CN113621732B - InDel labeled primer set and its application in purity identification of cauliflower ‘CB-30’ variety or seeds - Google Patents
InDel labeled primer set and its application in purity identification of cauliflower ‘CB-30’ variety or seeds Download PDFInfo
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Abstract
Description
技术领域Technical field
本发明涉及花椰菜分子标记引物组及其应用,尤其涉及花椰菜InDel标记引物组及其在花椰菜‘CB-30’品种或种子纯度鉴定中的应用,属于花椰菜‘CB-30’品种或种子纯度的分子鉴定领域。The present invention relates to a cauliflower molecular marker primer set and its application, in particular to a cauliflower InDel marker primer set and its application in cauliflower 'CB-30' variety or seed purity identification, and belongs to cauliflower 'CB-30' variety or seed purity molecules. identification field.
背景技术Background technique
花椰菜(Brassica oleracea var.Botrytis)是世界上最重要的蔬菜品种之一,因其花球营养丰富、风味鲜美而深受中西方消费者的喜爱。中国是世界上花椰菜种植和产量最大的国家。2018年,中国花椰菜产量达到1026万吨,占世界总产量的40.67%(FAO,2019)。作为高品质健康蔬菜的代表,其肉质茎与花序分生组织构成的花球富含维生素C与硫代葡萄糖苷类抗癌物质,符合当下国人对健康蔬菜的需求。Cauliflower (Brassica oleracea var.Botrytis) is one of the most important vegetable varieties in the world. It is deeply loved by Chinese and Western consumers because of its nutritious and delicious flower bulbs. China is the country with the largest cultivation and production of cauliflower in the world. In 2018, China's cauliflower production reached 10.26 million tons, accounting for 40.67% of the world's total production (FAO, 2019). As a representative of high-quality healthy vegetables, the curds composed of fleshy stems and inflorescence meristems are rich in vitamin C and glucosinolate anti-cancer substances, which meets the current Chinese people's demand for healthy vegetables.
随着花椰菜品种数量逐年增多,少数骨干亲本的集中应用,品种间的遗传差异越来越小,难以进行有效鉴别,从源头有效地管理和甄别遗传背景相似的花椰菜品种是亟待解决的一大难题。目前,花椰菜品种的鉴定主要是通过形态学标记研究等传统手段,时间周期长,得到的结论往往不够完善,且很难剔除环境以及人为因素的影响。因此,有必要建立基于基因型的快速鉴定方法。As the number of cauliflower varieties increases year by year, and a small number of backbone parents are used intensively, the genetic differences between varieties become smaller and smaller, making it difficult to effectively identify. Effectively managing and screening cauliflower varieties with similar genetic backgrounds from the source is a major problem that needs to be solved. . At present, the identification of cauliflower varieties is mainly through traditional methods such as morphological marker research, which takes a long time, and the conclusions obtained are often incomplete, and it is difficult to eliminate the influence of environmental and human factors. Therefore, it is necessary to establish a rapid identification method based on genotype.
分子标记是在基因水平上的标记,直接在DNA分子水平上检测遗传变异,不受组织和器官种类、发育阶段、生境条件等诸多因素的影响,多态性高、遗传稳定。插入缺失长度多态性(Insertion-Deletion Length Polymorphism,InDel)标记是在等位基因位点上一定数量的核苷酸插入或缺失而产生的长度多态性变异,属于第三代分子标记,主要基于全基因组测序而开发,在基因组中比SSR(Simple Sequence Repeat)标记密度大,具有标记特异性高、稳定性好、检测方法简单、经济等优点,已成功应用于水稻、大豆、棉花等品种鉴定方面,克服了仅依据形态特征鉴定新品种的不确定性。Molecular markers are markers at the gene level that directly detect genetic variation at the DNA molecular level. They are not affected by tissue and organ types, developmental stages, habitat conditions and many other factors. They are highly polymorphic and genetically stable. Insertion-Deletion Length Polymorphism (InDel) marker is a length polymorphism variation caused by the insertion or deletion of a certain number of nucleotides at the allelic site. It is a third-generation molecular marker and is mainly Developed based on whole-genome sequencing, it has a higher marker density than SSR (Simple Sequence Repeat) in the genome. It has the advantages of high marker specificity, good stability, simple and economical detection methods, and has been successfully used in rice, soybean, cotton and other varieties. In terms of identification, it overcomes the uncertainty of identifying new varieties based only on morphological characteristics.
花椰菜品种‘CB-30’是由天津市农业科学院培育的高产、高品质的花椰菜杂交品种,是花椰菜胞质不育系‘GT-42’和优良自交系‘GS-57’选育而成的早熟杂交种。‘CB-30’属于春季栽培品种,成熟期55~60天,株形质粒、紧凑,叶片深绿色,合抱护球性优。花球高圆、紧实、雪白、细嫩、平整。单球质量1.21kg,种植密度37500株/hm2,平均产量45290kg/hm2。迄今为止,尚未有适于花椰菜品种‘CB-30’,开发适用于花椰菜品种‘CB-30’的分子鉴定标记,有利于规范花椰菜品种登记、加强市场监管和强化知识产权保护等。Cauliflower variety 'CB-30' is a high-yielding, high-quality cauliflower hybrid variety cultivated by the Tianjin Academy of Agricultural Sciences. It is selected from the cauliflower cytoplasmic sterile line 'GT-42' and the excellent inbred line 'GS-57' Early maturing hybrids. 'CB-30' is a spring cultivar with a maturity period of 55 to 60 days, a compact plant shape, dark green leaves, and excellent ball protection. The flower bulbs are round, firm, white, tender and flat. The weight of a single ball is 1.21kg, the planting density is 37500 plants/hm 2 , and the average yield is 45290kg/hm 2 . So far, there is no molecular identification marker suitable for cauliflower variety 'CB-30'. The development of molecular identification markers suitable for cauliflower variety 'CB-30' will help standardize cauliflower variety registration, strengthen market supervision and strengthen intellectual property protection.
