测,且检测结果几乎没有下限,结果准确可靠,是现有技术达不到的。The beneficial effects brought by the technical solutions provided by the embodiments of the present invention are: the detection method provided by the present invention can be used universally among different samples to be tested and different detected target genes, and can detect any number of transgenic components that need to be detected at one time, thereby To determine whether the sample to be tested contains genetically modified ingredients, this method can realize quantitative detection, and the detection result has almost no lower limit, and the result is accurate and reliable, which is beyond the reach of the existing technology.

具体实施方式detailed description

为使本发明的目的、技术方案和优点更加清楚,下面将对本发明实施方式作进一步地详细描述。本发明实施例中未注明或详细描述的操作流程或操作规范均为普通分子生物学技术人员所熟知的操作。本发明实施例中未注明的试剂或生物材料均为市场上销售的常用试剂或生物材料,均为普通分子生物学技术人员所熟知的,且可以在市场上购买到。In order to make the purpose, technical solution and advantages of the present invention clearer, the implementation manners of the present invention will be further described in detail below. The operating procedures or operating specifications not indicated or described in detail in the embodiments of the present invention are operations well known to those skilled in molecular biology. Reagents or biological materials not indicated in the examples of the present invention are common reagents or biological materials sold in the market, are well known to ordinary molecular biology technicians, and can be purchased in the market.

实施例Example

通过农杆菌介导法将双丙氨酰磷抗性(Biolaphosresistance,Bar)基因导入贵油恢15油菜品种,自交纯化3代后,获得改造的贵油恢15油菜品种种子,作为本实施例的待测油菜品种。其中,贵油恢15油菜是转基因油菜受体品种,由贵州农学院油菜研究室育成,本实施例中使用的贵油恢15油菜种子由江汉大学保存和繁殖。The biolaphos resistance (Bar) gene was introduced into Guiyouhui 15 rape variety by Agrobacterium-mediated method, and after selfing and purification for 3 generations, the transformed Guiyouhui 15 rape variety seeds were obtained as this example Rapeseed varieties to be tested. Among them, Guiyouhui 15 rapeseed is a transgenic rapeseed recipient variety, bred by the Rapeseed Research Laboratory of Guizhou Agricultural College, and Guiyouhui 15 rapeseed seeds used in this example were preserved and propagated by Jianghan University.

油菜植物品种转基因成分检测方法,具体步骤如下:The method for detecting genetically modified components of rape plant varieties, the specific steps are as follows:

步骤1、确定待测样品中需要检测的转基因成分、待测样品中的内源标准基因和待测样品的外源标准基因,具体方法如下:待测样品为油菜植株或油菜植株的一部分,其中,油菜植株可以为油菜植株的根、茎、叶、花、果实和种子等器官,也可以是2种及2种以上的不同器官的混合物,如叶和茎的混合物,油菜植株的一部分可以为油菜植株的根、茎、叶、花、果实和种子等至少一个器官中的一部分。在本实施例中,待测样品为改造后的贵油恢15油菜的种子,转基因成分、内源标准基因和外源标准基因均≥1个,转基因成分可以为外源功能基因、抗性标记基因、启动子、终止子和外源插入旁侧序列中的至少一种,即通过转基因技术手段向贵油恢15油菜品种中转入不存在于贵油恢15油菜品种中的外源核酸序列;内源标准基因为待测样品的基因组中的单拷贝基因。在本实施例中,内源标准基因通过NCBI(http://www.ncbi.nlm.nih.gov/)在待测样品基因组上比对时为单一序列;外源标准基因不存在于所有生物中,在本实施例中,所使用的外源标准基因为ERCC04基因,其在NCBI上同源比对时,未发现同源序列,可以判定外源标准基因不存在于所有生物中。在本实施例中,检测的转基因成分共5种,内源标准基因1种,外源标准基因1种,其相关信息见表1,表1中所列转基因成分不仅包括Bar基因,Bar基因为外源功能基因,还包括其他转基因成分,这些转基因成分在转基因作物中广泛使用,因此,本实施例提供的检测方法具有通用性。表1中的基因序列有两种表示方式,一种是直接写出基因序列,另一种是NBCI的基因编号,表1中的测序区域中的数字代表碱基的位置,该基因的第1个碱基的位置定义为1。Step 1. Determine the transgenic components to be detected in the sample to be tested, the endogenous standard gene in the sample to be tested, and the exogenous standard gene of the sample to be tested. The specific method is as follows: the sample to be tested is a rape plant or a part of a rape plant, wherein Rapeseed plants can be organs such as roots, stems, leaves, flowers, fruits and seeds of rapeseed plants, or a mixture of two or more different organs, such as the mixture of leaves and stems, and a part of rapeseed plants can be A part of at least one organ such as roots, stems, leaves, flowers, fruits and seeds of rapeseed plants. In this embodiment, the sample to be tested is the seed of Guiyouhui 15 rapeseed after transformation, and the transgenic component, endogenous standard gene and exogenous standard gene are all ≥ 1, and the transgenic component can be exogenous functional gene, resistance marker At least one of genes, promoters, terminators, and foreign-inserted flanking sequences, that is, the introduction of exogenous nucleic acid sequences that do not exist in Guiyouhui 15 rapeseed varieties into Guiyouhui 15 rapeseed varieties by means of transgenic technology ; The endogenous standard gene is a single-copy gene in the genome of the sample to be tested. In this embodiment, the endogenous standard gene is a single sequence when compared on the genome of the sample to be tested by NCBI (http://www.ncbi.nlm.nih.gov/); the exogenous standard gene does not exist in all organisms Among them, in this example, the exogenous standard gene used is the ERCC04 gene, and no homologous sequence was found when it was homologously compared on NCBI, so it can be determined that the exogenous standard gene does not exist in all organisms. In this example, there are 5 types of genetically modified components detected, 1 type of endogenous standard gene, and 1 type of exogenous standard gene. Exogenous functional genes also include other transgenic components, which are widely used in transgenic crops, therefore, the detection method provided in this example is universal. The gene sequence in Table 1 has two representations, one is to write the gene sequence directly, and the other is the gene number of NBCI. The numbers in the sequencing area in Table 1 represent the position of the base, and the first The position of a base is defined as 1.

