CN105255878B - It is used for SNP marker and its application traced to the source on No. 6 chromosomes of pig - Google Patents
It is used for SNP marker and its application traced to the source on No. 6 chromosomes of pig Download PDFInfo
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Abstract
The invention discloses SNP marker and its application for being used to trace to the source on No. 6 chromosomes of pig, described SNP marker is obtained by ncbi database sequence alignment, the SNP marker is by TaiI restriction enzyme specific recognitions, common 550bp, there is a base to replace at 362nd bit base, for 362A or 362G, its sequence is as shown in SEQ ID NO.1.By analyzing distribution situation of the SNP marker in experiment colony allelic in the experiment colony including 10 pig varieties or strain, it was found that gene frequency of the SNP marker of the present invention in different kinds or strain approaches, rich polymorphism, gene frequency distributional difference is small between kind or strain, and heterozygosity is both greater than 0.3, the SNP marker can be used as DNA source tracing of pork products.
Description
Technical field
The invention belongs to field of food safety, be related to the SNP marker that is used for tracing to the source on No. 6 chromosomes of a pig and its
Detection method.
Background technology
With the development of society, the link in agri-food supply chains is being continuously increased, from farm, pasture to food enterprise plus
There is the potential safety hazard of food in work, packaging, storage, transport and sale, the links of food supply, food-safety problem often has
Occur.Therefore need to carry out meat products can tracing management, establish the retrospect systems of the links from the place of production to dining table, so as to
The information of accurate and detailed article is provided for consumer, is advantageous to operator and finds in time present in each link
Hidden danger.Since the food security crisis of mid-term the 1990s, the retrospect of meat product is as a kind of safety
Control measure, by the multiple national great attentions in the world.Meat product traceability system strengthens government department to meat product quality
The ability to supervise of safety, therefore many countries establish meat product traceability system one after another and existed to reduce in meat product quality safety
Risk.
Meat product tracing technology has label tracing technology, isotopic traceability technology, mineral element fingerprint tracing technology, organic
Thing tracing technology iris feature technology and DNA marker tracing technology (or DNA tracing technologies) etc., wherein DNA tracing technologies because
Detection means is simple, it is quick, be difficult to turn into the wide variety of quick tracing technology in countries in the world the features such as forgery.With other marks
Method is compared, and DNA marker, which has, peculiar is put into superiority:It directly occurs with DNA form, each tissue in organism, each
Developmental stage is detectable, is not influenceed by environmental factor, and marker number is more, throughout organism whole gene group.
SNP marker refers to the variation of single nucleotide acid on the same site of genome, normally behaves as two allele, very
Suitable high throughput automated analysis, so having become animal identification identifies molecular labeling of greatest concern.
But the SNP marker traced to the source for meat product is different from general SNP marker, for single SNP marker, it must
Must at least have following characteristics:(1) degree of variation is high, is approached in kind or strain allelic frequency;(2) equipotential base between kind
Because distribution frequency difference is small;(3) heterozygosity is more than or equal to 0.3.
In long-term breeding work, researcher have accumulated substantial amounts of SNP marker, because single SNP marks of tracing to the source are nothings
Method completes what is traced to the source, therefore, it is necessary to one group of separate SNP marker could be realized and traced to the source.With existing 13 known SNP points
Son mark combines as mark of tracing to the source, in the swinery body introduced by height selection, when being traced to the source using the group echo, and meeting
There are some undistinguishable situations of individual.
In addition, in long-term breeding work, the substantial amounts of SNP marker of accumulation often integrated distribution in some chromosomes
On, and other part chromosome, such as No. 5, No. 6, No. 8, No. 14, No. 15 and No. 18 chromosomes etc. then lack SNP marker, easily lead
Cause cascade phenomenon occur between molecular labeling, can not be independent mutually between molecular labeling, the detection range for experiment of tracing to the source is reduced, is caused
Actual detectable scope is less than expected detectable scope.Therefore, in order to meet the requirement traced to the source pork product progress DNA, need
The SNP marker for being used to trace to the source is developed on other chromosomes, improves trace to the source detection range and the degree of accuracy.
The content of the invention
, should it is an object of the invention to provide SNP marker and its application for being used to trace to the source on No. 6 chromosomes of a pig
SNP marker can be widely applied to DNA source tracing of pork products, the particularly peace for pork product in market pig is cultivated
Full property is traced to the source, perfect existing mark combination, and raising is traced to the source accuracy in detection, and expansion is traced to the source scale.