发明内容Contents of the invention
本发明的目的之一是提供用于鉴定花椰菜品种‘CB-30’品种真实性或种子纯度的InDel标记引物对组;One of the objects of the present invention is to provide an InDel marker primer pair for identifying the authenticity or seed purity of the cauliflower variety 'CB-30';
本发明的目的之二是提供用于鉴定花椰菜品种‘CB-30’真实性或者鉴定花椰菜杂交种’CB-30’种子纯度的PCR检测试剂盒;The second object of the present invention is to provide a PCR detection kit for identifying the authenticity of cauliflower variety ‘CB-30’ or identifying the purity of cauliflower hybrid ‘CB-30’ seeds;
本发明的目的之三是将所述的InDel标记引物对组应用于鉴定花椰菜品种‘CB-30’真实性或种子纯度等方面。The third object of the present invention is to apply the InDel marker primer pair set to identify the authenticity or seed purity of cauliflower variety 'CB-30'.
本发明的上述目的是通过以下技术方案来实现的:The above objects of the present invention are achieved through the following technical solutions:
本发明一方面提供了一种基于InDel标记的鉴定花椰菜品种‘CB-30’引物对组,所述引物对组由以下引物对1-引物对8共8对引物组成,所述8对引物的核苷酸序列分别为如下所示:On the one hand, the present invention provides a primer pair set for identifying cauliflower variety 'CB-30' based on InDel markers. The primer pair set consists of the following primer pair 1 - primer pair 8, a total of 8 pairs of primers. The 8 pairs of primers The nucleotide sequences are as follows:
引物对1:由SEQ ID NO.1所示的正向引物和SEQ ID NO.2所示的反向引物组成;Primer pair 1: consists of the forward primer shown in SEQ ID NO.1 and the reverse primer shown in SEQ ID NO.2;
引物对2:由SEQ ID NO.3所示的正向引物和SEQ ID NO.4所示的反向引物组成;Primer pair 2: consists of the forward primer shown in SEQ ID NO.3 and the reverse primer shown in SEQ ID NO.4;
引物对3:由SEQ ID NO.5所示的正向引物和SEQ ID NO.6所示的反向引物组成;Primer pair 3: consists of the forward primer shown in SEQ ID NO.5 and the reverse primer shown in SEQ ID NO.6;
引物对4:由SEQ ID NO.7所示的正向引物和SEQ ID NO.8所示的反向引物组成;Primer pair 4: consists of the forward primer shown in SEQ ID NO.7 and the reverse primer shown in SEQ ID NO.8;
引物对5:由SEQ ID NO.9所示的正向引物和SEQ ID NO.10所示的反向引物组成;Primer pair 5: consists of the forward primer shown in SEQ ID NO.9 and the reverse primer shown in SEQ ID NO.10;
引物对6:由SEQ ID NO.11所示的正向引物和SEQ ID NO.12所示的反向引物组成;Primer pair 6: consists of the forward primer shown in SEQ ID NO.11 and the reverse primer shown in SEQ ID NO.12;
引物对7:由SEQ ID NO.13所示的正向引物和SEQ ID NO.14所示的反向引物组成;Primer pair 7: consists of the forward primer shown in SEQ ID NO.13 and the reverse primer shown in SEQ ID NO.14;
引物对8:由SEQ ID NO.15所示的正向引物和SEQ ID NO.16所示的反向引物组成。Primer pair 8: consists of the forward primer shown in SEQ ID NO. 15 and the reverse primer shown in SEQ ID NO. 16.
本发明的另一方面是提供一种用于鉴定花椰菜品种‘CB-30’真实性或者鉴定花椰菜杂交种’CB-30’种子纯度的PCR检测试剂盒,该PCR检测试剂盒包括:dNTPs、Taq酶、MgCl2、由正向引物和反向引物组成的PCR引物对,扩增缓冲液和灭菌水;其中,所述的PCR引物对是所述InDel标记引物对组(上述引物对1-引物对8)中的任何一对。Another aspect of the present invention is to provide a PCR detection kit for identifying the authenticity of cauliflower variety 'CB-30' or identifying the purity of cauliflower hybrid 'CB-30' seeds. The PCR detection kit includes: dNTPs, Taq enzyme, MgCl 2 , a PCR primer pair consisting of a forward primer and a reverse primer, an amplification buffer and sterilized water; wherein the PCR primer pair is the InDel labeled primer pair set (the above primer pair 1- Any pair of primers 8).