表1为实施例一中被检测基因的相关信息与检测结果Table 1 is the relevant information and detection results of the detected genes in Example 1

表1中“/”表示无。"/" in Table 1 means none.

步骤2、制备用于扩增转基因成分、内源标准基因和外源标准基因的多重扩增引物,具体方法如下:Step 2, preparing multiple amplification primers for amplifying transgenic components, endogenous standard genes and exogenous standard genes, the specific method is as follows:

多重扩增引物的获取过程如下:登录赛默飞世尔公司多重PCR引物在线设计网页https://ampliseq.com/,在“Applicationtype”选项选择“DNAHotspotdesigns(single-pool)”。若选择multi-pool,则多重PCR将分多管进行,成本会有所增加,而single-pool的引物只需要一次多重PCR即可,节省成本,所以本实施例选择single-pool。将表1中所列的每一个基因的序列用100个N连接起来,形成一个人工参考基因组,并在“Selectthegenomeyouwishtouse”选项中选择“Custom”后,上传人工参考基因组。DNAType(类型)选项选择“StandardDNA”(标准DNA)。在AddHotspot选项中,为表1中的每一个基因随机选择1个通过NCBI同源比对获得的同源序列的同源性均低于80%的测试区域。其中,测试区域是指多重PCR的扩增区域,也是高通量测序的区域,由于测试区域与其它物种比较,无明显的同源序列,因此,可以代表被检测的基因,在高通量测序后,测试区域存在测序片段,则表明被检测的基因存在,测试区域的测序片段的数量,代表了被检测基因的量。此外,同源序列不包括转基因成分的原始来源物种中的序列,例如,表1中的CryIAc基因的原始来源物种为苏云金芽胞杆菌(Bacillusthuringiensis,简称Bt),因此,同源比对的对像不包括苏云金芽胞杆菌的基因组。为了保证本发明实施例的通用性,在NCBI上下载内源标准基因的种内的不同序列,通过同源比对,获得序列间的保守的区域,内源标准基因的测试区域选择为在种内边界序列保守的区域。进一步填写获得的每个测试区域的起始和终止位置,最后点击“Submittargets”按钮提交,获得扩增表1中每一个基因的扩增引物的序列。多重扩增引物中每重引物的扩增效率均在95%~105%之间,因此,需要验证多重扩增引物的扩增效率。具体验证方法为:由生工生物工程(上海)股份有限公司合成表1中Bar基因的序列和扩增Bar基因的测试区域的扩增引物序列,以合成的Bar基因的序列为模板,按照美国赛默飞世尔公司的StepOne实时定量PCR仪的操作手册(PartNumber4376784Rev.E)检测扩增Bar基因的测试区域的扩增引物的扩增效率,若扩增效率不在95%-105%之间,则需要重新确定Bar基因的测试区域,设计并验证Bar基因的新的扩增引物的效率,直至其效率在95%-105%之间为止。按同样的方法,验证表1中其它基因的扩增引物的扩增效率。最终入选的扩增引物的扩增效率、序列以及对应的扩增区域见表1,所有最终入选的扩增引物称为多重扩增引物,多重扩增引物由美国赛默飞世尔公司合成并以混合液体的形式提供给使用者。本实施例采用美国赛默飞世尔公司提供的多重PCR技术,其能够同时扩增多至12000个测试区域,因此,本发明有能力一次性检测现有的所有需要检测的转基因成分。The process of obtaining multiplex amplification primers is as follows: log in to Thermo Fisher’s multiplex PCR primer online design website https://ampliseq.com/, and select “DNAHotspotdesigns (single-pool)” in the “Application type” option. If multi-pool is selected, the multiplex PCR will be carried out in multiple tubes, and the cost will increase, while the primers of single-pool only need one multiplex PCR, which saves cost, so single-pool is selected in this embodiment. Connect the sequences of each gene listed in Table 1 with 100 Ns to form an artificial reference genome, and upload the artificial reference genome after selecting "Custom" in the "Selectthegenomeyouwishtouse" option. DNAType (type) option select "StandardDNA" (standard DNA). In the AddHotspot option, for each gene in Table 1, randomly select a test region whose homology of homologous sequences obtained through NCBI homologous alignment is lower than 80%. Among them, the test area refers to the amplification area of multiplex PCR, which is also the area of high-throughput sequencing. Compared with other species, the test area has no obvious homologous sequence, so it can represent the detected gene. Finally, the presence of sequenced fragments in the test area indicates the presence