CN112813183B - SSR marker fingerprint of Hypsizigus marmoreus Finc-B-6 strain and construction method and application thereof - Google Patents
SSR marker fingerprint of Hypsizigus marmoreus Finc-B-6 strain and construction method and application thereof Download PDFInfo
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Abstract
The invention discloses an SSR marker fingerprint of a Hypsizygus marmoreus Finc-B-6 strain, a construction method and application thereof, wherein the fingerprint consists of 6 pairs of SSR markers. The construction method comprises the following steps: (1) hypha culture; (2) extracting genome DNA; (3) detecting SSR molecular markers; and (4) detecting by capillary electrophoresis. The application comprises the following steps: and performing SSR marker amplification on the hypsizigus marmoreus strain, comparing the obtained banding pattern with the fingerprint spectrum, and obtaining the hypsizigus marmoreus Finc-B-6 strain if the banding pattern is consistent with the fingerprint spectrum. Compared with conventional morphological detection, antagonism test and fruiting test, the method has the advantages of short detection time, high accuracy and good repeatability, and has the specificity of the hypsizigus marmoreus Finc-B-6 strain in the collected 56 hypsizigus marmoreus cultivation main culture strains at home and abroad.
Description
Technical Field
The invention belongs to the technical field of detection of hypsizigus marmoreus strains, and particularly relates to an SSR marker fingerprint of a hypsizigus marmoreus Finc-B-6 strain, and a construction method and application thereof.
Background
Hypsizigus marmoreus (Peck) H.E.Bigelow, a species of Basidiomycota, agaricales, lyophyllaceae, is named due to marble patches on the surface of its pileus. The seafood soup is attractive in appearance, crisp and tender in texture, unique in seafood flavor and economical in price, and is popular with consumers. The hypsizigus marmoreus not only contains abundant vitamins and 18 amino acids, but also has the functions of hemolysis, antioxidation, leukemia and lymphoma cell inhibition, blood fat reduction, inflammation resistance, antioxidation and the like in components such as micromolecular compounds, polysaccharide, polypeptide and the like contained in the hypsizigus marmoreus through recent research, and is edible and medicinal fungi with high economic value. Since the first industrialized culture enterprise of hypsizygus marmoreus in China established in 2001, hypsizygus marmoreus becomes one of novel edible fungi which are developed in markets of China quickly. The industrialized total yield of the hypsizigus marmoreus in 2019 is 32.8 ten thousand tons, the yield is increased by 58.63% in comparison with the yield increased by 2018, the yield accounts for 9.6% of the industrialized total yield of the edible fungi, and the rate is the third in the industrialized edible fungi production amount in China.
The high-quality strain plays a very important role in the industrial cultivation of the hypsizigus marmoreus. At present, hypsizigus marmoreus strains used by industrialized production enterprises in China are mainly introduced into Japan or further bred by hybridization on the basis of the introduced strains, the cultivated hypsizigus marmoreus has brown fruiting bodies called as crab-flavor mushrooms, and the cultivated hypsizigus marmoreus has white fruiting bodies called as white beech mushrooms or yulong mushrooms. Although the yield of factory production is improved year by year, partial strains still have the problems of long cultivation period, low yield per unit, poor appearance uniformity of single fruiting body, easy occurrence of cap formation and the like, and the defects can cause the increase of production cost and reduce the market competitiveness of products. On the other hand, the industrialized production strains of the hypsizigus marmoreus are not high in diversity and similar in product appearance, so that the diversified requirements of market consumers cannot be met. The method has rich wild and natural hypsizigus marmoreus cultivation resources in China, efficiently utilizes the high-quality resources, expands the genetic basis of strains, and is beneficial to breeding of high-yield, high-quality and characteristic hypsizigus marmoreus strains in China.
With the promulgation and implementation of the protection law of new species of international plants, the establishment of a mature, rapid and accurate molecular biology identification technical system becomes a powerful means for protecting the intellectual property rights of edible fungus varieties.