To achieve the above object, the technical solution adopted by the present invention is as follows:
It is used for the SNP marker traced to the source, the DNA sequence dna such as SEQ ID of the SNP marker on No. 6 chromosomes of one pig
Shown in NO.1, common 550bp, and there is a base to replace at the 362nd bit base, it is 362A or 362G.
Further, described SNP marker is by TaiI restriction enzyme specific recognitions.
Described SNP marker is obtained by ncbi database sequence alignment, and including 10 pig varieties or
In the experiment colony (amounting to 245 individuals) of strain, distribution feelings of the SNP marker in experiment colony allelic are analyzed
Condition, it is found that gene frequency of the molecular labeling in different kinds and strain approaches, rich polymorphism, kind or strain
Between gene frequency distributional difference it is small, the preliminary judgement SNP marker can be used as DNA source tracing of pork products.
The preparation method of one on described No. 6 chromosomes of the pig SNP marker that can be used for tracing to the source, using PCR-
TaiI-RFLP methods are carried out, and are comprised the following steps:
1) the DNA sequence dna information of No. 6 chromosomes of pig is searched on NCBI, designs forward and reverse primer separation No. 6 chromosomes of pig
DNA fragmentation;
2) sequence alignment is carried out online using ncbi database, find the site that base replacement be present;
3) PCR-TaiI-RFLP detection methods are established and site is replaced in detection;
4) the ear tissue sample of 10 kinds and strain is gathered, altogether 245 individuals;
5) distribution of the SNP marker in experiment colony, statistical analysis are detected, and further whether verification experimental verification is applied to
During pork product is traced to the source.
Wherein, in the method for above-mentioned acquisition SNP marker, on described separation No. 6 chromosomes of pig DNA fragmentation just,
Reverse primer sequences are as follows:
Forward primer:5 '-AAATGAAGAACAGGCAAGG-3 ' (as shown in SEQ ID NO.2);
Reverse primer:5 '-CTTCCCAGTAAACTTAGGAGATA-3 ' (as shown in SEQ ID NO.3).
During DNA traces to the source, often increase a site of tracing to the source, just can further expand the number of detection sample, accurately
Property it is also just higher, preferable SNP site should be generally evenly distributed on the different chromosome of pig, and in existing SNP site lack
Mark of tracing to the source on weary No. 6 chromosome.
The present invention detects the existing SNP marker on No. 6 chromosomes of pig by ncbi database sequence alignment,
In experiment colony including 10 pig varieties or strain, distribution of the SNP marker in experiment colony allelic is analyzed
Situation, it is found that gene frequency of the molecular labeling in different kinds or strain approaches, rich polymorphism, kind or product
Gene frequency distributional difference is small between system, and heterozygosity is both greater than 0.3, and the preliminary judgement SNP marker can be used as pork production
During product DNA is traced to the source and the security of pork product is traced to the source.
It can not complete to trace to the source because single SNP traces to the source to mark, therefore in simulated test of tracing to the source, the present invention is obtained
No. 6 chromosomes of pig on Novel SNP molecular marker site be combined together with other existing published SNP marker sites
(amounting to 14 SNP sites) carries out experiment of tracing to the source.The present invention increases market pig source, chosen altogether in slaughterhouse in experiment of tracing to the source
300 individuals from multiple different pig farms have been selected, have selected 100 individuals at random from 300 individuals, have detected this 100
The genotype of 14 SNP sites in body, the genotype results of each individual are counted, it is found that 100 individuals possess respective difference
Genotype, can realize individual differentiation;Meanwhile 20 parts of muscle samples of picking, same detection statistics 14 in this 100 individuals at random
The genotype in individual SNP marker site, be then compared with 100 individual genotype, discovery can find with
The completely the same individual of 20 parts of muscle samples genotype, i.e., the source of 20 parts of pig muscles is found in 100 individuals by tracing to the source
Individual, therefore, it is determined that the SNP marker of the present invention can be used for pork product and trace to the source.
Compared with prior art, beneficial effects of the present invention:
The SNP marker of the present invention is located on No. 6 chromosomes of pig, can further improve the detection coverage rate of mark,
The accuracy traced to the source is improved, and expands the detection range of existing molecular labeling.
Embodiment
Technical scheme is described in further detail below in conjunction with specific embodiment.