of the detected gene, and the number of sequenced fragments in the test area represents the amount of the detected gene. In addition, the homologous sequence does not include the sequence in the original source species of the transgenic component, for example, the original source species of the CryIAc gene in Table 1 is Bacillus thuringiensis (abbreviated as Bt), therefore, the object of the homologous comparison is not Includes the genome of Bacillus thuringiensis. In order to ensure the versatility of the embodiments of the present invention, download the different sequences of the endogenous standard gene in the species on NCBI, and obtain the conserved regions between the sequences through homologous comparison. The test region of the endogenous standard gene is selected as the A region where the inner boundary sequence is conserved. Further fill in the start and end positions of each test region obtained, and finally click the "Submit targets" button to submit, and obtain the sequence of the amplification primers for amplifying each gene in Table 1. The amplification efficiency of each primer in the multiple amplification primers is between 95% and 105%. Therefore, the amplification efficiency of the multiple amplification primers needs to be verified. The specific verification method is as follows: the sequence of the Bar gene in Table 1 and the amplification primer sequence for amplifying the test region of the Bar gene are synthesized by Sangon Bioengineering (Shanghai) Co., Ltd., and the sequence of the synthesized Bar gene is used as a template. The operating manual (PartNumber4376784Rev.E) of the StepOne real-time quantitative PCR instrument of Thermo Fisher Corporation detects the amplification efficiency of the amplification primer of the test region of amplifying the Bar gene, if the amplification efficiency is not between 95%-105%, Then it is necessary to re-determine the test region of the Bar gene, design and verify the efficiency of the new amplification primers for the Bar gene until the efficiency is between 95% and 105%. In the same way, verify the amplification efficiencies of the amplification primers for other genes in Table 1. The amplification efficiency, sequence and corresponding amplification region of the final selected amplification primers are shown in Table 1. All the final selected amplification primers are called multiple amplification primers, and the multiple amplification primers were synthesized by Thermo Fisher Corporation of the United States and produced Provided to the user in the form of a mixed liquid. This embodiment adopts the multiplex PCR technology provided by Thermo Fisher Corporation of the United States, which can simultaneously amplify up to 12,000 test regions. Therefore, the present invention has the ability to detect all existing transgenic components that need to be detected at one time.