本发明的再一方面是提供一种鉴定花椰菜品种‘CB-30’真实性或种子纯度的方法:应用所述的基于InDel标记引物对组,通过PCR扩增,经琼脂糖凝胶电泳检测,即可显示InDel位点在不同个体间的多态性,从而达到鉴定的目的。Another aspect of the present invention is to provide a method for identifying the authenticity or seed purity of cauliflower variety 'CB-30': applying the InDel-based marker primer pair, amplifying by PCR, and detecting by agarose gel electrophoresis, The polymorphism of the InDel site among different individuals can be displayed to achieve the purpose of identification.
具体的,本发明提供了一种应用所述的InDel标记引物对组在花椰菜杂交种’CB-30’品种真实性鉴定中的应用,包括:Specifically, the present invention provides an application of the InDel marker primer pair set in the authenticity identification of cauliflower hybrid 'CB-30' variety, including:
(1)提取待检测的花椰菜植株样品的基因组DNA;(1) Extract the genomic DNA of the cauliflower plant sample to be tested;
(2)以所提取的样品基因组DNA为模板,分别以8对引物对为正反向引物建立PCR扩增体系分别进行PCR扩增;(2) Using the extracted sample genomic DNA as a template, establish a PCR amplification system using 8 pairs of primer pairs as forward and reverse primers to perform PCR amplification respectively;
(3)如果8种扩增产物中的每一种扩增产物的带型均同时具有花椰菜杂交种’CB-30’父母本的带型,则待测花椰菜品种为花椰菜杂交种’CB-30’;如果8种扩增产物中的任何一种扩增产物的带型不同时具有花椰菜杂交种’CB-30’父母本的带型,则待测花椰菜品种则不是花椰菜杂交种’CB-30’。(3) If the banding pattern of each of the 8 amplification products has the banding pattern of the parents of the cauliflower hybrid 'CB-30', then the cauliflower variety to be tested is the cauliflower hybrid 'CB-30' '; If the banding pattern of any one of the 8 amplification products does not have the banding pattern of the parents of the cauliflower hybrid 'CB-30', then the cauliflower variety to be tested is not the cauliflower hybrid 'CB-30' '.
其中,步骤(2)中所述的PCR扩增体系优选为:10×buffer 1.0μL,25mM MgCL2 1.0μL,2mM dNTPs 1.0μL,10μM正向引物与反向引物各1.0μL,0.5单位的Taq DNA聚合酶0.2μL,模板50ng,加ddH2O至10μL;Among them, the PCR amplification system described in step (2) is preferably: 10× buffer 1.0 μL, 25mM MgCL 2 1.0 μL, 2mM dNTPs 1.0 μL, 10 μM forward primer and reverse primer 1.0 μL each, 0.5 units of Taq DNA polymerase 0.2μL, template 50ng, add ddH 2 O to 10μL;
所述的PCR扩增程序为:95℃3min;95℃15s,58℃15s,72℃20s,循环35次;72℃5min。The PCR amplification program is: 95°C for 3 minutes; 95°C for 15 seconds, 58°C for 15 seconds, 72°C for 20 seconds, 35 cycles; 72°C for 5 minutes.
所述的花椰菜杂交种’CB-30’的母本为GT-42,所述花椰菜杂交种’CB-30’的父本为GS-57。The female parent of the cauliflower hybrid 'CB-30' is GT-42, and the male parent of the cauliflower hybrid 'CB-30' is GS-57.
具体的,本发明提供了一种应用所述的基于InDel标记引物对组应用于花椰菜杂交种’CB-30’种子纯度的鉴定,该鉴定方法包括:Specifically, the present invention provides a method for identifying the purity of cauliflower hybrid 'CB-30' seeds using the InDel marker primer pair set. The identification method includes:
(1)提取待检测的花椰菜种子样品的基因组DNA;(1) Extract the genomic DNA of the cauliflower seed sample to be tested;
(2)以所提取的种子样品基因组DNA为模板,分别以8对引物对为正反向引物建立PCR扩增体系分别进行PCR扩增;(2) Using the extracted genomic DNA of the seed sample as a template, establish a PCR amplification system using 8 pairs of primer pairs as forward and reverse primers to perform PCR amplification respectively;
(3)如果8种扩增产物中的每一种扩增产物的带型均同时具有花椰菜杂交种’CB-30’父母本的带型,则待测花椰菜种子为花椰菜杂交种’CB-30’种子;如果8种扩增产物中的任何一种扩增产物的带型不同时具有花椰菜杂交种’CB-30’父母本的带型,则待测花椰菜种子则不是花椰菜杂交种’CB-30’;(3) If the banding pattern of each of the eight amplification products has the banding pattern of the parents of the cauliflower hybrid 'CB-30', then the cauliflower seed to be tested is the cauliflower hybrid 'CB-30' 'Seeds; if the banding pattern of any one of the eight amplification products does not have the banding pattern of the parents of the cauliflower hybrid 'CB-30', then the cauliflower seeds to be tested are not the cauliflower hybrid 'CB- 30';
(4)计算真实的’CB-30’花椰菜杂交种个数占总检测种子个数的比率,得到’CB-30’花椰菜杂交种的种子纯度。(4) Calculate the ratio of the true number of 'CB-30' cauliflower hybrids to the total number of tested seeds, and obtain the seed purity of 'CB-30' cauliflower hybrids.
