CN109825565A - A kind of Cynoglossus semilaevis true and false milter discriminating method based on fluorescent molecule label system - Google Patents
A kind of Cynoglossus semilaevis true and false milter discriminating method based on fluorescent molecule label system Download PDFInfo
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- CN109825565A CN109825565A CN201910059872.8A CN201910059872A CN109825565A CN 109825565 A CN109825565 A CN 109825565A CN 201910059872 A CN201910059872 A CN 201910059872A CN 109825565 A CN109825565 A CN 109825565A
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- 241001014350 Cynoglossus semilaevis Species 0.000 title claims abstract description 43
- 238000000034 method Methods 0.000 title abstract description 16
- 108091028043 Nucleic acid sequence Proteins 0.000 claims abstract description 5
- 239000007850 fluorescent dye Substances 0.000 claims description 4
- 238000001514 detection method Methods 0.000 abstract description 6
- 210000003765 sex chromosome Anatomy 0.000 abstract description 6
- 238000002372 labelling Methods 0.000 abstract description 4
- 238000003556 assay Methods 0.000 abstract description 3
- 238000013461 design Methods 0.000 abstract description 3
- 238000011529 RT qPCR Methods 0.000 abstract description 2
- 230000003321 amplification Effects 0.000 abstract 1
- 238000007622 bioinformatic analysis Methods 0.000 abstract 1
- 230000035772 mutation Effects 0.000 abstract 1
- 238000003199 nucleic acid amplification method Methods 0.000 abstract 1
- 108020004414 DNA Proteins 0.000 description 8
- 210000000349 chromosome Anatomy 0.000 description 8
- 230000002068 genetic effect Effects 0.000 description 6
- 238000003753 real-time PCR Methods 0.000 description 6
- 238000011160 research Methods 0.000 description 6
- 239000003550 marker Substances 0.000 description 5
- 238000012216 screening Methods 0.000 description 4
- 241000251468 Actinopterygii Species 0.000 description 3
- 208000005652 acute fatty liver of pregnancy Diseases 0.000 description 3
- 238000009395 breeding Methods 0.000 description 3
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- 239000012634 fragment Substances 0.000 description 3
- 239000013535 sea water Substances 0.000 description 3
- 238000007862 touchdown PCR Methods 0.000 description 3
- 108091092878 Microsatellite Proteins 0.000 description 2
- 241000269978 Pleuronectiformes Species 0.000 description 2
- 241001595453 Symphurus nigrescens Species 0.000 description 2
- 230000008901 benefit Effects 0.000 description 2
- 239000003153 chemical reaction reagent Substances 0.000 description 2
- 238000010586 diagram Methods 0.000 description 2
- 238000005516 engineering process Methods 0.000 description 2
- 239000012452 mother liquor Substances 0.000 description 2
- 238000002205 phenol-chloroform extraction Methods 0.000 description 2
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- 210000001519 tissue Anatomy 0.000 description 2
- 229920000936 Agarose Polymers 0.000 description 1
- 108700028369 Alleles Proteins 0.000 description 1
- 241001417984 Cynoglossidae Species 0.000 description 1
- 238000012408 PCR amplification Methods 0.000 description 1
- 230000009286 beneficial effect Effects 0.000 description 1
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- 230000007246 mechanism Effects 0.000 description 1
- 230000003020 moisturizing effect Effects 0.000 description 1
- 239000003147 molecular marker Substances 0.000 description 1
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- 230000020509 sex determination Effects 0.000 description 1
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Abstract
The present invention is a kind of Cynoglossus semilaevis true and false milter discriminating method that system is marked based on fluorescent molecule.The design and detection of molecular labeling are to hinder mutation system (i.e. PARMS) based on five primer amplifications.The SNP polymorphic site between Z/W sex chromosome on DNA sequence dna is successfully found and be confirmed using the bioinformatic analysis to Cynoglossus semilaevis Z/W sex chromosome DNA sequence dna and molecular biology method, and designs and demonstrate 1 group of fluorescent molecule label based on PARMS.Show that the PARMS molecular labeling can true and false milter in all samples of successful identification by the verifying of high-throughput qPCR typing assay to Cynoglossus semilaevis fish sample known to 60 genders.Compared to current identification method and label, the label and corresponding detection method make to operate faster under the premise of guaranteeing accuracy rate, and cost is less expensive, and recall rate is higher, and can realize high-throughput detection.
Description
Technical field
The invention belongs in aquatic wholesale market seawater fish genetic sex identification and Sex Control field, be one
Kind is glimmering based on the codominance high throughput that can screen its gender that the SNP site between Cynoglossus semilaevis sex chromosome Z/W developed
Optical molecule label.
