CN118813847A - Grape SSR (simple sequence repeat) marker based on microRNA (micro ribonucleic acid) and application thereof - Google Patents
Grape SSR (simple sequence repeat) marker based on microRNA (micro ribonucleic acid) and application thereof Download PDFInfo
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- 241001251761 Riparia Species 0.000 claims 1
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Abstract
The invention discloses a microRNA-based grape SSR marker and application thereof, and belongs to the technical field of grape breeding and molecular markers. The grape SSR marker comprises VMIRSSR166b and/or VMIRSSR3633a, the primer sequences of VMIRSSR166b are shown in SEQ ID NO. 1 and SEQ ID NO. 2, and the primer sequences of VMIRSSR3633a are shown in SEQ ID NO. 3 and SEQ ID NO. 4, so that the grape SSR marker is used for grape variety identification, cold resistance evaluation and grape breeding. The invention combines the traditional SSR molecular markers and sequencing technology to newly develop miRNA-SSR molecular markers, greatly promotes the progress of grape molecular marker assisted breeding research, and remarkably improves the efficiency of germplasm resource identification.
Description
Technical Field
The invention belongs to the technical field of grape breeding and molecular markers, and particularly relates to a microRNA-based grape SSR marker and application thereof, in particular to application in grape variety identification, cold resistance evaluation and grape breeding.
Background
The molecular marking technology is a common and economical method, and can be used for variety identification and classification, germplasm resource evaluation and screening, auxiliary breeding and other aspects. SSR molecular markers, also called microsatellite (microsatellite) markers, are an analysis method based on simple repeated sequences in DNA sequences, wherein the SSR consists of repeated 2-6 base sequence units, the repeated sequences are widely distributed in a genome, and DNA fragments with polymorphism can be obtained by PCR amplification and analysis of the repeated sequences and are used for identifying the differences among different varieties. The SSR molecular marker technology has low cost, relatively simple and rapid amplification and analysis processes and simpler data analysis, and is suitable for large-scale and rapid sample identification.
The traditional SSR molecular marking method generally adopts polyacrylamide gel electrophoresis for separation and analysis, and in the electrophoresis process, different DNA band modes can appear among different varieties due to the difference of fragment lengths. The method is quick and economical, but mainly relies on the difference of the length and the number of the repeated sequences to perform difference analysis, has low resolution, and cannot capture the variation of the bases in the PCR band. In addition, the fluorescent dye moiety required for electrophoresis is toxic, and the comparison and interpretation of the electropherograms requires experimenters to possess a certain experience and expertise. The traditional molecular marker resolution can not reach single base, in order to make up for the deficiency in quality, the polymorphism analysis combined by a plurality of pairs of marker primers is often adopted to achieve the purpose of accurate identification, and the development time and the economic cost of the molecular marker are greatly increased.
Whole genome high throughput sequencing is a commonly used method for identifying and analyzing DNA sequences of different varieties of grapes, which can provide single base resolution, and can detect subtle variations and diversity in DNA sequences. The continuous development and maturation of gene sequencing technology provides more accurate tools for variety identification and breeding, and accelerates the progress of variety improvement and resource protection. However, when the high-throughput gene sequencing technology is used for identifying grape varieties, the generated data volume is huge, complicated data processing and analysis are required, and the cost of library construction and high-throughput sequencing is high, so that the wide application of the technology is limited.
Disclosure of Invention
Aiming at the problems that the resolution of the traditional grape molecular marker in the prior art cannot reach single base, the polymorphism analysis combined by a plurality of pairs of marker primers greatly increases the time and economic cost of molecular marker development, the data volume generated by high-throughput sequencing is huge, complicated data processing and analysis are needed, the cost of library construction and high-throughput sequencing is high, and the like, the main purpose of the invention is to provide a grape SSR marker based on microRNA.
The invention further aims to provide application of the microRNA-based grape SSR marker in grape variety identification, cold resistance evaluation and grape breeding.
