CN110241225A - The SNP marker of species identification for river Puffer combines - Google Patents
The SNP marker of species identification for river Puffer combines Download PDFInfo
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- CN110241225A CN110241225A CN201910355432.7A CN201910355432A CN110241225A CN 110241225 A CN110241225 A CN 110241225A CN 201910355432 A CN201910355432 A CN 201910355432A CN 110241225 A CN110241225 A CN 110241225A
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Abstract
The invention discloses a kind of combinations of the SNP marker of species identification for river Puffer, comprising: the SNP marker combination of Fugu Bimaculatus Puffer identification;The SNP marker combination of takifugu flavidus identification;The SNP marker combination of tun kusafugu Puffer identification;The SNP marker combination of Fugu rubripes identification;The SNP marker combination of fugu obscurus identification.The invention also discloses it is a kind of using different SNP marker combinations for river Puffer species, river Puffer seed species, hybridize river Puffer Parent species identification method.Species identification of the present invention to river Puffer, it can be ensured that detection river Puffer is legal edible river Puffer species;To the species identification of river Puffer seed, it can be ensured that seed is edible river Puffer species, guarantees raiser's interests and food safety;To the species identification of the cenospecies of river Puffer, cultivation HePuffer group is enable clearly to trace Parent species information.SNP marker quantity is big, genome coverage rate is high, and parting is easy to operate quickly, and parting accuracy is high.
Description
Technical field
The present invention relates to river Puffer Germplasm Identification field, the SNP marker of specifically a kind of species identification for river Puffer
Combination.
Background technique
River Puffer belongs to Osteichthyes (Osteichthyes), Actinopterygii (Actinopterygii), Tetraodontiformes
(Tetraodontiformes), be a kind of delicious meat, nutritive value and the very high fish of economic value, have both consumption and
Medical.River Puffer body is cylindrical, and body back ash is brown, outside of belly white, and body back, the speckle of side are different and different with type, there is gas
Capsule contains a kind of alkaloid -- fugutoxin in vivo.China has 54 kinds of Molidae fish, wherein 21 kinds of edible kind.It is edible
River Puffer be concentrated mainly on Puffer suborder (Tetraodontoidei), common are Molidae (Tetraodontidae) Fugu category
(Takifugu) Fugu Bimaculatus Puffer (Takifugu bimaculatus) Fugu rubripes (Takifugu rubripes), dark
Line Fugu (Takifugu obscurus), takifugu flavidus (Takifugu flavidus), tun kusafugu Puffer (Takifugu
Niphobles), yellowfin Fugu (Takifugu xanthopterus) etc..
From in September, 2016, China, which has ready conditions, decontrols cultivation Fugu rubripes and fugu obscurus processing operation, significantly pushes away
The development of river Puffer industry is moved.But nonstandard cultivation still can bring hidden danger to river Puffer aquaculture industry and edible river Puffer.Due to river
Puffer has virose particularity, currently, China eats the cultivation of river Puffer using poison cultivation is controlled, according to toxin source and enrichment original
Reason, control bait, the toxin of truncation production toxicity reach nontoxic rank, using stringent working process, ensure river Puffer
Edible safety.The Fugu rubripes of artificial breeding and fugu obscurus can reach safe edible by long-term stringent breeding
Non-toxic level.But in coastal area, a variety of Fugus inhabit that sea area, mating period are close, and Yi Fasheng germplasm is mixed hands over, and cause to plant
Matter is impure.In addition domestic also to have carried out a certain number of cenospecies cultivation in recent years, if chrysanthemum Huang Yuhong fin hybridizes, chrysanthemum Huang and dark line
Hybridization, red fin hybridize with false eyeball.If hybridizing river Puffer kind and source being unknown, it is more likely that making cenospecies, there are toxicity wind
Danger, it is extremely dangerous to human body to eat toxic river Puffer by mistake.In addition, economic value differs greatly between the Puffer species of different rivers, it would be highly desirable to carry out
The identification work of river Puffer species and seed.Its meaning causes toxic river first is that avoiding the higher species of toxicity that inter-species is caused to pollute
Puffer is eaten by mistake, second is that guaranteeing the purity of breed variety, is avoided germplasm impure, is guaranteed the characteristic of excellent variety, ensure raiser's
Interests.
