CN105331696B - A kind of method and primer special for identifying pig rib data/coherency shape - Google Patents
A kind of method and primer special for identifying pig rib data/coherency shape Download PDFInfo
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- CN105331696B CN105331696B CN201510741083.4A CN201510741083A CN105331696B CN 105331696 B CN105331696 B CN 105331696B CN 201510741083 A CN201510741083 A CN 201510741083A CN 105331696 B CN105331696 B CN 105331696B
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Abstract
The invention discloses a kind of methods and primer special for identifying pig rib data/coherency shape.The present invention provides the single nucleotide polymorphism of SNP site following in pig genome to identify or assist to identify the application in the rib cage data/coherency shape of pig to be measured;The SNP site are as follows: using pig genomic DNA as template, the 144th nucleotide from 5 ' ends of PCR amplification products therefrom is carried out using the primer pair that two articles of single stranded DNAs form shown in sequence 1 and sequence 2;Nucleotide at the SNP site is A or G.It is demonstrated experimentally that the rib cage number that the rib cage number of the pig of GG genotype is noticeably greater than the pig of AG genotype is noticeably greater than the rib cage number of AA genotype pig.Early screening can be carried out to pig using the present invention, effectively solve the problems, such as that the selection excellent boar time in actual production is long, reduce breeding and spend, and accuracy is high, testing cost is low, and can realize automatic detection, has very high practical application value in terms of pig breeding.
Description
Technical field
The invention belongs to field of biotechnology, are related to a kind of method and primer special for identifying pig rib data/coherency shape.
Background technique
It is one of highest pig carcass position of Chinese market pork product price in view of Pig spareribs, and chop is mainly by rib
Bone and its adherent meat composition, therefore pig rib number also just becomes important economic characters.The rib cage of Chinese native pig breed is general
There is 14-15 section, and west business pig kind generally has 15-17 to save (Zhang ZG, Li BD, Chen XH:Pig breeds in
China.Shanghai Scientific and Technical Publisher,Shang,China 1986.).Therefore, shadow
The major gene resistance and molecule marking research for ringing rib cage number variation become one of research hotspot.
Based on the importance of pig rib data/coherency shape, carrying out breeding work for it becomes one of current breeding work
Emphasis.But due to the features such as traditional breeding way speed is slow, order of accuarcy is low, and molecular breeding is with its accuracy and rapidity
Have become the technical way of current breeding work.
Summary of the invention
The first purpose of the invention is to provide a kind of SNP site relevant to pig rib number and its applications.
It is provided by the present invention application it is concretely any one of following: (1) in pig genome following SNP site list
Nucleotide polymorphisms are being identified or are assisting to identify the application in the rib cage data/coherency shape of pig to be measured;(2) for detecting pig gene
The substance of the single nucleotide polymorphism of following SNP site is being identified or is being assisted in the rib cage data/coherency shape for identifying pig to be measured in group
Application.
The SNP site are as follows: using pig genomic DNA as template, using the single stranded DNA as shown in sequence 1 in sequence table and
The primer pair that single stranded DNA shown in sequence 2 forms in sequence table carry out amplified production obtained by PCR amplification the from 5 ' ends
144 nucleotide;Nucleotide at the SNP site is A or G.
The SNP site is located on intragenic international pig genome No. 7 chromosomes of 10.2 version reference sequences of LTBP2 the
103637930 nucleotide site A > G are mutated (being denoted as g.103637930A > G).
A second object of the present invention is to provide a kind of for identifying or assisting to identify the rib cage data/coherency shape of pig to be measured
Reagent.
The reagent provided by the present invention for being used to identify or assist to identify the rib cage data/coherency shape of pig to be measured, is for examining
Survey the substance of the single nucleotide polymorphism of SNP site (g.103637930A > G) in pig genome;
It is described can be identified " for detecting the substance of the single nucleotide polymorphism of following SNP site in pig genome "
Any substance of the single nucleotide polymorphism of SNP site (g.103637930A > G), for example following (a) or (b) shown in primer
It is right:
(a) primer that single stranded DNA shown in sequence 2 forms in the single stranded DNA shown in sequence 1 in sequence table and sequence table
It is right;
(b) by by the substitution of one or several nucleotide and/or missing and/or adding sequence 1 in sequence table and sequence 2
Two single strand dnas shown in rear gained sequence are added to form, and primer pair identical with primer pair function described in (a).