In order to achieve the above purpose, the invention adopts the following technical scheme:
the invention provides a microRNA-based grape SSR marker, which comprises VMIRSSR and 166b and/or VMIRSSR and 3633a;
the primer sequences of VMIRSSR and 166b are shown as SEQ ID NO.1 and SEQ ID NO. 2;
The primer sequences of VMIRSSR and 3633a are shown as SEQ ID NO. 3 and SEQ ID NO. 4; the method comprises the following steps:
Vvi-MIR166b:
Forward primer: TCGACCATCTCCCAACTCTCT (SEQ ID NO: 1);
reverse primer: GGACCTACCCTTTCAAAGTCA (SEQ ID NO: 2);
Vvi-MIR3633a:
Forward primer: TTCTCTTGGTGCTCGCTGTT (SEQ ID NO: 3);
Reverse primer: CATGCTCGTGTCCACAGTCT (SEQ ID NO: 4).
Preferably, the microRNA-based grape SSR marker is VMIRSSR166b, and the primer sequences are shown in SEQ ID NO.1 and SEQ ID NO. 2.
The invention also provides application of the microRNA-based grape SSR marker in grape variety identification, cold resistance evaluation and grape breeding.
Preferably, the grape variety is selected from the group formed by: river bank No. 7, river bank No. 8, river bank No. 、588054lowa7riparia、gbc12aestivalis、DVIT1296acerifolia、DVIT2227.2Palmata、Beaumont、DVIT3235、Paulsen 1447、venus、 beda, 5C, erigeron breviscapus (large), zheng Guo No. 6 (0856), crystal, sira, bai Jixin, pecan, damina, rubratado, sweet sapphire, bai Hali li (0080), black agland (0305), red queen (0347), wonderful coreless, lingbao mulberry leaf 1, aril (riber) (0010), mutamof Thompson seedless1219, min Jiang xi grape water 1614.
Compared with the prior art, 23 pairs of primers related to grape miRNA-SSR molecular markers are independently developed by utilizing the result of the miRbase database annotation of grape miRNA sequences, the primers are used for carrying out PCR amplification and sequencing on the DNA of 10 cold-resistant and sensitive grape varieties, the sequencing result and the cold resistance are analyzed in a combined way, and 2 SSR markers highly related to the cold resistance are screened out. The primer pair corresponding to the 2 SSRs is used for carrying out PCR amplification and sequencing on 30 parts of germplasm resources (15 parts of cold resistance and sensitivity respectively), and the cold resistance is predicted according to the sequencing result, wherein the predicted success rate of VMIRSSR166b on the cold resistance and sensitivity of the grape can reach 93% and 93%, and the predicted success rate of VMIRSSR3633a on the cold resistance and sensitivity of the grape is 86% and 93%.
The invention combines the traditional SSR molecular marker and sequencing technology to newly develop the miRNA-SSR molecular marker, greatly promotes the progress of grape molecular marker assisted breeding research, remarkably improves the efficiency of germplasm resource identification, and has the following beneficial effects:
(1) The time efficiency is high. The SSR markers related to cold resistance can be obtained in a short time, and compared with the traditional molecular marker development and identification process, the SSR markers have greatly shortened time and have important significance for grape breeding and cold resistance variety screening.
(2) The flow is simple. Only a pair of molecular marker primers are needed to verify cold resistance, so that the complex process of combined analysis of a plurality of pairs of primers is avoided, the experimental steps are simplified, and the operation complexity is reduced.
(3) The cost is saved. Due to the reduction of the use of multiple pairs of labeled primers and the complicated data processing steps, the overall experimental cost is significantly reduced, and a more economical choice is provided compared with a high-throughput sequencing and multiple SSR site combined analysis method.
(4) And the identification is accurate. The method combines SSR molecular markers and sequencing technology, has higher resolution and accuracy, can capture single-base variation, and provides reliable technical support for accurate identification and cold resistance evaluation of grape varieties.