其中,步骤(2)中所述的PCR扩增体系优选为:10×buffer 1.0μL,25mM MgCL2 1.0μL,2mM dNTPs 1.0μL,10μM正向引物与反向引物各1.0μL,0.5单位的Taq DNA聚合酶0.2μL,模板50ng,加ddH2O至10μL;Among them, the PCR amplification system described in step (2) is preferably: 10× buffer 1.0 μL, 25mM MgCL 2 1.0 μL, 2mM dNTPs 1.0 μL, 10 μM forward primer and reverse primer 1.0 μL each, 0.5 units of Taq DNA polymerase 0.2μL, template 50ng, add ddH 2 O to 10μL;
所述的PCR扩增程序为:95℃3min;95℃15s,58℃15s,72℃20s,循环35次;72℃5min。The PCR amplification program is: 95°C for 3 minutes; 95°C for 15 seconds, 58°C for 15 seconds, 72°C for 20 seconds, 35 cycles; 72°C for 5 minutes.
所述的花椰菜杂交种’CB-30’的母本为‘GT-42’,所述花椰菜杂交种’CB-30’的父本为GS-57。The female parent of the cauliflower hybrid 'CB-30' is 'GT-42', and the male parent of the cauliflower hybrid 'CB-30' is GS-57.
本发明使用Perl语言脚本筛选花椰菜品种‘CB-30’父母本基因组中特有的InDel位点,InDel大小设定为20-500bp,且测序深度大于4。基于参考基因组信息,将筛选的位点定位在基因组上,提取InDel标记位点上下游200bp的核苷酸序列。使用Primer3.0和自编程Perl语言脚本批量设计引物,利用设计合成的引物,对花椰菜‘CB-30’品种及其父母本进行PCR扩增,筛选得到8对InDel标记引物,利用所筛选的8对InDel标记引物,在短时间内能快速精确完成‘CB-30’花椰菜品种和杂交种子纯度鉴定,解决了现有花椰菜‘CB-30’品种鉴定存在的周期长,人工投入大等问题,能够快捷、高效、稳定、准确地基于InDel分子标记检测出花椰菜品种‘CB-30’。The present invention uses a Perl language script to screen the unique InDel sites in the parental genome of the cauliflower variety 'CB-30'. The InDel size is set to 20-500 bp, and the sequencing depth is greater than 4. Based on the reference genome information, the screened sites were positioned on the genome, and the 200 bp upstream and downstream nucleotide sequences of the InDel marker site were extracted. Primer3.0 and self-programmed Perl language scripts were used to design primers in batches. The designed and synthesized primers were used to conduct PCR amplification of the cauliflower 'CB-30' variety and its parents. 8 pairs of InDel marker primers were screened and the 8 screened primers were used. InDel labeled primers can quickly and accurately complete the purity identification of 'CB-30' cauliflower varieties and hybrid seeds in a short time, solving the existing problems of long cycle and high labor investment in the identification of existing cauliflower 'CB-30' varieties. The cauliflower variety 'CB-30' was detected quickly, efficiently, stably and accurately based on InDel molecular markers.
与现有技术相比,本发明主要具有以下有益效果:Compared with the prior art, the present invention mainly has the following beneficial effects:
1.本发明利用花椰菜品种‘CB-30’的父母本重测序数据在全基因组范围内筛选差异InDel位点并设计特异性引物,准确性高、结果稳定可靠。1. The present invention uses the resequencing data of the parents of the cauliflower variety 'CB-30' to screen differential InDel sites across the entire genome and design specific primers, with high accuracy and stable and reliable results.
2.本发明利用琼脂糖凝胶电泳进行检测,与聚丙烯酰胺凝胶电泳凝胶电泳相比,具有操作简便、成本低、速度快、适用范围广等优点。2. The present invention uses agarose gel electrophoresis for detection. Compared with polyacrylamide gel electrophoresis, it has the advantages of simple operation, low cost, fast speed, and wide application range.
3.本发明基于PCR扩增反应,利用8个位点上的InDel分子标记,在短时间内能快速精确完成‘CB-30’花椰菜品种和杂交种子纯度鉴定,方法简便快捷、检测周期短、节省人工成本,具有很好的应用推广前景。3. This invention is based on PCR amplification reaction and uses InDel molecular markers at 8 sites to quickly and accurately complete the purity identification of 'CB-30' cauliflower varieties and hybrid seeds in a short time. The method is simple and fast, and the detection cycle is short. It saves labor costs and has good application and promotion prospects.
4.本发明除了根据引物组扩增的带型鉴定花椰菜品种‘CB-30’,还可以根据引物组在不同花椰菜品种间带型不同,对不同品种包括‘津品74’、‘津品79’、‘津品80’、‘春雪30’、‘BX-110’、‘BX-120’或‘SX-60’等花椰菜品种进行区分。4. In addition to identifying the cauliflower variety 'CB-30' based on the band pattern amplified by the primer set, the present invention can also identify the different band patterns among different cauliflower varieties based on the primer set. Different varieties include 'Jinpin 74', 'Jinpin 79' ', 'Jinpin 80', 'Chunxue 30', 'BX-110', 'BX-120' or 'SX-60' and other cauliflower varieties to distinguish.