步骤3、对待测样品进行抽样并混合,得到混合样品,具体方法如下:Step 3, sample and mix the sample to be tested to obtain a mixed sample, the specific method is as follows:

将待测样品按照标准《转基因植物及其产品成分检测抽样》(标准号:农业部2031号公告-19-2013)的散装货物中油菜种子的抽样方法进行抽样,由于待测样品仅1种简单的来源,因此,抽样点改为1个,抽样样品的样本量>1000粒种子,将所抽取的待测植物样本充分混合,得到混合样品。The sample to be tested is sampled according to the sampling method of rapeseed in bulk goods in the standard "Detection and Sampling of Genetically Modified Plants and Their Product Components" (Standard No.: Announcement No. 2031 of the Ministry of Agriculture-19-2013). Therefore, the sampling point is changed to 1, the sample size of the sampling sample is >1000 seeds, and the extracted plant samples to be tested are fully mixed to obtain a mixed sample.

步骤4、提取混合样品的基因组,具体方法如下:Step 4, extracting the genome of the mixed sample, the specific method is as follows:

参照标准《转基因植物及其产品成分检测DNA提取和纯化》(标准号:农业部1485号公告-4-2010)中固态试样进行预处理后提取混合样品的基因组,提取出的为混合样品的基因组核酸。Refer to the standard "DNA Extraction and Purification for Detection of Components of Transgenic Plants and Their Products" (Standard Number: Ministry of Agriculture Announcement No. 1485-4-2010) in which the solid sample is pretreated to extract the genome of the mixed sample, and the extracted genome of the mixed sample genomic nucleic acid.

步骤5、向混合样品的基因组中加入外源标准基因,得到混合核酸,具体方法如下:Step 5, adding an exogenous standard gene to the genome of the mixed sample to obtain a mixed nucleic acid, the specific method is as follows:

利用分光光度计(美国Quawell公司生产,型号为Q5000)中的双链DNA程序,检测获得的混合样品的基因组的浓度。外源标准基因的质量与混合样品的基因组的总质量的比例大于1/100000,该比例用于保证在正常测序通量(≥1M测序片段)下,高通量测序数据中可以检测到≥10条外源标准基因,若高通量测序通量更低或更高,可以对该比例做相应的调整。本实施例中,混合样品的基因组的总质量为1003ng,加入的外源标准基因为1.003ng,加入比例为1/1000,获得混合核酸。Using the double-stranded DNA program in the spectrophotometer (manufactured by Quawell, USA, model Q5000), the concentration of the genome in the obtained mixed sample was detected. The ratio of the mass of the exogenous standard gene to the total mass of the genome of the mixed sample is greater than 1/100000, and this ratio is used to ensure that ≥10 If the throughput of high-throughput sequencing is lower or higher, the ratio can be adjusted accordingly. In this embodiment, the total mass of the genome of the mixed sample is 1003ng, the exogenous standard gene added is 1.003ng, and the addition ratio is 1/1000, and the mixed nucleic acid is obtained.

步骤6、利用多重扩增引物对混合核酸进行扩增,得到扩增产物,利用扩增产物构建高通量测序文库,具体方法如下:Step 6, using multiple amplification primers to amplify the mixed nucleic acid to obtain amplified products, and using the amplified products to construct a high-throughput sequencing library, the specific method is as follows:

利用文库构建试剂盒2.0(由美国LifeTechnology公司生产,货号为4475345)构建高通量测序文库。该文库构建试剂盒包括以下试剂:5×IonAmpliSeqTMHiFiMix、FuPa试剂、转换试剂、测序接头溶液和DNA连接酶。文库构建的方法按该文库构建试剂盒的操作手册《IonAmpliSeqTMLibraryPreparation》(出版号:MAN0006735,版本:A.0)进行。多重PCR的扩增体系如下:5×IonAmpliSeqTMHiFiMix4μl、制备的多重扩增引物的混合液体4μl、混合核酸10ng和无酶水11μl。多重PCR的扩增程序如下:99℃,2分钟;(99℃,15秒;60℃,4分钟)×25个循环;10℃保温。利用FuPa试剂消化掉多重PCR扩增产物中多余的引物后,再进行磷酸化,具体方法为:向多重PCR的扩增产物中加入2μlFuPa试剂,混匀后,在PCR仪上按如下程序反应:50℃,10分钟;55℃,10分钟;60℃,10分钟;10℃保存,得到混合物a,混合物a为含有经过磷酸化的扩增产物的溶液。将磷酸化的扩增产物连接上测序接头,具体方法为:向混合物a中加入转换试剂4μl、测序接头溶液2μl和DNA连接酶2μl,混匀后,在PCR仪上按如下程序反应:22℃,30分钟;72℃,10分钟;10℃保存,得到混合液b。利用标准的乙醇沉淀方法纯化混合液b后溶解于10μl无酶水中。利用美国Invitrigen公司生产的dsDNAHSAssayKit(货号为Q32852)并按照其说明书进行检测,获得混合液b的质量浓度后,将纯化后的混合液b稀释至15ng/ml,得到浓度约100pM的高通量测序文库。A high-throughput sequencing library was constructed using the library construction kit 2.0 (produced by LifeTechnology, USA, product number 4475345). The library construction kit includes the following reagents: 5×IonAmpliSeq TM HiFiMix, FuPa reagent, conversion reagent, sequencing adapter solution and DNA ligase. The method of library construction was carried out according to the operation manual "IonAmpliSeq TM Library Preparation" (publication number: MAN0006735, version: A.0) of the library construction kit. The multiplex PCR amplification system was as follows: 5×IonAmpliSeq TM HiFiMix 4 μl, prepared multiple amplification primer mixed liquid 4 μl, mixed nucleic acid 10 ng and enzyme-free water 11 μl. The multiplex PCR amplification program is as follows: 99°C, 2 minutes; (99°C, 15 seconds; 60°C, 4 minutes) x 25 cycles; 10°C incubation. Use FuPa reagent to digest the redundant primers in the multiple PCR amplification products, and then phosphorylate them. The specific method is: add 2 μl FuPa reagent to the multiple PCR amplification products, mix well, and react on the PCR instrument according to the following procedure: 50° C. for 10 minutes; 55° C. for 10 minutes; 60° C. for 10 minutes; and 10° C. for storage to obtain mixture a, which is a solution containing phosphorylated amplification products. Connect the phosphorylated amplification product to the sequencing adapter. The specific method is: add 4 μl of conversion reagent, 2 μl of sequencing adapter solution and 2 μl of DNA ligase to mixture a, mix well, and react on the PCR machine according to the following procedure: 22°C , 30 minutes; 72 ° C, 10 minutes; 10 ° C storage, to obtain the mixture b. Mixture b was purified by standard ethanol precipitation and dissolved in 10 μl of enzyme-free water. Produced by Invitrigen Company of the United States dsDNAHSAssayKit (Cat. No. Q32852) was tested according to its instructions. After obtaining the mass concentration of the mixed solution b, the purified mixed solution b was diluted to 15 ng/ml to obtain a high-throughput sequencing library with a concentration of about 100 pM.

步骤7、对高通量测序文库进行高通量测序,得到测序片段组,具体方法如下:Step 7. Perform high-throughput sequencing on the high-throughput sequencing library to obtain the sequenced fragment group. The specific method is as follows:

利用获得的高通量测序文库和试剂盒IonPITemplateOT2200Kitv2(美国invirtrigen公司生产,货号为4485146)进行测序前的ePCR(EmulsionPCR,乳化聚合酶链反应)扩增,操作方法按该试剂盒的操作手册进行。利用ePCR产物和试剂盒IonPISequencing200Kitv2(美国invirtrigen公司生产,货号为4485149)在Proton二代高通量测序仪上进行高通量测序,操作方法按该试剂盒的操作手册进行。在本实施例中,高通量测序量设置为1M测序片段(1M=100万),测序长度设置为500cycle(循环),测序结束后,获得测序片段组。The obtained high-throughput sequencing library and kit IonPITemplateOT2200Kitv2 (produced by Invirtrigen, USA, product number 4485146) were used for ePCR (EmulsionPCR, emulsion polymerase chain reaction) amplification before sequencing, and the operation method was carried out according to the operation manual of the kit. High-throughput sequencing was performed on a Proton second-generation high-throughput sequencer using the ePCR product and the kit IonPISequencing200Kitv2 (produced by Invirtrigen, USA, product number 4485149), and the operation method was carried out according to the operation manual of the kit. In this embodiment, the high-throughput sequencing volume is set to 1M sequencing fragments (1M=1 million), and the sequencing length is set to 500 cycles (cycles). After the sequencing is completed, a sequenced fragment group is obtained.