Therefore, the present invention develops the genetic tool being simple and efficient, and can be used for species identification, seed identification and the hybridization of river Puffer
Kind of identification is cultivated for preferred purebred seed, the purity that avoids germplasm from obscuring, maintain cultured population provides technology guarantee.
Summary of the invention
It is an object of the invention to solve at least the above problems, and provide the advantages of at least will be described later.
It is a still further object of the present invention to provide the combinations of the SNP marker of the species identification for river Puffer.The present invention mentions
For the SNP marker combination for river Puffer fish species identification, the SNP marker combination are as follows: base sequence such as ID:
Fugu001~Fugu110.SNP marker combination provided by the invention as a result accurately can be efficient for five kinds of river Puffer fish
Rate, high throughput, using easy identification river Puffer species.
It is a still further object of the present invention to provide utilize the SNP marker combination of the species identification for river Puffer to carry out river
The method of Puffer species identification.
It is miscellaneous it is a still further object of the present invention to provide utilizing the SNP marker combination of the species identification for river Puffer to carry out
The method for handing over the species identification of the Parent of river Puffer.
It is a still further object of the present invention to provide utilize the SNP marker combination of the species identification for river Puffer to carry out river
The method of the species identification of Puffer seed.
In order to realize these purposes and other advantages according to the present invention, the SNP of the species identification for river Puffer is provided
Molecular labeling combination, comprising:
SNP marker combination for the identification of Fugu Bimaculatus Puffer: base sequence is as shown in ID:Fugu001~Fugu022
Nucleotide sequence:
SNP marker combination for takifugu flavidus identification: base sequence is as shown in ID:Fugu023~Fugu044
Nucleotide sequence:
SNP marker combination for the identification of tun kusafugu Puffer: base sequence is as shown in ID:Fugu045~Fugu066
Nucleotide sequence:
SNP marker combination for Fugu rubripes identification: base sequence is as shown in ID:Fugu067~Fugu088
Nucleotide sequence:
SNP marker combination for fugu obscurus identification: base sequence is as shown in ID:Fugu089~Fugu110
Nucleotide sequence:
A method of for river Puffer species identification, comprising the following steps:
Step 1: obtaining the genomic DNA of river Puffer to be assessed;
Step 2: constructing full-length genome SNP micro-array chip using the river Puffer genomic DNA obtained by step 1, obtain
The genotype in multiple SNP marker sites of every tail river Puffer;
Step 3: by described in the result of the genotype in multiple SNP marker sites of river Puffer to be assessed and claim 1
The species identification for river Puffer SNP marker combination be compared, the species information of river Puffer to be assessed is sentenced
It is disconnected.
Preferably, in step 1, the fin ray, muscle or blood of the genomic DNA of river Puffer to be assessed from the river Puffer
It obtains.
A method of for hybridizing the species identification of the Parent of river Puffer, comprising the following steps:
S1, the genomic DNA for obtaining river Puffer to be assessed;
S2, full-length genome SNP micro-array chip is constructed using the river Puffer genomic DNA obtained by S1, obtains every tail river Puffer
Multiple SNP marker sites genotype;
S3, by the result of the genotype in multiple SNP marker sites of river Puffer to be assessed and use described in claim 1
Be compared in the SNP marker combination of the species identification of river Puffer, to the species information of the Parent of river Puffer to be assessed into
Row judgement.
Preferably, in S1, the genomic DNA of river Puffer to be assessed is obtained from the fin ray, muscle or blood of the river Puffer
It arrives.
A method of the species identification for river Puffer seed, comprising the following steps:
Step a, the genomic DNA of river Puffer seed to be assessed is obtained;
Step b, full-length genome SNP micro-array chip is constructed using the river Puffer seed genomic DNA obtained by step a, obtained
Obtain the genotype in multiple SNP marker sites of every tail river Puffer seed;
Step c, by the result of the genotype in multiple SNP marker sites of Puffer seed in river to be assessed and claim 1
The SNP marker combination of the species identification for river Puffer is compared, and believes the species of river Puffer seed to be assessed
Breath is judged.