(5) Applications in a number of fields. The molecular marker is not only suitable for grape breeding and cold resistance variety screening, but also can be applied to molecular marker assisted breeding of other fruit trees and crops in an expanding way, and provides a new technical means for development of agricultural science and horticulture.
Drawings
FIG. 1 is a growth state diagram of 40 parts of grape germplasm resources in an example.
FIG. 2 shows DNA bands obtained by PCR amplification of VMIRSSR b labeled primers from different varieties of grape in the example.
FIG. 3 shows DNA bands obtained by PCR amplification of VMIRSSR3633a labeled primers in the examples.
Detailed Description
The technical effects produced by the present invention will be described in further detail and fully in connection with the specific embodiments for a more complete understanding of the technical aspects, objects, and advantages of the present invention. It will be apparent that the described embodiments are only some, but not all, embodiments of the invention. It should be noted that other embodiments obtained without departing from the inventive concept are within the scope of protection of the present invention for a person skilled in the art.
Example 1
1. Experimental materials
A total of 40 grape varieties in Vitaceae grape genus are selected for experiment, the grape varieties are all from Shanghai university agriculture and biology college greenhouses, and standard management methods are adopted for the grape seedlings to ensure that external factors such as illumination, temperature, insect damage and the like are consistent as much as possible, grape leaves are taken from the growth and development period of the leaves, and grape sources can be divided into European and Asia populations, east Asia populations, american populations and hybrid populations, and are shown in table 1 and figure 1.
2. Acquisition of DNA samples
High quality DNA was extracted from grape leaf samples using the modified CTAB method. After DNA extraction, the concentration of DNA is detected by using Nanodrop and recorded, and if the concentration reaches the requirement, a small amount of sample is taken and the quality of the sample is detected by agarose gel electrophoresis. After passing the test, the DNA sample was diluted to 50ng/uL and stored at-20℃for later use.
3. Development of grape miRNA-SSR
SSR predictions were made by MISA tools on the pre-existing 153 miRNAs of MiRbase database grapes around 500bp upstream and downstream based on the Nibino grape reference genome. Combining miRNAs responding to cold stress in predecessor and laboratory researches and the prediction results, screening 23 candidate miRNAs-SSRs. A total of 23 Primer pairs were designed for these 23 candidate miRNA-SSR using Primer 5.0 software, as shown in table 2. After primers were synthesized by Rui Zhi Biotechnology Co., ltd, the primers were used to PCR amplify the DNAs of 5 cold-resistant and 5 sensitive grape varieties, and the PCR products were sent to Beijing Biotechnology Co., ltd for sequencing. And analyzing a sequencing result by DNAMAN software, and analyzing the sequencing result and cold resistance in a combined way, wherein 2 SSR sites with strong cold resistance are selected, namely VMIRSSR b and VMIRSSR3633a, and the 2 sites have obvious differences in cold resistance and sensitive grape, so that the method can be used as candidate markers for predicting the cold resistance of the grape.
4. Identification of grape miRNA-SSR
The DNA of 30 grape varieties was amplified, PCR and sequenced using the primers developed in step 3 for the 2 candidate miRNA-SSR sites, as shown in tables 3-6, figures 2 and 3. According to the sequencing result, the cold resistance of 30 grape varieties is predicted, and the predicted result is compared with the actual resistance, wherein the predicted success rate of VMIRSSR166b on the cold resistance and the sensitivity of the grape is 93% and 93%, and the predicted success rate of VMIRSSR3633a on the cold resistance and the sensitivity of the grape is 86% and 93%.