Disclosure of Invention
The invention aims to solve the technical problem of providing an SSR marker fingerprint of a Hypsizygus marmoreus Finc-B-6 strain and a construction method and application thereof, wherein the fingerprint has the advantages of short detection time, high accuracy and good repeatability compared with conventional morphological detection, antagonism test and fruiting test.
Hypsizigus marmoreus (Hypsizygus marmoreus) Finc-B-6, which is deposited in China general microbiological culture Collection center (CGMCC) at 28 days 11 and 2016, with the address of No. 3 of Ministry of West Lu 1 of Beijing republic of oriented Yang, and the number of deposit at the institute of microbiology of China academy of sciences, CGMCC No.13194.
The invention relates to an SSR marker fingerprint of hypsizigus marmoreus 'Finc-B-6' strain, which consists of 6 pairs of SSR markers, is an SSR primer developed based on simple repetitive sequence segments of hypsizigus marmoreus genome, has good amplification band type and high repeatability, and detailed marker information is shown in Table 1:
TABLE 1 SSR tag detailed information List
The invention relates to a method for constructing an SSR marker fingerprint of a Hypsizigus marmoreus Finc-B-6 strain, which comprises the following steps:
(1) Hypha culture: inoculating Hypsizigus marmoreus strain to potato glucose agar solid culture medium, culturing at 22 deg.C for 10-14d, and collecting mycelium;
(2) Extraction of genomic DNA: the fungal DNA extraction kit is used, the genomic DNA is extracted according to the kit experimental steps, and 2 mu L of DNA is taken for carrying out 1.2% agarose gel electrophoresis detection. Detecting the concentration and purity of the total genome DNA by an ultraviolet spectrophotometry, and adjusting the concentration of the sample DNA to be consistent;
(3) SSR molecular marker primer development: selecting a polymorphic sequence to design an SSR primer and synthesizing according to the genome re-sequencing result of the hypsizigus marmoreus strain;
(4) Detection of SSR molecular markers: carrying out PCR amplification of gene SSR markers on the extracted DNA;
(5) And (3) electrophoresis detection: mixing the product obtained by PCR amplification with formamide sample adding buffer solution, denaturing, and detecting on a computer;
(6) GeneMapper data analysis.
The method for constructing the SSR marker fingerprint of the Hypsizigus marmoreus Finc-B-6 strain is characterized by comprising the following steps of: the step (2) of extracting the genome DNA comprises the following specific steps:
(1) Adding a fungus sample into liquid nitrogen for fully grinding;
(2) Rapidly adding 360 mu LBuffersSTE and 40 mu L Buffer SDS into the ground powder, rapidly vortexing and uniformly mixing, placing the centrifugal tube in a water bath at 65 ℃ for 15min, and reversing the centrifugal tube in the water bath process to mix the sample for a plurality of times;
(3) Adding 5 mu L of RNase Solution into the lysate, uniformly mixing by vortex, and standing for 15-30min at room temperature;
(4) Adding 140 μ L Buffer PS, vortexing and shaking for 30s, and standing on ice for 10min;
(5) 13000g was centrifuged for 5min at room temperature, and 400. Mu.L of the supernatant was carefully transferred to a new centrifuge tube;
(6) Adding 600 mu L of Buffer PBD into the sample, and uniformly mixing by vortex for 30s;
(7) Loading the DNA binding column in a collecting tube, transferring half of the mixed solution to the column, and centrifuging at 8000g for 1min;
(8) Pouring off the filtrate, putting the column back into the collecting pipe, transferring the residual mixed solution into the column, and centrifuging for 1min at 8000 g;
(9) Pouring the filtrate and putting the column back into the collecting pipe, adding 600 mu L of Buffer GW2 into the column, and centrifuging for 1min at 8000 g;
(10) Repeating the step 9;
(11) Pouring off the filtrate, putting the column back into the collecting pipe, centrifuging at 10000g for 2min to remove the residual ethanol in the column;
(12) Transferring the column to a new 1.5mL centrifuge tube, adding 30. Mu.L of Buffer AE preheated to 65 ℃ to the center of the membrane of the column, standing at room temperature for 2min, and centrifuging at 10000g for 1min;
(13) mu.L of DNA was subjected to 1.2% agarose gel electrophoresis, 2. Mu.L of DNA was subjected to NanoDrop spectrophotometry, and the remaining DNA was stored at-20 ℃.