附图说明Description of the drawings
图1为花椰菜品种‘CB-30’母本GT-42、花椰菜品种‘CB-30’父本GS-57、花椰菜品种‘CB-30’的8对引物对的PCR扩增产物电泳图;图中M为Marker,每对引物分别有9个泳道,从左至右依次为花椰菜品种‘CB-30’母本、父本和‘CB-30’的各3个单株。Figure 1 is the electrophoresis pattern of PCR amplification products of 8 primer pairs of cauliflower variety 'CB-30' female parent GT-42, cauliflower variety 'CB-30' male parent GS-57, and cauliflower variety 'CB-30'; Figure M in the middle is Marker, and each pair of primers has 9 lanes. From left to right, there are 3 individual plants each of the female parent, male parent and 'CB-30' of the cauliflower variety 'CB-30'.
图2为花椰菜品种‘CB-30’以及津品74’、‘津品79’、‘津品80’、‘春雪30’、‘BX-110’、‘BX-120’或‘SX-60’的8对引物对的PCR扩增产物电泳图;图中M为Marker,泳道01~08分别为CB30-36、CB30-46、CB30-48、CB30-57、CB30-63、CB30-67、CB30-98、CB30-99等8对引物,每对引物对应1个泳道,分别为5个单株混样。。Figure 2 shows the cauliflower variety 'CB-30' and Jinpin 74', 'Jinpin 79', 'Jinpin 80', 'Chunxue 30', 'BX-110', 'BX-120' or 'SX-60' Electrophoresis diagram of PCR amplification products of 8 pairs of primers; M in the picture is Marker, and lanes 01 to 08 are CB30-36, CB30-46, CB30-48, CB30-57, CB30-63, CB30-67, and CB30 respectively. -98, CB30-99 and other 8 pairs of primers, each pair of primers corresponds to 1 lane, and each is a mixed sample of 5 individual plants. .
图3为分别使用引物CB30-36、CB30-48、CB30-57检测花椰菜品种‘CB-30’的种子纯度的部分电泳图;图中M为Marker,泳道01为花椰菜品种‘CB-30’母本,泳道02为花椰菜品种‘CB-30’父本,03-24泳道为待测样品的22个单株。Figure 3 is a partial electrophoresis diagram of using primers CB30-36, CB30-48, and CB30-57 to detect the seed purity of cauliflower variety 'CB-30'; M in the figure is the Marker, and lane 01 is the mother of cauliflower variety 'CB-30' In this example, lane 02 is the male parent of cauliflower variety 'CB-30', and lanes 03-24 are the 22 individual plants of the sample to be tested.
具体实施方式Detailed ways
以下结合具体实施例来进一步描述本发明,本发明的优点和特点将会随着描述而更为清楚。但这些实施例仅是范例性的,并不对本发明的范围构成任何限制。本领域技术人员应该理解的是,在不偏离本发明的精神和范围下可以对本发明的细节和形式进行修改或替换,但这些修改和替换均落入本发明的保护范围内。The present invention will be further described below in conjunction with specific embodiments, and the advantages and features of the present invention will become clearer with the description. However, these embodiments are only exemplary and do not constitute any limitation on the scope of the present invention. Those skilled in the art should understand that the details and forms of the present invention can be modified or replaced without departing from the spirit and scope of the present invention, but these modifications and substitutions all fall within the protection scope of the present invention.
试验例1全基因组范围内筛选差异InDel位点并设计筛选特异性引物Test Example 1: Screen differential InDel sites across the entire genome and design screening-specific primers
1试验方法1Test method
1.1 Illumina高通量测序1.1 Illumina high-throughput sequencing
提取花椰菜品种‘CB-30’的母本胞质不育系‘GT-42’、父本优良自交系‘GS-57’、以及其他PN-601、PN-602、PN-603、PN-604、PN-643、PN-644、PN-737等7个优良自交系等的基因组DNA,对各个不育系和自交系的基因组DNA进行Illumina双末端测序,获得的原始数据去除接头序列和数据质控后,有效测序数据通过BWA软件,与花椰菜参考基因组进行比对,比对结果经SAMTOOLS去除重复。使用GATK HaplotypeCaller模块对样本中的InDel变异进行检测分析;Extract the maternal cytoplasmic sterile line 'GT-42' of cauliflower variety 'CB-30', the male superior inbred line 'GS-57', and other PN-601, PN-602, PN-603, PN- Genomic DNA of 7 excellent inbred lines, including 604, PN-643, PN-644, and PN-737, was analyzed. Illumina paired-end sequencing was performed on the genomic DNA of each sterile line and inbred line. The obtained raw data removed the adapter sequences. After data quality control, the effective sequencing data was compared with the cauliflower reference genome through BWA software, and the comparison results were removed by SAMTOOLS to remove duplicates. Use the GATK HaplotypeCaller module to detect and analyze InDel mutations in samples;
1.2差异InDel位点筛选及特异性引物设计1.2 Differential InDel site screening and specific primer design
使用Perl语言脚本筛选花椰菜品种‘CB-30’父母本基因组中特有的InDel位点,InDel大小设定为20-500bp,且测序深度大于4。基于参考基因组信息,将筛选的位点定位在基因组上,提取InDel标记位点上下游200bp的核苷酸序列。使用Primer3.0和自编程Perl语言脚本设计引物,设置参数为Tm值为(58±3)℃,引物长度为(20±2)bp,PCR产物预计长度为100~400bp,其他参数为默认。Use a Perl language script to screen the unique InDel sites in the parental genome of cauliflower variety 'CB-30'. The InDel size is set to 20-500bp, and the sequencing depth is greater than 4. Based on the reference genome information, the screened sites were positioned on the genome, and the 200 bp upstream and downstream nucleotide sequences of the InDel marker site were extracted. Use Primer3.0 and self-programmed Perl language script to design primers. Set the parameters as T m value is (58±3)℃, primer length is (20±2)bp, the expected length of PCR product is 100~400bp, and other parameters are default .