Preferably, in step a, the fin ray, muscle or blood of the genomic DNA of river Puffer to be assessed from the river Puffer
It obtains.
The present invention is include at least the following beneficial effects:
The present invention develops special SNP site 110 of five species river Puffer, wherein the specific site of each species 22,
The molecular labeling combination special as river Puffer.The present invention has carried out the species identification of river Puffer using 110 SNP sites of the group, really
Protecting detection river Puffer is legal edible river Puffer species.The present invention has carried out object to the seed of river Puffer using 110 SNP sites of the group
Kind identification, it is ensured that seed is edible river Puffer species, guarantees raiser's interests and food safety.The present invention utilizes 110 SNP of the group
Site has carried out species identification to the cenospecies of river Puffer, and cultivation HePuffer group is enable clearly to trace Parent species information.SNP
Molecular labeling quantity is big, genome coverage rate is high, and parting is easy to operate quickly, and parting accuracy is high.The present invention is based on current SNP
The characteristics of typing method, screens SNP marker site.
Further advantage, target and feature of the invention will be partially reflected by the following instructions, and part will also be by this
The research and practice of invention and be understood by the person skilled in the art.
Specific embodiment
The present invention will be further described in detail below with reference to the embodiments, to enable those skilled in the art referring to specification
Text can be implemented accordingly.
Core technology: 110SNP array
Firstly, obtaining river Puffer genomic DNA (DNA concentration range is 60~100ng/ μ L), DNA sample source is live fish fin
Item, muscle, blood (in the case where not influencing fish survival).Then with 110SNP array (the results are shown in Table 1) to river Puffer
Genomic DNA carries out SNP parting.
It is yellow to 30 tail fugu obscurus, 29 tail Fugu rubripes, 15 tail tun kusafugu Puffer, 8 tail Fugu Bimaculatus Puffer and 8 tail chrysanthemums
90 tail river Puffer of totally five species carry out full-length genome and resurvey sequence Fugu, and after carrying out SNP calling to sequencing data, altogether
Meter obtains the SNP site homozygous more than 2,900,000.Wherein fugu obscurus, Fugu rubripes, tun kusafugu Puffer, double spots
Fugu and the species specific homozygous polymorphic site of the object of takifugu flavidus are respectively 140603,1139,270770,4807
It is a and 4992.The reference postgenome for comparing Fugu further selects 22 special homozygous SNP in each species
Site amounts to 110 SNP polymorphic sites (110SNP array).
In order to verify the feasibility that a whole set of SNP marker is inferred in practical group, inventor has selected river Puffer
The 90 tail fishes of the different population in source carry out species identification.Specific sample information is shown in Table 2.
<embodiment 1>
A tail therein is arbitrarily selected to carry out object as species identification object in the 90 tail river Puffer that source is different population
Kind identification, specifically the step of identification include:
Step 1: obtaining the genomic DNA of the river Puffer from the fin ray, muscle or blood of tail Fugu to be assessed;
Step 2: constructing full-length genome SNP micro-array chip using the river Puffer genomic DNA obtained by step 1, obtain
The genotype in multiple SNP marker sites of the tail river Puffer.
Step 3: utilizing bioinformatics software east to be assessed according to obtained in mendelian inheritance analytical procedure two
The genotype in multiple SNP marker sites of square Puffer, analysis obtain the parting information of Fugu to be assessed, judge wait reflect
Determine the species ownership of Fugu.
If the genotype of its corresponding SNP site complies fully with genotype information listed by Fugu001~Fugu022, then
It can determine that Fugu to be identified is Fugu Bimaculatus Puffer.
If the genotype of its corresponding SNP site complies fully with genotype information listed by Fugu023~Fugu044, then
It can determine that Fugu to be identified is takifugu flavidus.
If the genotype of its corresponding SNP site complies fully with genotype information listed by Fugu045~Fugu066, then
It can determine that Fugu to be identified is tun kusafugu Puffer.