Background technique
Cynoglossus semilaevis (Cynoglossus semilaevis) belongs to Pleuronectiformes, Cynoglossidae, tongue sole category, is that China sea area is peculiar
A kind of warm warm nature coastal waters large size demersal fishes, be distributed mainly on the littoral area of the Huanghai Sea, the Bohai Sea.Due to Cynoglossus semilaevis nature
Stock number is few, delicious delicious, and smooth in taste is full of nutrition, therefore has wide breeding prospect, is important rare seawater and supports
Breeding fish.Cynoglossus semilaevis as flatfish, the growth rate of female individuals be 3 times of male or more (Chen Songlin etc.,
2013), and milter have the characteristics that slow growth, individual it is small, reduce the cultured output of Cynoglossus semilaevis, while making to cultivate
Increased costs.Cynoglossus semilaevis, which forms middle milter, even can achieve 80% -90%.Research is found in 80% -90% ratio
Having part in milter is pseudo-milter.Some researches show that Cynoglossus semilaevis Sex Determination Mechanism be sex chromosome Z and W, wherein homotype contaminate
Colour solid ZZ is Genetic male individual, heterotypical chromosomes ZW type be hereditary female individuals (Zhuang et al., 2006;Zhou Liqing
Deng 2005).The normal milter of Cynoglossus semilaevis has the chromosome of ZZ type, and normal raun has the chromosome of ZW type.And pseudo-milter is lost
What is passed is x chromosome, and genotype is all ZW type.But male characteristic is shown as from its figure and features feature and reproductive organs,
Fertile sperm and breeding offspring can be generated as milter.If using pseudo-milter as male parent, offspring can also be lost
The feature for passing male parent becomes pseudo-milter.In this way by accumulating by generation, physiology female in cynoglossus semilaevis cultivation group is had led to
Unbalance (i.e. milter is more and more, and raun is fewer and fewer) of ratio, to seriously affect cynoglossus semilaevis cultivation yield.Therefore, right
The exploitation of Rapid identification Cynoglossus semilaevis gender especially true and false milter efficient molecular labeling screened and detection method, to its heredity
Sex identification and production cultivation, have important scientific meaning and application value.
In terms of the screening of Cynoglossus semilaevis sex specific molecular marker and genetic sex identification, forefathers pass through AFLP
It is sliding that (amplified fragment length polymorphism, amplified fragment length polymorphism) labelling technique is separated to half
Tongue sole female specific AFLP label (Chen et al., 2007) cannot distinguish between in since AFLP label is dominant inheritance
ZW female and WW poly-x female individual, it is difficult to avoid false negative as a result, to generate erroneous judgement to ZZ milter and ZW raun.By half-and-half
The special microsatellite scaffold68-2 label screening of sliding-tongue sole codominance gender (Liu Yang etc., 2014) can be directed to codominance gender
Specific mark site design primer identifies Cynoglossus semilaevis genetic sex, but INDEL is short (small in microsatellite in practical application
In 50bp), cause two kinds of pcr amplification product fragment length differences from Z chromosome and W chromosome smaller, in gel electricity
Swimming determines that its length causes no small difficulty in short-term.Simultaneously the technology detection in need with concentration be 4% Ago-Gel to help
Distinguish the band (such as less than 50bp) of small difference in length, and the agarose of high concentration is not easy to prepare, electrophoresis duration, expense
The problems such as high, this all further limits the popularization of this method.
Therefore, the fluorescent molecule that Cynoglossus semilaevis gender includes true and false milter can be screened by inventing a kind of codominance based on SNP
It marks particularly necessary to solve the above problems.
Summary of the invention
1, it to solve the problems, such as
The purpose of the present invention is to provide a kind of fluorescent molecule labels that can screen Cynoglossus semilaevis gender, utilize Cynoglossus semilaevis
Sex-specific SNP site parting, to solve the problems mentioned above in the background art.
2, technical solution
To achieve the above object, the present invention provides the following technical solutions.
A kind of high-throughput Cynoglossus semilaevis true and false milter gender screening techniques based on fluorescent molecule label system, step packet
It includes:
S1, downloading disclose the public ZW DNA sequence sequence of inscience property right;
S2, it is compared in the ZW homology of chromosome allelic sequences searched out, ZW dye can be distinguished by filtering out
The candidate SNP locus of colour solid;
S3, the SNP site SNP_chr_8936186_C_G based on above-mentioned screening, designing one group can be used for Cynoglossus semilaevis
The PARMS fluorescent dye primer of sex identification;
S4, using phenol chloroform extraction method from Cynoglossus semilaevis fin tissue extraction genomic DNA;
S5, typing assay is carried out using real-time quantitative PCR (qPCR), it is female whether verifying PARMS fluorescent marker can identify
Male Cynoglossus semilaevis.