2试验结果2 test results
根据预测的InDel位点,共计得到125个InDel位点及其特异性引物。经PCR检测发现,125对引物在‘GT-42’、‘GS-57’及F1‘CB-30’中均能扩增出条带,且扩增产物大小与预测大小相吻合,8对InDel引物在‘CB-30’中可以同时扩增到父母本的特征性条带,可用于鉴定花椰菜品种‘CB-30’及其种子纯度(图1)。Based on the predicted InDel sites, a total of 125 InDel sites and their specific primers were obtained. After PCR testing, it was found that 125 pairs of primers could amplify bands in 'GT-42', 'GS-57' and F1'CB-30', and the size of the amplified product was consistent with the predicted size, and 8 pairs of InDel The primers in 'CB-30' can simultaneously amplify the characteristic bands of both parents, which can be used to identify the cauliflower variety 'CB-30' and its seed purity (Figure 1).
表1基于InDel标记的花椰菜杂交种’CB-30’鉴定的引物对Table 1 Primer pairs for identification of InDel-labeled cauliflower hybrid ‘CB-30’
以下试验例1和试验例2中用于鉴定‘CB-30’花椰菜品种或‘CB-30’花椰菜杂交种子纯度的8对InDel标记引物对为表1所示。The eight pairs of InDel marker primers used to identify the purity of ‘CB-30’ cauliflower variety or ‘CB-30’ cauliflower hybrid seeds in the following Test Examples 1 and 2 are shown in Table 1.
试验例2‘CB-30’花椰菜品种快速鉴定试验Test Example 2 ‘CB-30’ Cauliflower Variety Rapid Identification Test
1鉴定方法1 identification method
1.1叶片基因组DNA提取1.1 Extraction of genomic DNA from leaves
花椰菜杂交种‘CB-30’及其母本GT-42和父本GS-57、‘津品74’、‘津品79’、‘津品80’、‘春雪30’、‘BX-110’、‘BX-120’或‘SX-60’花椰菜品种的各5个单株混样DNA。Cauliflower hybrid 'CB-30' and its female parent GT-42 and male parent GS-57, 'Jinpin 74', 'Jinpin 79', 'Jinpin 80', 'Chunxue 30', and 'BX-110' , 'BX-120' or 'SX-60' cauliflower varieties, mixed DNA samples of five individual plants each.
1.2 PCR扩增1.2 PCR amplification
以1.1所述的各个花椰菜品种的基因组DNA为模板,以CB30-36、CB30-46、CB30-48、CB30-57、CB30-63、CB30-67、CB30-98和CB30-99为引物,分别进行PCR扩增;Use the genomic DNA of each cauliflower variety described in 1.1 as the template, and use CB30-36, CB30-46, CB30-48, CB30-57, CB30-63, CB30-67, CB30-98 and CB30-99 as primers, respectively. Perform PCR amplification;
PCR扩增体系为:10×buffer 1.0μL,25mM MgCL2 1.0μL,2mM dNTPs 1.0μL,10μM正向引物与反向引物各1.0μL,0.5单位的Taq DNA聚合酶0.2μL,模板50ng,加ddH2O至10μL;The PCR amplification system is: 10× buffer 1.0μL, 25mM MgCL 2 1.0μL, 2mM dNTPs 1.0μL, 10μM forward primer and reverse primer 1.0μL each, 0.5 unit Taq DNA polymerase 0.2μL, template 50ng, add ddH 2 O to 10 μL;
PCR扩增程序为:95℃3min,(95℃15s,58℃15s,72℃20s)循环35次,72℃5min。The PCR amplification program was: 95°C for 3 min, 35 cycles of (95°C for 15 s, 58°C for 15 s, 72°C for 20 s), and 72°C for 5 min.
1.3 PCR扩增产物检测分析1.3 Detection and analysis of PCR amplification products
加入1μL10×Loding Buffer于1.2所述扩增的产物中,在120V/cM恒定电压下,经2%琼脂糖凝胶电泳90min后,Gelred染色,凝胶成像系统照相。根据电泳带型鉴定品种,如果8个InDel位点的带型同时具有花椰菜杂交种‘CB-30’父母本的带型,则确定待测花椰菜品种为花椰菜杂交种‘CB-30’。Add 1 μL of 10× Loding Buffer to the amplified product described in 1.2, conduct 2% agarose gel electrophoresis for 90 min at a constant voltage of 120 V/cM, Gelred staining, and take pictures with a gel imaging system. Identification of varieties based on electrophoresis band patterns. If the band patterns of the eight InDel sites also have the band patterns of the parents of the cauliflower hybrid ‘CB-30’, the cauliflower variety to be tested is determined to be the cauliflower hybrid ‘CB-30’.