If the genotype of its corresponding SNP site complies fully with genotype information listed by Fugu067~Fugu088, then
It can determine that Fugu to be identified is fugu obscurus.
If the genotype of its corresponding SNP site complies fully with genotype information listed by Fugu089~Fugu110, then
It can determine that Fugu to be identified is fugu obscurus.
<embodiment 2>
A tail therein is arbitrarily selected to identify that object carries out river as seed in the 90 tail river Puffer that source is different population
The identification of Puffer seed, specifically the step of identification include:
Step 1: obtaining the genome of the river Puffer from the fin ray, muscle or blood of tail Fugu fry to be assessed
DNA;
Step 2: constructing full-length genome SNP micro-array chip using the river Puffer genomic DNA obtained by step 1, obtain
The genotype in multiple SNP marker sites of the tail river Puffer.
Step 3: utilizing bioinformatics software east to be assessed according to obtained in mendelian inheritance analytical procedure two
The genotype in multiple SNP marker sites of square Puffer fry, analysis obtain the parting information of Fugu fry to be assessed, sentence
The species ownership of disconnected Fugu seed to be identified out.
If the genotype of its corresponding SNP site complies fully with genotype information listed by Fugu001~Fugu022, then
It can determine that Fugu to be identified is Fugu Bimaculatus Puffer.
If the genotype of its corresponding SNP site complies fully with genotype information listed by Fugu023~Fugu044, then
It can determine that Fugu to be identified is takifugu flavidus.
If the genotype of its corresponding SNP site complies fully with genotype information listed by Fugu045~Fugu066, then
It can determine that Fugu to be identified is tun kusafugu Puffer.
If the genotype of its corresponding SNP site complies fully with genotype information listed by Fugu067~Fugu088, then
It can determine that Fugu to be identified is Fugu rubripes.
If the genotype of its corresponding SNP site complies fully with genotype information listed by Fugu089~Fugu110, then
It can determine that Fugu to be identified is fugu obscurus.
<embodiment 3>
Hybridize the species identification of river Puffer Parent, specifically the step of identification includes:
Step 1: obtaining the genomic DNA of the river Puffer from the fin ray, muscle or blood of tail Fugu to be assessed;
Step 2: constructing full-length genome SNP micro-array chip using the river Puffer genomic DNA obtained by step 1, obtain
The genotype in multiple SNP marker sites of the tail river Puffer;
Step 3: utilizing bioinformatics software east to be assessed according to obtained in mendelian inheritance analytical procedure two
The genotype in multiple SNP marker sites of square Puffer, analysis obtain the parting information of Fugu to be assessed, as it is corresponding
The genotype part of SNP site meet Fugu001~Fugu022 or Fugu023~Fugu044 or Fugu045~Fugu066 or
Any one in genotype information listed by Fugu067~Fugu088 or Fugu089~Fugu110, also partially meets
Fugu001~Fugu022 or Fugu023~Fugu044 or Fugu045~Fugu066 or Fugu067~Fugu088 or
Any one in genotype information listed by Fugu089~Fugu110 (two kinds of genotype are not identical at this time), then can determine that
Identify that Fugu is the filial generation of Fugu corresponding to two kinds of genotype.
In the present invention, we choose five species of river Puffer totally 90 tails identify of the invention 110 as experiment sample
SNP marker combines the applicability in species identification, the experimental results showed that, which can be used for river Puffer
The seed of fish is identified and Hybridization identification.
The heredity that can be used for Puffer breeding parent in river for the SNP marker combination of Hybridization identification of exploitation is explored in this research
Screening provides convenience for the artificial propagation and breeding work of river Puffer.Screening is used for object respectively on different linkage groups (chromosome)
The site of kind identification obtains the one group 110 site clusters that can be used for seed identification and Hybridization identification, and in breeding populations
It is verified and has been applied.