步骤8、分析测序片段组,获得待测样品中转基因成分的测序片段的数量、内源标准基因的测序片段的数量和外源标准基因的测序片段的数量,具体方法如下:Step 8. Analyze the sequenced fragment group to obtain the number of sequenced fragments of the transgenic component in the sample to be tested, the number of sequenced fragments of the endogenous standard gene, and the number of sequenced fragments of the exogenous standard gene. The specific methods are as follows:

根据测序片段的引物,利用blastall(version2.2.26)软件,按其默认的参数设置,将测序片段组比对到表1中各对应检测基因上,比对成功的测序片段即代表检测到基因,从而分别获得待测样品中各种转基因成分的测序片段的数量、各种内源标准基因的测序片段的数量和外源标准基因的测序片段的数量,其结果见表1。According to the primers of the sequenced fragments, use the blastall (version2.2.26) software, according to its default parameter settings, compare the sequenced fragments to the corresponding detection genes in Table 1, and the sequenced fragments that are successfully compared represent the detected genes. The number of sequenced fragments of various transgenic components, the number of sequenced fragments of various endogenous standard genes, and the number of sequenced fragments of exogenous standard genes in the sample to be tested were respectively obtained. The results are shown in Table 1.

步骤9、根据外源标准基因的测序片段的数量,判断实验是否成功,具体方法如下:Step 9. According to the number of sequenced fragments of the exogenous standard gene, judge whether the experiment is successful, the specific method is as follows:

当外源标准基因的测序片段的数量和内源标准基因的测序片段的数量均≥α1时,则实验成功;当外源标准基因的测序片段的数量或内源标准基因的测序片段的数量<α1时,则实验失败,实验失败后需要重新进行实验,直至实验成功为止;其中,α1为判定阈值,其大小依据要求的严格程度和经验人为判定,一般来说,若在高通量测序数据中,可以检测到10条以上的测序片段,表明所检测的基因是存在的。在本实施例中,α1可以取10条测序片段,从表1中可以看出,外源标准基因的测序片段的数量和内源标准基因的测序片段的数量均≥10条,因此证实,本次实验是成功的。When the number of sequenced fragments of the exogenous standard gene and the number of sequenced fragments of the endogenous standard gene are both ≥α1, the experiment is successful; when the number of sequenced fragments of the exogenous standard gene or the number of sequenced fragments of the endogenous standard gene< When α1, the experiment fails. After the experiment fails, the experiment needs to be repeated until the experiment succeeds; among them, α1 is the judgment threshold, and its size is judged manually according to the strictness of requirements and experience. Generally speaking, if the high-throughput sequencing data Among them, more than 10 sequencing fragments can be detected, indicating that the detected gene exists. In this embodiment, α1 can take 10 sequencing fragments. It can be seen from Table 1 that the number of sequencing fragments of exogenous standard genes and the number of sequencing fragments of endogenous standard genes are both ≥ 10, so it is confirmed that this The experiment was successful.

步骤10、若实验成功,则计算待测样品种中转基因成分的含量,具体方法如下:Step 10, if the experiment is successful, then calculate the content of the transgenic component in the sample species to be tested, the specific method is as follows:

第m种转基因成分的含量的计算公式为其中,i为第m种转基因成分的第i个测试区域,n1为第m种转基因成分的测试区域的个数,bi为第m种转基因成分的第i个测试区域的测序片段的数量,k为第k种内源标准基因,n3为内源标准基因的个数,j为第k种内源标准基因的第j个测试区域,n2为第k种内源标准基因的测试区域的个数,aj为第k种内源标准基因的第j种测试区域的测序片段的数量;N为所有内源标准基因的测试区域的总数。The formula for calculating the content of the mth genetically modified ingredient is Among them, i is the i-th test area of the m-th genetically modified component, n1 is the number of test areas of the m-th genetically modified component, bi is the number of sequencing fragments in the i-th test area of the m-th genetically modified component, k is the kth endogenous standard gene, n3 is the number of endogenous standard genes, j is the jth test area of the kth endogenous standard gene, n2 is the number of test areas of the kth endogenous standard gene , aj is the number of sequenced fragments of the jth test region of the kth endogenous standard gene; N is the total number of test regions of all endogenous standard genes.