The PCR amplification system in the step (3) is as follows: total volume 10 μ L, including: 10 XPCR buffer 1 uL, 2.5mmol/L dNTP 0.8 uL, 5U/uL TAKARA HSTaq enzyme 0.1 uL, 5 umol/L TP-M130.5 uL, 5 umol/L SSR mark specific primer total volume 0.6 uL respectively, concentration 20 ng-30 ng/uL extracted template DNA 1.2 uL, ddH 2 O 5.2μL；
And (3) PCR reaction conditions: 5min at 95 ℃; 30s at 95 ℃, 30s at 59 ℃, 30s at 72 ℃ and 30 cycles; 5min at 95 ℃; 30s at 95 ℃, 30s at 53 ℃, 30s at 72 ℃ and 10 cycles; 30min at 60 ℃.
The sample adding buffer solution in the step (5) is 9 mu L of a mixed solution of a molecular weight internal standard and formamide (0.5; the amount of the PCR amplification product added was 1. Mu.L.
The specific process of denaturation in the step (5) is to denature at 95 ℃ for 3min, and then to cool in an ice-water mixture for 3min.
The electrophoresis in the step (5) has the following process parameters: the modified polyacrylamide gel is commercial POP7 gel, the electrophoresis buffer solution is 3730buffer EDTA, the injection voltage is 2000V, the operation voltage is 15000V, the sample injection time is 10s, the temperature is 60 ℃, the capillary length is 50cm, the power is 200W, the electrophoresis is performed for 20min, and the current and the power are dynamic.
The data analysis in the step (6) specifically comprises the following steps: and (3) importing the detected original data file into analysis software GeneMapper ID3.2, and performing group structure analysis, clustering and heterozygosity analysis and core germplasm resource calculation analysis by using POPGENE, NTSYS and other software. Allele factors (Na, ne), nei's genetic diversity index (He), shannon's diversity information index (I) and gene observation heterozygosity (Ho) were analyzed.
TABLE 2 summary of allelic fragment information from SSR primer amplification
The invention discloses an application of SSR marker fingerprint of hypsizigus marmoreus 'Finc-B-6' strain, which is characterized in that 6 pairs of SSR primers developed by simple repetitive sequence segments of hypsizigus marmoreus genomes are utilized, a large number of SSR primers are screened, the number and the number of allelic fragments of the 6 pairs of SSR primers amplified in each hypsizigus marmoreus cultivated variety are determined and numbered (table 2) by performing banding amplification on the SSR primers of 56 collected hypsizigus marmoreus main cultivated varieties, and the 'Finc-B-6' strain can be effectively identified in 56 collected main cultivated varieties by the number combination of different SSR allelic sites. The relative molecular weight of the amplified allelic locus of each SSR primer can be determined by analyzing by capillary electrophoresis combined software, the strain with the specific SSR allelic fragment combination of the strain 'Finc-B-6' is the strain 'Finc-B-6' of hypsizigus marmoreus, and the numbering combination of the strain is as follows: 14/(5+6)/(2+5+8)/(1+10)/(12+16)/(4+10).
The invention has the beneficial effects that: compared with conventional morphological detection, antagonism test and fruiting test, the method has the advantages of short detection time, high accuracy and good repeatability. The operation time required for detection is within 24h (including genome DNA extraction, PCR amplification, electrophoresis analysis and data analysis), while the time required for a conventional antagonism test is at least two weeks, and the time required for a fruiting test is at least 3 months; the method has specificity of 'Finc-B-6' in the collected 56 commercial hypsizigus marmoreus main culture strains, and has good application prospect.