2鉴定结果2 identification results
使用上述方法对花椰菜杂交种花椰菜品种‘CB-30’以及‘津品74’、‘津品79’、‘津品80’、‘春雪30’、‘BX-110’、‘BX-120’或‘SX-60’进行品种鉴定,8对引物在花椰菜品种中验证均具有多态性,均为3种带型,为了直观表示,一般将同一引物对扩增图谱中依最小扩增产物的分子量大小来分类,当最小产物的分子量相同时以次二的分子量分类,以此类推。低分子量谱带的类型定义为1,高分子量谱带的类型定义为2,杂合共显带类型定义为3,无条带定义为0。把相应的图谱类型转换成像身份证号一样独一无二的编码,用编码来区分品种的差异。Use the above method to test the cauliflower hybrid cauliflower variety 'CB-30' and 'Jinpin 74', 'Jinpin 79', 'Jinpin 80', 'Chunxue 30', 'BX-110', 'BX-120' or 'SX-60' was used for variety identification. The 8 pairs of primers were verified to be polymorphic in cauliflower varieties, with 3 banding types. For intuitive representation, the amplification map of the same primer pair is generally based on the molecular weight of the smallest amplification product. Classify by size. When the molecular weight of the smallest product is the same, it is classified by the second molecular weight, and so on. The type of low molecular weight band is defined as 1, the type of high molecular weight band is defined as 2, the type of hybrid co-banding is defined as 3, and the type of no band is defined as 0. Convert the corresponding map type into a unique code like an ID number, and use the code to distinguish the differences in varieties.
花椰菜杂交种品种‘CB-30’以及‘津品74’、‘津品79’、‘津品80’、‘春雪30’、‘BX-110’、‘BX-120’或‘SX-60’的8对引物扩增琼脂糖凝胶电泳图如图2所示。图2中M为Marker,泳道01~08分别为CB30-36、CB30-46、CB30-48、CB30-57、CB30-63、CB30-67、CB30-98和CB30-99等8对引物的扩增产物;其编码表如表2所示。Cauliflower hybrid varieties 'CB-30' and 'Jinpin 74', 'Jinpin 79', 'Jinpin 80', 'Spring Snow 30', 'BX-110', 'BX-120' or 'SX-60' The agarose gel electrophoresis diagram amplified by 8 pairs of primers is shown in Figure 2. In Figure 2, M is Marker, and lanes 01 to 08 are respectively the amplification results of eight pairs of primers: CB30-36, CB30-46, CB30-48, CB30-57, CB30-63, CB30-67, CB30-98 and CB30-99. Increased product; its coding table is shown in Table 2.
表2花椰菜品种‘CB-30’的父母本、杂交种‘CB-30’以及7份花椰菜杂交品种指纹图谱编码Table 2 Fingerprint codes of the parents of cauliflower variety ‘CB-30’, hybrid ‘CB-30’ and 7 cauliflower hybrid varieties
根据检测结果可见,花椰菜杂交种‘CB-30’的8个InDel位点的带型同时具有花椰菜杂交种‘CB-30’父母本的带型,‘津品74’、‘津品79’、‘津品80’、‘春雪30’、‘BX-110’、‘BX-120’以及‘SX-60’的8个InDel位点的带型不同时具有花椰菜杂交种‘CB-30’父母本的带型;根据鉴定结果可见,采用本发明设计的引物组能够将花椰菜杂交种‘CB-30’与其它的花椰菜品种进行准确鉴定。According to the test results, it can be seen that the banding patterns of the eight InDel sites of the cauliflower hybrid 'CB-30' also have the banding patterns of the parents of the cauliflower hybrid 'CB-30', 'Jinpin 74', 'Jinpin 79', The banding patterns of the eight InDel loci of 'Jinpin 80', 'Chunxue 30', 'BX-110', 'BX-120' and 'SX-60' are different and they all have the parental parent of the cauliflower hybrid 'CB-30'. The band pattern; according to the identification results, it can be seen that the cauliflower hybrid 'CB-30' and other cauliflower varieties can be accurately identified using the primer set designed in the present invention.
试验例3‘CB-30’花椰菜杂交种子纯度的鉴定Test Example 3 Identification of Purity of ‘CB-30’ Cauliflower Hybrid Seeds
1.鉴定方法1. Identification method
1.1叶片基因组DNA提取1.1 Extraction of genomic DNA from leaves
一批‘CB-30’花椰菜杂交种子中随机94份杂交种样品种子。94 random hybrid sample seeds from a batch of ‘CB-30’ cauliflower hybrid seeds.
将父母本(母本GT-42和父本GS-57)的种子和样品种子同时播种于72孔穴盘中,定期浇水,直至长出两片真叶;将父母本各5株单株分别混合取样,94份杂交样品种子分别单株取样叶片。按照常规CTAB方法分别提取基因组DNA,-20℃保存备用。Seeds from the parent parent (female parent GT-42 and male parent GS-57) and sample seeds were sown in a 72-hole hole tray at the same time, and watered regularly until two true leaves grew; 5 plants from each parent were planted separately. Mixed sampling was conducted, and the leaves of each of the 94 hybrid sample seeds were sampled from individual plants. Genomic DNA was extracted separately according to the conventional CTAB method and stored at -20°C for later use.
1.2 PCR扩增1.2 PCR amplification
同试验例2中的PCR扩增条件。The same PCR amplification conditions as in Test Example 2.
1.3 PCR扩增产物检测分析1.3 Detection and analysis of PCR amplification products
PCR扩增产物检测及杂交种品种鉴定方法同试验例1。The methods for detecting PCR amplification products and identifying hybrid varieties are the same as those in Experimental Example 1.