Preferably, in the S2, sex-specific SNP site is filtered out in Cynoglossus semilaevis ZW sex chromosome DNA sequence dna
SNP_chr_8936186_C_G:GCTGAAGGTGCAGTTGTGA [C/G], wherein C is the variation of raun specificity.C/G genotype
For raun or pseudo-milter, G/G genotype is true milter.
Preferably, the PARMS fluorescent dye primer of Cynoglossus semilaevis sex identification is filtered out in the S3 are as follows:
8936186_PR_CIt takes
GAAGGTGACCAAGTTCATGCTGCTGAAGGTGCAGTTGTGAc;
8936186_PR_GIt takes
GAAGGTCGGAGTCAACGGATTGCTGAAGGTGCAGTTGTGAg;
8936186_PFIt takesGGCAACAAGGACAGAATCTACATC。
3, beneficial effect
Compared with the prior art, the invention has the benefit that
The present invention is based on the SNP sites between the Cynoglossus semilaevis ZW sex chromosome of discovery, only need to be by qPCR typing assay
Male and female sex identification can be achieved.This method only needs 5 μ l reaction systems that automatic parting direction can be realized and identify male and female.Compared to mesh
The method of preceding identification Cynoglossus semilaevis genetic sex, for this method under the premise of guaranteeing accuracy rate, operation is faster, and cost is lower
Honest and clean, detection flux is higher, and primary first-order equation can detect a samples up to a hundred.
Detailed description of the invention
Fig. 1 is the site SNP_chr_8936186_C_G PARMS fluorescent marker qPCR points of sample 1-30 Cynoglossus semilaevis fish
Type result diagram, black color dots are male × 30 homozygote ZZ (3 repetitions of each sample);Grey Point is heterozygote ZW female
Individual × 30 (3 repetitions of each sample).
Fig. 2: the site the SNP_chr_8936186_C_G PARMS fluorescent marker qPCR of sample 31-60 Cynoglossus semilaevis fish point
Type result diagram, black color dots are male × 30 homozygote ZZ (3 repetitions of each sample);Grey Point is
Female individuals × 30 heterozygote ZW (3 repetitions of each sample).
Specific embodiment
In order to be easy to understand the technical means, the creative features, the aims and the efficiencies achieved by the present invention, tie below
Specific embodiment is closed the present invention is further described.
Based on the embodiments of the present invention, those of ordinary skill in the art are obtained under the premise of not making innovative labor
The every other embodiment obtained, shall fall within the protection scope of the present invention.
Genome sequence used in the present invention derives from the China Aquatic Science Research Institute's Huang for having published no property right protection
Seawater produces research institute's aquatic products genome and cell engineering research department and heads the list of signers the Cynoglossus semilaevis sequencing data of whole genome completed.
The present invention provides one kind to be based on Cynoglossus semilaevis sex-specific SNP site PARMS fluorescent molecule marker development skill
Art, comprising the following steps:
S1: selected ZW homology of chromosome allelic sequences and searching candidate SNP locus;
S2: the allele containing candidate SNP locus can be expanded by designing in conjunction with the online primer-design software of Primer3Plus
The primer pair of sequence;
S3: the PCR product that second step is amplified send a generation to be sequenced, by determining sex-specific to generation sequencing result
SNP site SNP_chr_8936186_C_G;
S4: the SNP site SNP_chr_8936186_C_G verified based on third step is drawn online in conjunction with Primer3Plus
Object design software designs one group of PARMS fluorescent dye primer that can be used for Cynoglossus semilaevis sex identification, and (each PARMS label contains
3 primers, are shown in claims 3;Wuhan Jing Tai Biotechnology Co., Ltd);
S5: genome is extracted from the Cynoglossus semilaevis fin tissue of 60 known genetic sexs using phenol-chloroform extraction method
DNA;
S6: configuration 10 × PARMS primer mother liquor is configured according to 200 reaction requirements:
Reagent | Volume (μ l) |
Primer 8935925_PF_C (10 μM) | 15 |
Primer 8935925_PF_T (10 μM) | 15 |
8935925_PR(10μM) | 40 |
ddH2O | 30 |
Total volume | 100 |
S7: PARMS Touchdown PCR (touchdown PCR) reaction system and ABI Q6 platform of 5 μ l and included point are used
It analyses software and carries out automatic parting direction.