Drawings
In order to more clearly illustrate the technical solutions of the embodiments of the present invention, the drawings needed to be used in the description of the embodiments will be briefly introduced below, and it is obvious that the drawings in the following description are only some embodiments of the present invention, and it is obvious for those skilled in the art to obtain other drawings based on these drawings without inventive exercise. Wherein:
FIG. 1 is a diagram of the relative molecular weight peaks of the allelic sites obtained by sequentially detecting the primer HMSSR5 in the selected hypsizigus marmoreus cultivation material 'Finc-B-6' and several main cultivation commercial varieties respectively;
FIG. 2 is a diagram of the peaks of the relative molecular weights of the allelic sites obtained by the primer HMSSR15 respectively and sequentially detected in the selected hypsizigus marmoreus cultivation material "Finc-B-6" and several main cultivation commercial varieties;
FIG. 3 is a diagram of the relative molecular weight peaks of the allelic sites obtained by the primer HMSSR32 respectively and sequentially detected in the selected hypsizigus marmoreus cultivation material 'Finc-B-6' and several main cultivation commercial varieties;
FIG. 4 is a diagram of the peaks of the relative molecular weights of the allelic sites obtained by the primer HMSSR36 respectively and sequentially detected in the selected hypsizigus marmoreus cultivation material "Finc-B-6" and several main cultivation commercial varieties;
FIG. 5 is a diagram of the peaks of the relative molecular weights of the allelic sites obtained by the primer HMSSR51 sequentially detected in the selected Hypsizygus marmoreus cultivation material "Finc-B-6" and several main cultivation commercial varieties respectively;
FIG. 6 is a diagram of the peak of the relative molecular weight of the allelic site obtained by the primer HMSSR59 respectively and sequentially detected in the selected hypsizigus marmoreus cultivation material "Finc-B-6" and several main cultivation commercial varieties.
Detailed Description
In order to make the aforementioned objects, features and advantages of the present invention more comprehensible, embodiments accompanying specific embodiments of the present invention are described in detail below.
In the following description, numerous specific details are set forth in order to provide a thorough understanding of the present invention, however, the present invention may be practiced otherwise than as specifically described herein, and it will be appreciated by those skilled in the art that the present invention may be practiced without departing from the spirit and scope of the present invention and that the present invention is not limited by the specific embodiments disclosed below.
Furthermore, reference herein to "one embodiment" or "an embodiment" means that a particular feature, structure, or characteristic described in connection with the embodiment is included in at least one implementation of the invention. The appearances of the phrase "in one embodiment" in various places in the specification are not necessarily all referring to the same embodiment, nor are separate or alternative embodiments mutually exclusive of other embodiments.
Example 1:
(1) Hypha culture: inoculating Hypsizigus marmoreus strain to potato glucose agar solid culture medium, culturing at 22 deg.C for 10d, and collecting mycelium;
(2) Extraction of genomic DNA: the fungal DNA extraction kit is used, the genomic DNA is extracted according to the kit experimental steps, and 2 mu L of DNA is taken for carrying out 1.2% agarose gel electrophoresis detection. Detecting the concentration and purity of the total genome DNA by an ultraviolet spectrophotometry, and adjusting the concentration of the sample DNA to be consistent;
the CTAB method for extracting genome DNA of hyphae comprises the following steps:
(1) adding a fungus sample into liquid nitrogen for fully grinding;
(2) adding 360 mu L of Buffer STE and 40 mu L of Buffer SDS into the ground powder quickly, quickly whirling and uniformly mixing, placing the centrifuge tube in a water bath at 65 ℃ for 15min, and reversing the centrifuge tube in the water bath process to mix the sample for a plurality of times;