Third object of the present invention is to provide a kind of for identifying or assisting to identify the rib cage data/coherency shape of pig to be measured
Kit.
The kit provided by the present invention for being used to identify or assist to identify the rib cage data/coherency shape of pig to be measured, containing
State reagent.
The application in the rib cage data/coherency shape for identifying pig to be measured is being identified or assisted to the reagent or the kit
It belongs to the scope of protection of the present invention.
Fourth object of the present invention is to provide the side of a kind of identification or the rib cage data/coherency shape for assisting identification pig to be measured
Method.
The method that identification provided by the present invention or auxiliary identify the rib cage data/coherency shape of pig to be measured, specifically may include as
Lower step: detecting the nucleotide at SNP site in the genome of pig to be measured (g.103637930A > G) is A or G or A and G,
Genotype with the determination pig to be measured is AA or GG or AG, according to the genotype of the pig to be measured according to it is following determine to
Survey the rib cage data/coherency shape of pig: the rib cage number of the pig to be measured of GG genotype is more than or the candidate pig to be measured for being more than AG genotype;
The rib cage number of the pig to be measured of AG genotype is more than or the candidate pig to be measured for being more than AA genotype;
The GG genotype be using pig genomic DNA as template, using the single stranded DNA as shown in sequence 1 in sequence table and
The primer pair that single stranded DNA shown in sequence 2 forms in sequence table carry out the resulting amplified production of PCR amplification the from 5 ' ends
144 nucleotide are the homozygous (the 103637930th on i.e. international pig genome No. 7 chromosomes of 10.2 version reference sequences of G
Nucleotide is the homozygous of G);I.e. amplified production only has one kind, is DNA fragmentation shown in sequence 4 in sequence table.
The AA genotype be using pig genomic DNA as template, using the single stranded DNA as shown in sequence 1 in sequence table and
The primer pair that single stranded DNA shown in sequence 2 forms in sequence table carry out amplified production obtained by PCR amplification the from 5 ' ends
144 nucleotide are the homozygous (the 103637930th on i.e. international pig genome No. 7 chromosomes of 10.2 version reference sequences of A
Nucleotide is the homozygous of A);I.e. amplified production only has one kind, is DNA fragmentation shown in sequence 3 in sequence table.
The AG genotype be using pig genomic DNA as template, using the single stranded DNA as shown in sequence 1 in sequence table and
The primer pair that single stranded DNA shown in sequence 2 forms in sequence table carry out amplified production obtained by PCR amplification the from 5 ' ends
Heterozygous that 144 nucleotide are A and G is (the on i.e. international pig genome No. 7 chromosomes of 10.2 version reference sequences
The heterozygous that 103637930 nucleotide are A and G);I.e. there are two types of amplified productions, DNA shown in sequence 3 respectively in sequence table
DNA fragmentation shown in sequence 4 in segment and sequence table.
In the method, described " detect nucleotide in the genome of pig to be measured at following SNP site be A or G also
The method for being A and G " can be sequencing analysis;The sequencing analysis may include PCR amplification and to the PCR amplification products therefrom into
Row two steps of sequencing;The template of the PCR amplification is the genomic DNA of the pig to be measured, and primer pair used meets as follows
Condition: PCR amplification gained amplified production is carried out as template using the genomic DNA of pig to be measured and contains the nucleosides at the SNP site
Acid;
Specifically, the primer pair can be primer pair shown in (a) or (b) as described above.
When carrying out PCR amplification using the primer pair (sequence 1 and sequence 2), not according to the genomic DNA of pig to be measured
Together, the DNA fragmentation expanded is as shown in sequence 3 in sequence table or as shown in sequence 4 in sequence table.Wherein, the of sequence 3
144 nucleotide are A;144th nucleotide of sequence 4 is G.
The application of the reagent or the kit or the method in pig breeding also belongs to protection scope of the present invention.
In the method, the annealing temperature used when carrying out the PCR amplification is 57-62 DEG C (such as 58.5 DEG C).
Further, the amplification program used when carrying out the PCR amplification specifically: 95 DEG C of initial denaturation 5min;95 DEG C of denaturation
20s, 58.5 DEG C of annealing 30s, 72 DEG C of extension 30s, totally 35 recycle;Last 72 DEG C of extensions 10min.