The lookup of the molecular labeling of embodiment 1
(1) design of primers
With the DNA sequence dna (Genbank of No. 6 chromosomes of pig:FN675082 it is) template, the DNA pieces of design primer separation pig
Section (template expanded using the DNA of a duroc as PCR), primer is as follows:
Forward primer:5 '-AAATGAAGAACAGGCAAGG-3 ' (as shown in SEQ ID NO.2)
Reverse primer:5 '-CTTCCCAGTAAACTTAGGAGATA-3 ' (as shown in SEQ ID NO.3)
PCR reaction cumulative volumes are 20 μ l, wherein pig genomic DNA about 100ng, containing 1 × buffer (Promega companies),
1.5mmol/L MgCl2, dNTP (Shanghai Sheng Gong biotech firms) final concentration of 150 μm of ol/L, the final concentration of 0.2 μm of ol/ of primer
L, 2U Taq archaeal dna polymerases (Promega companies).
PCR is expanded:94 DEG C of 4min, (94 DEG C of 30s, 60 DEG C of annealing 30s, 72 DEG C of 30s) circulation 30 times, last 72 DEG C of extensions
10min。
PCR reaction products are detected with 1% agarose gel electrophoresis.PCR reaction products are examined with 1% agarose gel electrophoresis
Survey.
(2) cloning and sequencing is analyzed
The DNA fragmentation of obtained No. 6 chromosome of pig is cloned as follows.
The purifying of PCR primer:The gel containing purpose fragment is cut from Ago-Gel under uviol lamp, is put into 1.5ml
In Ependorff pipes, purified with PCR primer purification kit (Tiangeng biochemical technology Co., Ltd).
Coupled reaction:The PCR primer of purifying is connected with pMD18-T carriers (Dalian treasured biotech firm), coupled reaction is total
Volume is 10 μ l, and including 5 μ l solution I (Dalian treasured biotech firm), (the precious biology in Dalian is public for 0.5 μ l carrier T
Department), 2.5 μ l purified pcr product, it is eventually adding 2 μ l aqua sterilisas and puts 4 DEG C of water-baths and stay overnight.
Conversion:100-120 μ l competent cells (Tiangeng biochemical technology Co., Ltd) are taken under germ-free condition in 1.5ml
In Ependorff pipes, 5 μ l connection product is added and mixed, 30min is placed on ice, 42 DEG C of heat shock 90s, not shaken therebetween
Dynamic Ependorff pipes, ice bath 3-4min after taking-up add the LB fluid nutrient mediums of 400 μ l antibiotic-frees, 37 DEG C keep flat 1h after fall
Put culture.
Bacterium colony PCR is identified:Bacterial strain after bacterium colony PCR identifications is in 37 DEG C of overnight incubations of LB culture mediums, and picking is multiple immediately
Clone is sent to the sequencing of Shanghai life work biology Co., Ltd.
After tested, the common 550bp of DNA sequence dna through spliced No. 6 chromosomes of pig, sequence is as shown in SEQ ID NO.1.
Find that a base at its 362nd base be present replaces through analysis, be 362A or 362G.By molecular biology software analysis and
Ncbi database is analyzed, it is found that the base at the 362nd base is replaced causes TaiI-RFLP (Restriction Fragment
LengthPolymorphism, i.e. TaiI-RFLP sites) polymorphism.
(3) foundation of PCR-TaiI-RFLP detection methods and the detection in replacement site
The μ l of endonuclease reaction cumulative volume 10, wherein 1 × buffer 10 μ l, PCR primer 3-5 μ l, restriction enzyme TaiI are
0.5 μ l (5U), use H2O supplies 10 μ l, 65 DEG C of water-bath 4h, weighs 0.6g agaroses and is dissolved in 15.75ml DEPC (Shanghai life work lifes
Thing company) handle in water, 5ml 5 × formaldehyde gel buffer solution and 4.25ml 37% formalin are added after slightly cooling down,
Glue is mixed, digestion result is detected after electrophoresis.
As a result find:A allele only has mono- fragment of 550bp in SEQ ID NO.1 sequences, and G allele has 363bp
With two fragments of 187bp, the two allele can form three kinds of genotype, AA, AG, GG.And in the SEQ ID NO.1 sequences
The 362nd bit base replace, A → G.
The distribution situation of the allele of embodiment 2
(1) design of colony is tested
Test group:Gather Pietrain (21), Shen Nong (17), great Bai (43), great Shen (52), long Shen (16),
(20) Du Shen (23), Pi great Shen (11), Shen of growing up (25), Du great Shen (17) and Du Pi great Shen individual ear groups
Knit, extract DNA, altogether 245 DNA samples.
The purpose of colony is tested in the distribution situation in detection SNP marker in different cultivars.