从表1可以看出,在本实施例中,共检测了5种转基因成分,所以m=5,每一种转基因成分分别检测了1个测试区域,所以,n1=1,共检测了1个内源标准基因,所以n3=1,每个内源标准基因共检测了1个测试区域,所以,n2=1,N=3,表1列出了每一种转基因成分与每一个内源标准基因的测序片段的数量,将它们代入转基因成分的含量的计算公式中可得到每一种转基因成分的含量,其结果见表1。从表1可以看出,本实施例通过5对多重扩增引物,一次性地定量检测了5种转基因成分的含量。在本实施例子的基础上,只需要增加更多的多重扩增引物,即可实现一次定量检测任意多种需要检测的转基因成分的含量。此外,也可以检测转基因成分、内源标准基因及外源标准基因的多个测试区域,通过平均数消除因不同基因或不同测试区域的不同扩增效率而造成的测试误差,本实施例由于将每一个检测的基因的每一个测试区域的扩增效率都控制在了95%-105%之间,误差较小,为节省成本,所以每一个基因只选择了一个测试区域。It can be seen from Table 1 that in this embodiment, 5 kinds of genetically modified components were detected, so m=5, and one test area was detected for each kind of genetically modified component, so, n1=1, a total of 1 test area was detected Endogenous standard gene, so n3=1, each endogenous standard gene detected a total of 1 test area, so, n2=1, N=3, Table 1 lists each transgenic ingredient and each endogenous standard The number of sequenced fragments of the gene can be substituted into the calculation formula of the content of the genetically modified ingredients to obtain the content of each genetically modified ingredient. The results are shown in Table 1. It can be seen from Table 1 that in this example, the contents of five transgenic components were quantitatively detected at one time through five pairs of multiple amplification primers. On the basis of this example, it is only necessary to add more multiplex amplification primers to achieve one-time quantitative detection of the contents of any number of transgenic components that need to be detected. In addition, multiple test areas of transgenic components, endogenous standard genes, and exogenous standard genes can also be detected, and the test error caused by different amplification efficiencies of different genes or different test areas can be eliminated by averaging. The amplification efficiency of each test region of each detected gene is controlled between 95%-105%, and the error is small. In order to save costs, only one test region is selected for each gene.

步骤11、根据转基因成分的含量判断待测样品中是否含有转基因成分,具体方法如下:Step 11. Determine whether the sample to be tested contains a genetically modified ingredient according to the content of the genetically modified ingredient. The specific method is as follows:

当需要检测的任意一种转基因成分的含量≥α2时,则判定待测样品含有转基因成分;当所有转基因成分的含量<α2时,判定待测样品不含有转基因成分;其中,α2为判定阈值。When the content of any genetically modified ingredient to be detected is ≥ α2, it is determined that the sample to be tested contains genetically modified ingredients; when the content of all genetically modified ingredients is < α2, it is judged that the sample to be tested does not contain genetically modified ingredients; where α2 is the judgment threshold.

在国标《转基因产品检测核酸定量PCR检测方法》(标准号:GB/T19495.5-2004)中设定的转基因成份检测下限为0.1%。本实施例中,将α2的值设定为0.1%,用于判定待测样品是否为转基因产品。由于本发明采用测序检测转基因成分,而测序技术得到的是数字信号,即测到与没有测到两种情况,因此,几乎没有技术下限,与传统的芯片检测技术或实时定量PCR检测技术比较,没有背景噪音干扰的问题,因此,判定待测样品是否为转基因产品的判定阈值可以根据具体情况要求的严格程度自由设定。从表1可以看出,本实施例子中,5种所检测的转基因成分之中,除CryIAc外,其余4种转基因成分的含量均≥α2=0.1%,因此,判定本实施例中的待测样品含有转基因成分,该待测样品为转基因植物。The lower limit of detection of genetically modified ingredients set in the national standard "Nucleic acid quantitative PCR detection method for detection of genetically modified products" (standard number: GB/T19495.5-2004) is 0.1%. In this embodiment, the value of α2 is set to 0.1%, which is used to determine whether the sample to be tested is a genetically modified product. Since the present invention uses sequencing to detect transgenic components, and the sequencing technology obtains digital signals, that is, detected and not detected, there is almost no technical lower limit. Compared with traditional chip detection technology or real-time quantitative PCR detection technology, There is no problem of background noise interference, therefore, the judgment threshold for judging whether the sample to be tested is a genetically modified product can be freely set according to the strictness required by the specific situation. It can be seen from Table 1 that in this example, among the five detected transgenic components, except for CryIAc, the contents of the other four transgenic components are all ≥α2=0.1%. Therefore, it is determined that the tested components in this embodiment The sample contains genetically modified components, and the sample to be tested is a genetically modified plant.

结果验证:根据《转基因植物及其产品成分检测Bar基因或pat基因定性PCR方法》(标准号:农业部1782号公告-6-2012)所提供的方法对待测样品进行了检测,检测结果表明待测样品含有转基因成分,这与本实施例的结果一致,由此可见,本实施例提供的检测方法是正确的。Result verification: According to the method provided by "Qualitative PCR method for Bar gene or pat gene detection of transgenic plants and their product components" (standard number: Ministry of Agriculture Announcement No. 1782-6-2012), the test samples were tested, and the test results showed that The test sample contains genetically modified components, which is consistent with the results of this example, so it can be seen that the detection method provided by this example is correct.