The specifying information of 110 SNP sites in table 1 " 110SNP array "
The sample information of 90 tail river Puffer in 2 embodiment of table
Although the embodiments of the present invention have been disclosed as above, but its is not only in the description and the implementation listed
With it can be fully applied to various fields suitable for the present invention, for those skilled in the art, can be easily
Realize other modification, therefore without departing from the general concept defined in the claims and the equivalent scope, the present invention is simultaneously unlimited
In specific details.
Claims (7)
1. the SNP marker combination of the species identification for river Puffer characterized by comprising
SNP marker combination for the identification of Fugu Bimaculatus Puffer: base sequence core as shown in ID:Fugu001~Fugu022
Nucleotide sequence:
SNP marker combination for takifugu flavidus identification: base sequence core as shown in ID:Fugu023~Fugu044
Nucleotide sequence:
SNP marker combination for the identification of tun kusafugu Puffer: base sequence core as shown in ID:Fugu045~Fugu066
Nucleotide sequence:
SNP marker combination for Fugu rubripes identification: base sequence core as shown in ID:Fugu067~Fugu088
Nucleotide sequence:
SNP marker combination for fugu obscurus identification: base sequence core as shown in ID:Fugu089~Fugu110
Nucleotide sequence:
2. the method for being used for river Puffer species identification, which comprises the following steps:
Step 1: obtaining the genomic DNA of river Puffer to be assessed;
Step 2: constructing full-length genome SNP micro-array chip using the river Puffer genomic DNA obtained by step 1, every tail is obtained
The genotype in multiple SNP marker sites of river Puffer;
Step 3: by the result of the genotype in multiple SNP marker sites of river Puffer to be assessed and use described in claim 1
It is compared in the SNP marker combination of the species identification of river Puffer, the species information of river Puffer to be assessed is judged.
3. as claimed in claim 2 for the SNP marker combination of the species identification of river Puffer, which is characterized in that in step
In one, the genomic DNA of river Puffer to be assessed is obtained from the fin ray, muscle or blood of the river Puffer.
4. the method for the species identification of the Parent for hybridizing river Puffer, which comprises the following steps:
S1, the genomic DNA for obtaining river Puffer to be assessed;
S2, full-length genome SNP micro-array chip is constructed using the river Puffer genomic DNA obtained by S1, obtains the more of every tail river Puffer
The genotype in a SNP marker site;
S3, the result of the genotype in multiple SNP marker sites of river Puffer to be assessed is used for river with described in claim 1
The SNP marker combination of the species identification of Puffer is compared, and sentences to the species information of the Parent of river Puffer to be assessed
It is disconnected.
5. as claimed in claim 4 for the SNP marker combination of the species identification of river Puffer, which is characterized in that in S1,
The genomic DNA of river Puffer to be assessed is obtained from the fin ray, muscle or blood of the river Puffer.
6. the method for the species identification for river Puffer seed, which comprises the following steps:
Step a, the genomic DNA of river Puffer seed to be assessed is obtained;
Step b, full-length genome SNP micro-array chip is constructed using the river Puffer seed genomic DNA obtained by step a, obtained every
The genotype in multiple SNP marker sites of tail river Puffer seed;
It step c, will be described in the result of the genotype in multiple SNP marker sites of Puffer seed in river to be assessed and claim 1
The SNP marker combination of the species identification for river Puffer be compared, to the species information of river Puffer seed to be assessed into
Row judgement.
7. as described in claim 1 for the SNP marker combination of the species identification of river Puffer, which is characterized in that in step a
In, the genomic DNA of river Puffer to be assessed is obtained from the fin ray, muscle or blood of the river Puffer.
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CN111057771A (en) * | 2020-01-14 | 2020-04-24 | 南京师范大学 | SNP molecular marker for distinguishing 'Zhongyang No. 1' from common fugu obscurus and application thereof |
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CN103805695A (en) * | 2013-12-05 | 2014-05-21 | 上海市水产研究所 | Primer pair for detecting growth rate of takifugu flavidus, kit and method |
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Cited By (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO2021097878A1 (en) * | 2019-11-21 | 2021-05-27 | 南京师范大学 | Takifugu fasciatus snp molecule marker and use thereof in genetic breeding |
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