(2) genetic test
Forward primer:5 '-AAATGAAGAACAGGCAAGG-3 ' (as shown in SEQ ID NO.2);
Reverse primer:5 '-CTTCCCAGTAAACTTAGGAGATA-3 ' (as shown in SEQ ID NO.3).
(amplification condition is with embodiment 1) is expanded, experiment colony is detected with identical PCR-TaiI-RFLP methods and owns
Idiotype.
(3) statistical analysis
All idiotypes of record experiment colony, and gene frequency and heterozygosity are calculated, as a result such as table 1 below.
Table 1
As known from Table 1:Gene frequency of the SNP marker of the present invention in each kind approaches, rich polymorphism;
Between kind or strain, gene frequency A and G distributional difference are small;The heterozygosity H of all kinds or strain is all higher than 0.3,
Therefore it was initially believed that the DNA that the SNP marker can be used for pork product traces to the source and traced to the source with security.
The SNP marker availability of embodiment 3 is traced to the source verification experimental verification
The SNP marker of the present invention can be used in traceability mark by tentative confirmation, in order to ensure in mark of tracing to the source
In availability, the present invention again resampled in different location, with existing 13 SNP markers (as described in Table 2)
It is used in combination (totally 14 SNP markers), carries out availability and trace to the source verification experimental verification, meanwhile, only to be divided with existing 13 SNP
Son mark trace to the source verification experimental verification work to ratio.
In the individual ear tissue of recovery slaughterhouse random acquisition pig and each 100 parts of muscle sample, (each pig individual is adopted simultaneously
Collect ear tissue sample and muscle sample), ear tissue sample numbering E1-E100, muscle sample numbering M1-M100, muscle sample and ear are extracted respectively
The DNA of tissue sample is standby.
The TaiI of the pig of the present invention is detected in 20 muscle samples selected in 100 individual ear tissue samples and at random
The genotype (amounting to 14 SNP marker sites) of SNP site and existing published 13 SNP sites, statistics is per each and every one
The genotype results of body.According to digestion banding pattern, a band is designated as 1, two bands occurs and is designated as 2, three bands are designated as 3.Record order
Arranged according to the site of table 2 order, the SNP marker site as the enzymes of Pvu II of ADAMTS-1 genes identify is 1, its genotype
Record result just makes number one, and the SNP marker site of the enzymes of Eam1104 I identification of ADD1 genes is 2, its genotype note
Record result just comes second, the like, the TaiI SNP markers site on No. 6 chromosomes of pig of the invention comes most
Afterwards, its genotype results is indicated as the 14th numeral from left to right, and individual genotype can be expressed as:
21232322223311。
Table 2
The genotype in 14 SNP marker sites of each individual of statistics and meat sample, 100 individuals and 20 parts of muscle samples
The genotype Statistical Comparison result of product is respectively such as table 3 below and table 4.
In table 3, No. 82 individuals and No. 91 individual genotype are closely similar, and preceding 13 tag values of two individual are equal
Unanimously, only difference is that the 14th mark is different.As can be seen here, traced back merely with existing 13 SNP markers
During source, it may appear that the situation that genotype repeats, the 14th is labeled as New SNP marker provided by the invention, illustrates to add the present invention
SNP marker after, it is possible to smoothly by this in two genotype make a distinction, the addition of Novel SNP molecular marker of the invention
The further perfect scale of tracing to the source for combination of tracing to the source, improves the accuracy traced to the source with SNP marker pork DNA.
The genotype results in 14 SNP marker sites of 20 parts of muscle samples are entered with 100 individual genotype
Row compares analysis (comparison result is referring to table 4), and discovery can find the individual completely the same with 20 parts of muscle samples genotype,
The source individual of 20 parts of pig muscles is found in 100 individuals by tracing to the source, realizes that meat sample is traced to the source to the accurate of individual.
Illustrate with reference to table 3 and table 4, experiment of tracing to the source, 100 individuals, 20 parts of muscle samples are carried out using 14 SNP markers
Possess different genotype with 14 SNP marker detections, individual differentiation can be realized.