本发明提供的检测方法可以在不同待测样品、不同检测的目标基因间通用,能够同时定量检测待测样品中的任意多种转基因成分,充分满足了转基因检测的现实需求,是现有技术达不到的。The detection method provided by the present invention can be commonly used among different samples to be tested and different target genes to be detected, and can quantitatively detect any variety of transgenic components in the samples to be tested at the same time, which fully meets the actual needs of genetically modified detection, and is an achievement of the prior art. less than.

以上所述仅为本发明的较佳实施例,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、改进等,均应包含在本发明的保护范围之内。The above descriptions are only preferred embodiments of the present invention, and are not intended to limit the present invention. Any modifications, equivalent replacements, improvements, etc. made within the spirit and principles of the present invention shall be included in the protection of the present invention. within range.

Claims (8)

1. the detection method of a Brassica campestris L transgene component, it is characterised in that described method includes:
Determining the external source standard gene of the endogenous standard gene and described testing sample needed in testing sample in the transgene component of detection, described testing sample, described testing sample is rapeseed plants or a part for described rapeseed plants;
Preparation is for expanding the multiplex amplification primer of the test zone of described transgene component, described endogenous standard gene and described external source standard gene;
Described testing sample it is sampled and mixes, obtaining biased sample;
Extract the genome of described biased sample;
In the genome of described biased sample, add described external source standard gene, obtain mixing nucleic acid;
Utilize mixing nucleic acid described in described multiplex amplification primer pair to expand, obtain amplified production, utilize described amplified production to build high-throughput sequencing library;
Described high-throughput sequencing library is carried out high-flux sequence, obtains order-checking fragment group;
Analyze described order-checking fragment group, it is thus achieved that the quantity of the order-checking fragment of the quantity of the order-checking fragment of transgene component described in described testing sample, the quantity of order-checking fragment of described endogenous standard gene and described external source standard gene;
The quantity of the order-checking fragment according to described external source standard gene, it is judged that whether experiment is successful;
If described Success in Experiment, then calculate the content of transgene component described in described testing sample kind;
Content according to described transgene component judges whether contain transgene component in described testing sample.
2. detection method according to claim 1, it is characterised in that described transgene component is at least one that external source functional gene, resistant maker gene, promoter, terminator and external source insert in flanking sequence.
3. detection method according to claim 1, it is characterised in that described endogenous standard gene is the single copy gene in the genome of described testing sample.
4. detection method according to claim 1, it is characterised in that described external source standard gene is not present in all biologies.
5. detection method according to claim 1, it is characterized in that, described judgment experiment whether successfully method is: when the quantity of the quantity of order-checking fragment of described external source standard gene and the order-checking fragment of described endogenous standard gene equal>=�� 1 time, then Success in Experiment; When the quantity of order-checking fragment of described external source standard gene or the order-checking fragment of described endogenous standard gene quantity<during �� 1, then the failure of an experiment; Wherein, �� 1 is decision threshold.
6. detection method according to claim 1, it is characterized in that, described judge described testing sample whether contain the method for transgene component as: as the content>=�� 2 of any one described transgene component of needs detection, it is determined that described testing sample contains transgene component; When the content of all described transgene components is<during �� 2, it is determined that described testing sample does not contain transgene component; Wherein, �� 2 is decision threshold.
7. detection method according to claim 1, it is characterised in that the method for the content of transgene component described in described testing sample kind that calculates is: described in m kind, the computing formula of the content of transgene component isWherein, i be described m kind transgene component i-th described in test zone, n1 is the number of the described test zone of described m kind transgene component, bi be described m kind transgene component i-th described in the quantity of described order-checking fragment of test zone, k is endogenous standard gene described in kth kind, n3 is the number of described endogenous standard gene, j is the jth test zone of endogenous standard gene described in kth kind, n2 is the number of the described test zone of the described endogenous standard gene of kth kind, aj be the described endogenous standard gene of kth kind jth kind described in the quantity of described order-checking fragment of test zone, N is the sum of the described test zone of all described endogenous standard genes.
8. detection method according to claim 1, it is characterised in that the ratio of the quality of described external source standard gene and the genomic gross mass of described biased sample is more than 1/100000.
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