Reagent/specimen | Dosage |
2 × PARMS Master Mix (Wuhan scape peptide biology) | 2.5μl |
10 × PARMS primer mother liquor | 0.5μl |
DNA template(50ng) | Moisturizing is to 5 μ l |
Single reaction total volume | 5μl |
Environmental parameter needed for qPCR PARMS TouchDown PCR response procedures are as follows: step 1: 94 DEG C of 3min;Step 2:
94℃20s;Step 3: 65 DEG C of (- 0.8 DEG C of every circulation) 1min;Step 4: step 2,10 circulations are returned;Step 5: 94 DEG C of 20s;6th
Step: 57 DEG C of 1min;Step 7: step 5,30 circulations are returned.
S8: Cynoglossus semilaevis gender is judged by qPCR automatic parting direction result.
One: 60 site Cynoglossus semilaevis SNP_chr_8936186_C_G PARMS Marker Identification result of table.
It is according to determining the accuracy of this technology qualification result with Cynoglossus semilaevis morphology sex identification result.
The basic principles, main features and advantages of the present invention have been shown and described above.This field it is common
Technical staff is it is to be appreciated that the present invention is not limited to the above embodiments, and what is described in the above embodiment and the description is only this
The principle of invention, without departing from the spirit and scope of the present invention, various changes and improvements may be made to the invention, these changes
Changing and improving should all fall into claimed invention.The claimed scope of the invention is by appended claims and its waits
Effect object defines.
Sequence table
<110>Tianjin Bohai Sea aquatic products research institute
<120>a kind of Cynoglossus semilaevis true and false milter discriminating method based on fluorescent molecule label system
<160> 5
<170> SIPOSequenceListing 1.0
<210> 1
<211> 41
<212> DNA
<213>artificial sequence (Artificial Sequence)
<400> 1
gaaggtgacc aagttcatgc tgctgaaggt gcagttgtga c 41
<210> 2
<211> 41
<212> DNA
<213>artificial sequence (Artificial Sequence)
<400> 2
gaaggtcgga gtcaacggat tgctgaaggt gcagttgtga g 41
<210> 3
<211> 24
<212> DNA
<213>artificial sequence (Artificial Sequence)
<400> 3
ggcaacaagg acagaatcta catc 24
<210> 5
<211> 21
<212> DNA
<213>artificial sequence (Artificial Sequence)
<400> 5
gaaggtgacc aagttcatgc t 21
<210> 5
<211> 21
<212> DNA
<213>artificial sequence (Artificial Sequence)
<400> 5
gaaggtcgga gtcaacggat t 21
Claims (2)
1. a kind of fluorescent molecule label that can screen Cynoglossus semilaevis true and false milter, which is characterized in that dyed in Cynoglossus semilaevis ZW
Sex-specific SNP site SNP_chr_8936186_C_G:GCTGAAGGTGCAGTTGTGA [C/ is filtered out in body DNA sequence dna
G], wherein C is the variation of raun specificity;C/G genotype is raun or pseudo-milter, and G/G genotype is true milter.
2. being marked according to a kind of PARMS fluorescent molecule based on Cynoglossus semilaevis sex-specific SNP site of claim 1, feature
It is: the PARMS fluorescent dye primer sequence are as follows:
8936186_PR_C takes
GAAGGTGACCAAGTTCATGCTGCTGAAGGTGCAGTTGTGAc;
8936186_PR_G takes
GAAGGTCGGAGTCAACGGATTGCTGAAGGTGCAGTTGTGAg;
8936186_PF takes GGCAACAAGGACAGAATCTACATC;Wherein, 8936186_PR_C connection FAM fluorophor is marked
Note: it is denoted as: FAMGAAGGTGACCAAGTTCATGCT;
8936186_PR_G connection HEX fluorophor marks
HEX:GAAGGTCGGAGTCAACGGATT。
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Cited By (3)
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CN110616256A (en) * | 2019-08-19 | 2019-12-27 | 天津渤海水产研究所 | Multi-site cynoglossus semilaevis true and false male fish screening system based on SNaPshot technology and application |
CN111676297A (en) * | 2020-06-19 | 2020-09-18 | 安徽微分基因科技有限公司 | Molecular marker and detection method for rapidly discriminating true and false male fish of cynoglossus semilaevis based on RAA-LFD |
CN113832219A (en) * | 2020-06-23 | 2021-12-24 | 安徽微分基因科技有限公司 | Nano-upgrade ultrahigh-flux SNP genotyping method based on PARMS technology |
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CN111676297A (en) * | 2020-06-19 | 2020-09-18 | 安徽微分基因科技有限公司 | Molecular marker and detection method for rapidly discriminating true and false male fish of cynoglossus semilaevis based on RAA-LFD |
CN113832219A (en) * | 2020-06-23 | 2021-12-24 | 安徽微分基因科技有限公司 | Nano-upgrade ultrahigh-flux SNP genotyping method based on PARMS technology |
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