Table 3
Numbering | Genotype | Numbering | Genotype | Numbering | Genotype |
E1 | 33332332132312 | E35 | 33333232131333 | E68 | 23311222133232 |
E2 | 21211233132123 | E36 | 21333321323232 | E69 | 23313333333223 |
E3 | 33333232331122 | E37 | 22213233131322 | E70 | 21231233333212 |
E4 | 23311232111313 | E38 | 31221211121113 | E71 | 21121333332233 |
E5 | 23113332231331 | E39 | 22333231121222 | E72 | 21231122211123 |
E6 | 23332221321322 | E40 | 33332223111331 | E73 | 31313113323221 |
E7 | 33231232321332 | E41 | 21233113113321 | E74 | 23131113231122 |
E8 | 23332222131121 | E42 | 33311312333123 | E75 | 31332213331111 |
E9 | 31313211221111 | E43 | 21233112131322 | E76 | 23333333321313 |
E10 | 23333333111333 | E44 | 33112113133133 | E77 | 23311232333323 |
E11 | 21211332123113 | E45 | 21312233331231 | E78 | 22131232333331 |
E12 | 12121313131111 | E46 | 33212323222112 | E79 | 12133233222322 |
E13 | 33312232313212 | E47 | 31212333333312 | E80 | 31211212311132 |
E14 | 32112212111322 | E48 | 21232312331231 | E81 | 21231222322321 |
E15 | 23113132231113 | E49 | 33333232133223 | E82 | 21231233333332 |
E16 | 23132311121121 | E50 | 31133211131322 | E83 | 21211212111332 |
E17 | 23123232113213 | E51 | 33332333331233 | E84 | 33331332333321 |
E18 | 32132231321322 | E52 | 21133232323222 | E85 | 31311222112213 |
E19 | 21213132321111 | E53 | 21232132123113 | E86 | 12132112133222 |
E20 | 21211212331331 | E54 | 21232332321112 | E87 | 23223212322223 |
E21 | 23313332323312 | E55 | 21213232131213 | E88 | 23311312333111 |
E22 | 33312233233213 | E56 | 33132122332311 | E89 | 23213331133213 |
E23 | 23111212323113 | E57 | 33132312131131 | E90 | 23311222132221 |
E24 | 13133331223211 | E58 | 31231221331212 | E91 | 21231333233331 |
E25 | 32113232321113 | E59 | 31332333113313 | E92 | 31212212123113 |
E26 | 21222223333331 | E60 | 21313232321132 | E93 | 33311232311131 |
E27 | 33312232132111 | E61 | 31313133231332 | E94 | 32131332233331 |
E28 | 32111222322223 | E62 | 32132211313331 | E95 | 23312332323112 |
E29 | 32311213123112 | E63 | 33313233213333 | E96 | 13332223323112 |
E30 | 32113213123221 | E64 | 21321332221312 | E97 | 21211132323333 |
E31 | 33123311113312 | E65 | 32112213231221 | E98 | 21332212132212 |
E32 | 11232131332233 | E66 | 31213133321131 | E99 | 32131331321112 |
E33 | 33131232232113 | E67 | 32131133113323 | E100 | 23313231323332 |
E34 | 31222212111132 |
Table 4
Numbering | Genotype | Corresponding individual | Numbering | Genotype | Corresponding individual |
M1 | 31213133321131 | E66 | M11 | 32131331321112 | E99 |
M2 | 21333321323232 | E36 | M12 | 31221211121113 | E38 |
M3 | 23123232113213 | E17 | M13 | 11232131332233 | E32 |
M4 | 21123123221123 | E9 | M14 | 33212323222112 | E46 |
M5 | 33123311113312 | E31 | M15 | 31332213331111 | E75 |
M6 | 13133331223211 | E24 | M16 | 32131133113323 | E67 |
M7 | 21121333332233 | E71 | M17 | 23131113231122 | E74 |
M8 | 33112113133133 | E44 | M18 | 23213331133213 | E89 |
M9 | 31313211221111 | E10 | M19 | 31212333333312 | E47 |
M10 | 31231221331212 | E58 | M20 | 33131232232113 | E33 |
Claims (4)
1. it is used for the SNP marker traced to the source, the DNA sequence dna such as SEQ ID NO.1 of the SNP marker on No. 6 chromosomes of pig
It is shown, common 550bp, and there is a base to replace at the 362nd bit base, it is 362A or 362G.
2. it is used for the SNP marker traced to the source on No. 6 chromosomes of pig according to claim 1, it is characterised in that the SNP
Molecular labeling is by TaiI restriction enzyme specific recognitions.
3. the primer pair for expanding the SNP marker for being used for tracing to the source on No. 6 chromosomes of pig described in claim 1, it is special
Sign is that it includes forward primer, reverse primer, and specific base sequence is as follows:
Forward primer:As shown in SEQ ID NO.2;
Reverse primer:As shown in SEQ ID NO.3.
4. the SNP marker for being used to trace to the source on No. 6 chromosomes of pig as claimed in claim 1 is in DNA source tracing of pork products
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