Further, the PCR reaction system specifically: template DNA 200ng, 10 × PCR amplification buffer 5 μ l, dNTPs
Final concentration of 10mM, each 50ng of upstream and downstream primer, Taq archaeal dna polymerase 0.75U, Mg2+2.5mmol/L uses ddH2O supplies body
It is to 50 μ l.
Fifth object of the present invention is to provide the methods of following (A) or (B):
(A) method for cultivating the pig of more rib cage numbers includes the steps that selecting the pig of GG genotype to carry out breeding;The GG base
Because type is using pig genomic DNA as template, using shown in sequence 2 in the single stranded DNA as shown in sequence 1 in sequence table and sequence table
The primer pair of single stranded DNA composition carry out the 144th nucleotide from 5 ' ends ing of the obtained amplified production of PCR amplification as G's
Homozygous (the homozygosis that the 103637930th nucleotide is G on i.e. international pig genome No. 7 chromosomes of 10.2 version reference sequences
Type);
(B) method for cultivating the pig of few rib cage number includes the steps that selecting the pig of AA genotype to carry out breeding;The GG base
Because type is using pig genomic DNA as template, using shown in sequence 2 in the single stranded DNA as shown in sequence 1 in sequence table and sequence table
The primer pair of single stranded DNA composition carry out the 144th nucleotide from 5 ' ends ing of the obtained amplified production of PCR amplification as A's
Homozygous (the homozygosis that the 103637930th nucleotide is A on i.e. international pig genome No. 7 chromosomes of 10.2 version reference sequences
Type).
In the present invention, the pig is big people's hybridized pig;Big people's hybridized pig is specifically hybridized by Large White and people pig
It arrives.
It is demonstrated experimentally that the rib cage number of the pig of GG genotype is noticeably greater than the rib cage number of the pig of AG genotype, AG genotype
The rib cage number of pig is noticeably greater than the rib cage number of AA genotype pig, and the rib cage number of the rib cage number ratio AA genotype pig of GG genotype pig is more
About 1.32 (P < 0.0001).So SNP site (g.103637930A > G) can be used as pig rib number trait molecular breeding label.
Method provided by the invention can carry out early screening to pig to be selected, efficiently solve the selection excellent boar time in actual production
Long problem reduces breeding cost, effectively reduces or increase the rib cage number of the pig in actual production, and this method accuracy is high,
Testing cost is low, and can realize automatic detection, has very high practical application value in terms of the breeding of pig.
Detailed description of the invention
Fig. 1 is AA genotype individuals (corresponding sequence 3) and GG genotype individuals (corresponding sequence 4) pig LTBP2 gene
G.105182819A the sequencing result of sequence near > G polymorphic site.
Specific embodiment
Experimental method used in following embodiments is conventional method unless otherwise specified.
The materials, reagents and the like used in the following examples is commercially available unless otherwise specified.
Big people's hybridized pig (Sus scrofa) in following embodiments is obtained, specially greatly by Large White and the hybridization of people pig
In white pig × people pig F2 generation, obtains according to the method in document: Luo W, Cheng D, Chen S, Wang L, Li Y, Ma X,
Song X,Liu X,Li W,Liang J,Yan H,ZhaoK,Wang C,Wang L,Zhang L.Genome-wide
association analysis of meat quality traits in a porcine Large White×Minzhu
intercross population.Int J Biol Sci.2012,8:580-595.The specific method is as follows: four-head Large White point
Not Jiao Pei 16 people pigs, obtain F1 generation group, 9 boars in this F1 generation group mate 46 sows, and three parity produce altogether
585 F2 generation individuals.
Embodiment 1, identify pig rib cage number how much
One, pig LTBP2 gene g.105182819A > determination of G polymorphic site
(1) using the big people's hybridized pig in both ends as experimental material, the genomic DNA of its ear-edge tissue is extracted respectively.
(2) design and synthesis of primer
According to the 10.2 version reference sequences of international pig genome of pig LTBP2 gene (http: //
Asia.ensembl.org/Sus_scrofa/Info/Index), following primer is designed and synthesized:
U (upstream primer): 5 '-CCAGCTAGGACCCTCTGC-3 ' (sequence 1);
D (downstream primer): 5 '-CCAACCCTGATTCAAAGACG-3 ' (sequence 2).