2.鉴定结果2. Identification results
使用上述方法对花椰菜杂交种‘CB-30’进行种子纯度鉴定的琼脂糖凝胶电泳图部分结果如图3所示。图中M为Marker,泳道01为花椰菜杂交种品种‘CB-30’母本,泳道02为花椰菜杂交种品种‘CB-30’父本,03-24泳道为待测样品的22个单株。Partial results of agarose gel electrophoresis for seed purity identification of cauliflower hybrid ‘CB-30’ using the above method are shown in Figure 3. In the figure, M is the marker, lane 01 is the female parent of the cauliflower hybrid variety 'CB-30', lane 02 is the male parent of the cauliflower hybrid variety 'CB-30', and lanes 03-24 are the 22 individual plants of the sample to be tested.
22份样品种子中真实的杂交种有22份,因此该批‘CB-30’杂交种子纯度为100%,符合国家标准且与田间调查结果一致。Among the 22 sample seeds, 22 are true hybrids, so the purity of this batch of ‘CB-30’ hybrid seeds is 100%, in line with national standards and consistent with field survey results.
SEQUENCE LISTINGSEQUENCE LISTING
<110> 天津市农业科学院<110> Tianjin Academy of Agricultural Sciences
<120> InDel标记引物组及其在花椰菜'CB-30'品种或种子纯度鉴定中的应用<120> InDel labeled primer set and its application in purity identification of cauliflower 'CB-30' variety or seeds
<130> TJ-2002-210704A<130> TJ-2002-210704A
<160> 16<160> 16
<170> PatentIn version 3.5<170> PatentIn version 3.5
<210> 1<210> 1
<211> 20<211> 20
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 1<400> 1
tggggataga gagagaccca 20tggggataga gagagaccca 20
<210> 2<210> 2
<211> 20<211> 20
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 2<400> 2
aaatcccagt gtccgaacga 20aaatcccagt gtccgaacga 20
<210> 3<210> 3
<211> 20<211> 20
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 3<400> 3
accattgtgc tcccagttcc 20accattgtgc tcccagttcc 20
<210> 4<210> 4
<211> 22<211> 22
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 4<400> 4
gctttgtttc agaccagtgt gt 22gctttgtttc agaccagtgt gt 22
<210> 5<210> 5
<211> 20<211> 20
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 5<400> 5
atactgacaa gccactgccc 20atactgacaa gccactgccc 20
<210> 6<210> 6
<211> 20<211> 20
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 6<400> 6
aatggacaat cagggcaggg 20aatggacaat cagggcaggg 20
<210> 7<210> 7
<211> 22<211> 22
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 7<400> 7
gcggatgcta ctgtagagaa ac 22gcggatgcta ctgtagagaa ac 22
<210> 8<210> 8
<211> 20<211> 20
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 8<400> 8
agcggcttct cattcccaat 20agcggcttct cattcccaat 20
<210> 9<210> 9
<211> 20<211> 20
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 9<400> 9
acgctgagtc gtttctggag 20acgctgagtc gtttctggag 20
<210> 10<210> 10
<211> 20<211> 20
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 10<400> 10
cggaaggttt cagtttgccg 20cggaaggttt cagtttgccg 20
<210> 11<210> 11
<211> 20<211> 20
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 11<400> 11
cggtctatca ggtcacaggc 20cggtctatca ggtcacaggc 20
<210> 12<210> 12
<211> 20<211> 20
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 12<400> 12
ctgtgcaact tccaacgtgg 20ctgtgcaact tccaacgtgg 20
<210> 13<210> 13
<211> 20<211> 20
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 13<400> 13
tctccgcatg ttcgtgtgaa 20tctccgcatg ttcgtgtgaa 20
<210> 14<210> 14
<211> 20<211> 20
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 14<400> 14
tttgcaggca aaccaatccg 20tttgcaggca aaccaatccg 20
<210> 15<210> 15
<211> 20<211> 20
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 15<400> 15
acggtccggc aaagaatctt 20acggtccggc aaagaatctt 20
<210> 16<210> 16
<211> 20<211> 20
<212> DNA<212> DNA
<213> Artifical sequence<213> Artificial sequence
<400> 16<400> 16
cgtatcaatg ccaccgtcct 20cgtatcaatg ccaccgtcct 20
Claims (9)
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Citations (2)
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CN111471786A (en) * | 2020-04-03 | 2020-07-31 | 天津科润农业科技股份有限公司 | Molecular marker related to cauliflower anthocyanin and application |
CN112391488A (en) * | 2020-10-21 | 2021-02-23 | 浙江省农业科学院 | SNP marker for identifying broccoli variety Zhe Qing 80 |
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CN101610668B (en) * | 2006-10-03 | 2013-11-20 | 塞米尼斯蔬菜种子公司 | Brilliant white cauliflower |
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Patent Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
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CN111471786A (en) * | 2020-04-03 | 2020-07-31 | 天津科润农业科技股份有限公司 | Molecular marker related to cauliflower anthocyanin and application |
CN112391488A (en) * | 2020-10-21 | 2021-02-23 | 浙江省农业科学院 | SNP marker for identifying broccoli variety Zhe Qing 80 |
Non-Patent Citations (1)
Title |
---|
吴鑫燕等.基于BSA重测序松花性状InDel标记的开发及应用.《分子植物育种》.2021,第1-17页. * |
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