(3) adding 5 μ L RNase Solution into the lysate, mixing by vortex, and standing at room temperature for 15-30min;
(4) adding 140 μ L Buffer PS, vortexing and shaking for 30s, and standing on ice for 10min;
(5) 13000g was centrifuged for 5min at room temperature, and 400. Mu.L of the supernatant was carefully transferred to a new centrifuge tube;
(6) add 600. Mu.L Buffer PBD (diluted with absolute ethanol) to the sample, vortex and mix for 30s;
(7) loading the DNA binding column in a collecting tube, transferring half of the mixed solution to the column, and centrifuging at 8000g for 1min;
(8) pouring off the filtrate, putting the column back into the collecting pipe, transferring the residual mixed solution into the column, and centrifuging for 1min at 8000 g;
(9) pouring off the filtrate, putting the column back into the collecting pipe, adding 600. Mu.L Buffer GW2 (diluted with absolute ethyl alcohol) into the column, and centrifuging at 8000g for 1min;
r repeats step 9;
(3) Detection of SSR molecular markers: carrying out PCR amplification of gene SSR markers on the extracted DNA;
the PCR amplification system is as follows: total volume 10 μ L, including: 10 XPCR buffer 1 uL, 2.5mmol/L dNTP 0.8 uL, 5U/uL TAKARA HSTaq enzyme 0.1 uL, 5 umol/L TP-M130.5 uL, 5 umol/L SSR mark specific primer total volume 0.6 uL respectively, concentration 20 ng-30 ng/uL extracted template DNA 1.2 uL, ddH 2 O 5.2μL；
And (3) PCR reaction conditions: 5min at 95 ℃; 30s at 95 ℃, 30s at 59 ℃, 30s at 72 ℃ and 30 cycles; 5min at 95 ℃; 30s at 95 ℃, 30s at 53 ℃, 30s at 72 ℃ and 10 cycles; 30min at 60 ℃. (4) electrophoretic detection: mixing 1 μ L of the product obtained by PCR amplification with 9 μ L of sample buffer solution, denaturing at 95 deg.C for 3min, and cooling in ice water mixture for 3min; applying 3 microlitres of sample to a modified polyacrylamide gel for electrophoresis, wherein the modified polyacrylamide gel is commercial POP7 gel, the electrophoresis buffer solution is 3730buffer EDTA, the injection voltage is 2000V, the operation voltage is 15000V, the sample injection time is 10s, the temperature is 60 ℃, the length of a capillary is 50cm, the power is 200W, the electrophoresis is 20min, and the current and the power are dynamic,
(5) Analysis of results
PCR amplification and capillary electrophoresis are carried out on the hypsizigus marmoreus strain by adopting 6 pairs of SSR primers, and the combination of Fu Gebian is found by analyzing the allelic gene factors (Na, ne), the Nei's genetic diversity index (He), the shannon's diversity information index (I) and the gene observation heterozygosity (Ho) and combining the peak diagram of the relative molecular weight of the allelic site: HMSSR5, HMSSR15, HMSSR32, HMSSR36, HMSSR51, HMSSR59, the corresponding banding patterns are: 14/(5+6)/(2 +5+ 8)/(1 + 10)/(12 + 16)/(4 + 10), and the strain is determined to be the Hypsizigus marmoreus 'Finc-B-6' strain. To ensure the accuracy of the identification, three replicates were recommended.
Taking several main-cultivated commercial varieties as examples, 6 pairs of primers are given for sequential detectionThe peak pattern of the relative molecular weights of the resulting allelic sites is shown in FIGS. 1 to 6 (sequentially (1); finc-B-6 (2); K (3B 2 (4); 15-X2 (5); 14-X1 (6); 13-X6 (7); H2 (8); BS027 (9); X5. RTM DTG)
B4)。
The fingerprint spectrum refers to the combination of the primer and the band type thereof.
It should be noted that the above-mentioned embodiments are only for illustrating the technical solutions of the present invention and not for limiting, and although the present invention has been described in detail with reference to the preferred embodiments, it should be understood by those skilled in the art that modifications or equivalent substitutions may be made on the technical solutions of the present invention without departing from the spirit and scope of the technical solutions of the present invention, which should be covered by the claims of the present invention.