(3) PCR amplification
The genomic DNA of the big people's hybridized pig obtained respectively using step (1) carries out PCR expansion as template, by primer of U and D
Increase, obtains pcr amplification product, be respectively designated as product 1 and product 2.
PCR amplification system: genomic DNA 200ng, 10 × PCR amplification buffer, the 5 μ final concentration of 10mM of l, dNTPs,
Each 50ng of upstream and downstream primer, Taq archaeal dna polymerase 0.75U, Mg2+2.5mmol/L uses ddH2O supplies system to 50 μ l.
PCR amplification program: 95 DEG C of initial denaturation 5min;95 DEG C of denaturation 20s, 58.5 DEG C of annealing 30s, 72 DEG C of extension 30s, totally 35
A circulation;Last 72 DEG C of extensions 10min.
(4) sequencing and sequence analysis
Product 1 and product 2 are sequenced, obtaining sequence (as shown in sequence 3 in sequence table) and the product 2 of product 1
Sequence (as shown in sequence 4 in sequence table).Sequence 3 and sequence 4 only exist the difference of a base, are in sequence 3 and sequence 4
The 144th from 5 ' ends, it is A that the base at this, which is in sequence 3, is G, as shown by the arrows in Figure 1, the position in sequence 4
On the world Dian Wei pig genome No. 7 chromosomes of 10.2 version reference sequences the 103637930th from 5 ' ends, therefore should
Site is named as g.103637930A > G.
By on No. 7 chromosomes of international 10.2 version reference sequences of pig genome the 103637930th from 5 ' ends
Base (i.e. the obtained pcr amplification product of step (3) the 144th base from 5 ' ends) be A homozygous individual base
Because type is named as AA;By on No. 7 chromosomes of international 10.2 version reference sequences of pig genome from 5 ' ends
103637930 bases (i.e. the obtained pcr amplification product of step (3) the 144th base from 5 ' ends) are homozygous for G
The genotype of type individual is named as GG;By on No. 7 chromosomes of international 10.2 version reference sequences of pig genome from 5 ' ends
The base (i.e. the obtained pcr amplification product of step (3) the 144th base from 5 ' ends ing) for playing the 103637930th is A
AG is named as with the genotype of the heterozygous individual of G.
Two, pig LTBP2 gene g.103637930A > association analysis of the rib cage number of G polymorphic site and pig
To determine whether g.103637930A > G polymorphic site and the rib cage number of pig are related, with 585 big people's hybridized pig
For experimental material, tested as follows:
(1) genomic DNA of the ear-edge tissue of every pig is extracted, carries out PCR according to the method for (three) in step 1 respectively
Amplification, obtains each pcr amplification product, determines that the genotype of every pig is AA, AG or GG according to the method for (four) in step 1.
(2) with the rib cage number for butchering posterior rib counting number method and detecting every pig.
(3) association analysis is carried out to the genotype of pig and rib cage number, specific method can be found in document " Zhang L, Wang
L,Li Y,Li W,Yan H,Liu X,Zhao K,Wang L.A substitution within erythropoietin
receptor gene D1 domain associated with litter size in Beijing Black pig,Sus
scrofa.Anim Sci J.2011,82(5):627-632”。
Model used is as follows:
Y=S+G+e
Wherein, Y is property determination value, and S is sex-effects, and G is genotype effects, and e is residual error effect.
The results are shown in Table 1.
The association analysis of the rib cage number of the genotype and pig of 1 pig of table
Genotype | Quantity | Rib cage number ± standard error |
AA | 15 | 14.48±0.03A |
AG | 203 | 15.08±0.04B |
GG | 377 | 15.80±0.13C |
Note: the different letters of same column subscript indicate significant difference (P < 0.001).
As seen from Table 1, in the rib cage number character of pig, the rib cage number of the pig of GG genotype is noticeably greater than the pig of AG genotype
Rib cage number, the rib cage number of the pig of AG genotype is noticeably greater than the rib cage number of AA genotype pig, the rib cage number ratio of GG genotype pig
The rib cage number of AA genotype pig mostly about 1.32 (P < 0.001).