Table 1: grape germplasm resource and source thereof
Table 2: grape VMIRSSR marker primer design
Table 3: alignment of DNA sequences after Vvi-MIR166b amplification
Table 4: alignment of DNA sequences after Vvi-MIR3633a amplification
Table 5: vvi-MIR166b amplified fragment SSR number statistics
Name of the name | Cold resistance | 166b |
River bank No. 7 | Cold-resistant | (TC)10 |
River bank number 8 | Cold-resistant | (TC)10 |
River bank number 9 | Cold-resistant | (TC)8 |
588054lowa7riparia | Cold-resistant | (TC)14 |
gbc12aestivalis | Cold-resistant | (TC)7 |
DVIT1296acerifolia | Cold-resistant | (TC)10 |
DVIT2227.2Palmata | Cold-resistant | (TC)12 |
Beaumont | Cold-resistant | (TC)12 |
DVIT3235 | Cold-resistant | (TC)13 |
Paulsen 1447 | Cold-resistant | (TC)14 |
venus | Cold-resistant | (TC)13 |
Beda | Cold-resistant | (TC)10 |
5C | Cold-resistant | (TC)10 |
Vitis Viniferae (Large) | Cold-resistant | / |
Zheng Guo 6 No. 6 (0856) | Cold-resistant | (TC)12 |
Crystal | Sensitivity to | (TC)16(TT)(TC)4 |
Sila device | Sensitivity to | (TC)7C(CT)18 |
Bai Jixin A | Sensitivity to | (TC)6C(CT)29 |
Bixiang seedless | Sensitivity to | (TC)19 |
Damina | Sensitivity to | (TC)7C(CT)15 |
Red baladox | Sensitivity to | (TC)7C(CT)26 |
Sweet sapphire | Sensitivity to | (TC)6C(CT)28 |
Bai Hali Li (0080) | Sensitivity to | (TC)7C(CT)18 |
Black gram (0305) | Sensitivity to | / |
Red queen (0347) | Sensitivity to | (TC)7C(CT)23 |
Wonderful coreless | Sensitivity to | (TC)7C(CT)24 |
"Lingbao" mulberry leaf 1 | Sensitivity to | (TC)25 |
Aryl (Rui Bier) (0010) | Sensitivity to | (TC)7C(CT)15 |
Mutamof Thompson seedless 1219 | Sensitivity to | (TC)6C(CT)23 |
Ganjing grape water 1614 | Sensitivity to | (TC)7C(CT)21 |
Table 6: vvi-MIR3633a amplified fragment SSR number statistics
The above is only a preferred embodiment of the present invention, and is not intended to limit the present invention, but various modifications and variations can be made to the present invention by those skilled in the art. Any modification, equivalent replacement, improvement, etc. made within the spirit and principle of the present invention should be included in the protection scope of the present invention.
Claims (4)
1. A microRNA-based grape SSR marker comprising VMIRSSR166b and/or VMIRSSR3633a;
the primer sequences of VMIRSSR and 166b are shown as SEQ ID NO.1 and SEQ ID NO. 2;
The primer sequences of VMIRSSR and 3633a are shown in SEQ ID NO. 3 and SEQ ID NO. 4.
2. The microRNA-based grape SSR marker of claim 1, wherein the primer sequence is VMIRSSR166b as shown in SEQ ID No. 1 and SEQ ID No. 2.
3. The use of the microRNA-based grape SSR marker of claim 1 or 2 in grape variety identification, cold resistance assessment and grape breeding.
4. Use according to claim 3, characterized in that the grape variety is selected from the group formed by: river bank No. 7, river bank No. 8, river bank No. 、588054lowa7 riparia、gbc12 aestivalis、DVIT1296 acerifolia、DVIT2227.2 Palmata、Beaumont、DVIT3235、Paulsen 1447、venus、 beda, 5C, erigeron breviscapus (large), zheng Guo No. 6 (0856), crystal, sira, bai Jixin, pecan, damina, rubratado, sweet sapphire, bai Hali li (0080), black agland (0305), red queen (0347), wonderful coreless, lingbao mulberry leaf 1, aril (riber) (0010), mutamof Thompson seedless 1219, min Jiang xi grape water 1614.
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