Sequence listing
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Claims (2)
1. A fingerprint identification method of SSR markers of Hypsizigus marmoreus Finc-B-6 strains is characterized by comprising the following steps: the fingerprint consists of 6 SSR marker loci, and the specific sequences of 6 corresponding pairs of primers are as follows:
HMSSR5 forward primer: CACACCTTACGAGGTGAGCA;
reverse primer: TGTTTGATGTTAGCCGAACG;
HMSSR15 forward primer: GATTGTTCGCTGGAACACCT;
reverse primer: ACTCACGATGAAGGCAAACG;
HMSSR32 forward primer: AACCTCCAGTCACAACCTGC;
reverse primer: CCTTGCTTCTTGTCGGATGT;
HMSSR36 forward primer: TCTTCTTGTAGAGCGCCTCG;
reverse primer: CTCTCGACGCGTGTTCCT;
HMSSR51 forward primer: CACCCCCTCATCCTACACAT;
reverse primer: TGGTCAGAAGAAACGTCGTG;
HMSSR59 forward primer: CACTGTTCCAGAGTGGGACC;
reverse primer: AGGGCCTTTTCAGAGACGAT;
the corresponding combination of the belt type numbers is as follows: 14/(5+6)/(2 +5+ 8)/(1 + 10)/(12 + 16)/(4 + 10);
wherein the corresponding band type number of the primer HMSSR5 is 14, and the band size of the corresponding allele segment is 222-222.99bp;
the belt type number corresponding to the primer HMSSR15 is 5+6, wherein the size of the belt of the allele segment corresponding to the number 5 is 227 to 227.99bp, and the size of the belt of the allele segment corresponding to the number 6 is 253 to 253.99bp;
the band type number corresponding to the primer HMSSR32 is 2+5+8, wherein the band size of the allele segment corresponding to the number 2 is 226 to 226.99bp, the band size of the allele segment corresponding to the number 5 is 231 to 231.99bp, and the band size of the allele segment corresponding to the number 8 is 237 to 237.99bp;
the band type number corresponding to the primer HMSSR36 is 1+10, wherein the band size of the allele segment corresponding to the number 1 is 152 to 152.99bp, and the band size of the allele segment corresponding to the number 10 is 168 to 168.99bp;
the band type number corresponding to the primer HMSSR51 is 12+16, wherein the band size of the allele segment corresponding to the number 12 is 163 to 163.99bp, and the band size of the allele segment corresponding to the number 16 is 206 to 206.99bp;
the band type number corresponding to the primer HMSSR59 is 4+10, wherein the size of the band of the allele segment corresponding to the number 4 is 160 to 160.99bp, and the size of the band of the allele segment corresponding to the number 10 is 169 to 169.99bp;
the preservation number of the Hypsizigus marmoreus Finc-B-6 strain is CGMCC No.13194.
2. The application of the SSR marked fingerprint of the Hypsizigus marmoreus Finc-B-6 strain according to claim 1 is characterized in that: the fingerprint of the SSR marker of the hypsizigus marmoreus Finc-B-6 strain is used for identifying the specific allelic variation of the hypsizigus marmoreus Finc-B-6 strain and/or identifying the specificity of the hypsizigus marmoreus Finc-B-6 strain.
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Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN101684487A (en) * | 2008-09-24 | 2010-03-31 | 上海市农业科学院 | Method for identifying industrially cultivated strains of hypsizygus marmoreus by using SSR molecular marker |
| CN102851364A (en) * | 2012-08-29 | 2013-01-02 | 上海市农业科学院 | SSR fingerprint of Cr02 strain of Lentinus edodes, and construction method and application thereof |
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| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN101684487A (en) * | 2008-09-24 | 2010-03-31 | 上海市农业科学院 | Method for identifying industrially cultivated strains of hypsizygus marmoreus by using SSR molecular marker |
| CN102851364A (en) * | 2012-08-29 | 2013-01-02 | 上海市农业科学院 | SSR fingerprint of Cr02 strain of Lentinus edodes, and construction method and application thereof |
Non-Patent Citations (1)
| Title |
|---|
| 真姬菇微卫星分子标记的开发及其种质资源分析;董岩;《万方数据》;20101231;第四章，表4.1 * |
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