The result shows that with the intragenic international 10.2 version reference sequences of pig genome of LTBP2 the from 5 ' ends
103637930 single nucleotide polymorphism can be used for identifying the rib cage data/coherency shape of pig.In actual pig breeding, to obtain
The pig of more rib cage numbers, the pig for being preferably selected GG genotype carry out breeding;For the pig for obtaining less rib cage number, it is preferably selected AA base
Because the pig of type carries out breeding.
Claims (4)
1. a kind of method that identification or auxiliary identify the rib cage data/coherency shape of pig to be measured, includes the following steps: to detect pig to be measured
Genome in nucleotide at following SNP site be A or G or A and G, the genotype with the determination pig to be measured is AA
Or GG or AG, according to the genotype of the pig to be measured according to the rib cage data/coherency shape for determining pig to be measured as follows: GG gene
The rib cage number of the pig to be measured of type is more than or the candidate pig to be measured for being more than AG genotype;The rib cage number of the pig to be measured of AG genotype is more than
Or the candidate pig to be measured for being more than AA genotype;
The SNP site are as follows: using pig genomic DNA as template, using the single stranded DNA as shown in sequence 1 in sequence table and sequence
In table single stranded DNA shown in sequence 2 form primer pair carry out PCR amplification obtained by amplified production the 144th from 5 ' ends
Nucleotide;Nucleotide at the SNP site is A or G;
The GG genotype is using pig genomic DNA as template, using the single stranded DNA as shown in sequence 1 in sequence table and sequence
In table single stranded DNA shown in sequence 2 form primer pair carry out the resulting amplified production of PCR amplification the 144th from 5 ' ends
Position nucleotide is the homozygous of G;
The AA genotype is using pig genomic DNA as template, using the single stranded DNA as shown in sequence 1 in sequence table and sequence
In table single stranded DNA shown in sequence 2 form primer pair carry out PCR amplification obtained by amplified production the 144th from 5 ' ends
Nucleotide is the homozygous of A;
The AG genotype is using pig genomic DNA as template, using the single stranded DNA as shown in sequence 1 in sequence table and sequence
In table single stranded DNA shown in sequence 2 form primer pair carry out PCR amplification obtained by amplified production the 144th from 5 ' ends
Nucleotide is the heterozygous of A and G;
The method of " detecting the nucleotide in the genome of pig to be measured at following SNP site is A or G or A and G " is to survey
Sequence analysis;The sequencing analysis includes PCR amplification and carries out two steps of sequencing to the PCR amplification products therefrom;The PCR
The template of amplification is the genomic DNA of the pig to be measured, and primer pair used is the single stranded DNA as shown in sequence 1 in sequence table
With the primer pair of the composition of single stranded DNA shown in sequence 2 in sequence table;
The pig is big people's hybridized pig;Big people's hybridized pig specifically is hybridized to obtain by Large White and people pig.
2. application of claim 1 the method in pig breeding;
The pig is big people's hybridized pig;Big people's hybridized pig specifically is hybridized to obtain by Large White and people pig.
3. the method for cultivating the pig of more rib cage numbers includes the steps that selecting the pig of GG genotype to carry out breeding;The GG genotype
For using pig genomic DNA as template, using single shown in sequence 2 in the single stranded DNA as shown in sequence 1 in sequence table and sequence table
The primer pair of chain DNA composition carries out the homozygosis that the 144th nucleotide is G from 5 ' ends for the amplified production that PCR amplification obtains
Type;
The pig is big people's hybridized pig;Big people's hybridized pig specifically is hybridized to obtain by Large White and people pig.
4. the method for cultivating the pig of few rib cage number includes the steps that selecting the pig of AA genotype to carry out breeding;The GG genotype
For using pig genomic DNA as template, using single shown in sequence 2 in the single stranded DNA as shown in sequence 1 in sequence table and sequence table
The primer pair of chain DNA composition carries out the homozygosis that the 144th nucleotide is A from 5 ' ends for the amplified production that PCR amplification obtains
Type;
The pig is big people's hybridized pig;Big people's hybridized pig specifically is hybridized to obtain by Large White and people pig.
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KR101312480B1 (en) * | 2012-12-31 | 2013-10-01 | 대한민국(농촌진흥청장) | Novel snp marker for discriminating number of rib of pig and use thereof |
CN104232630A (en) * | 2012-12-04 | 2014-12-24 | 江西农业大学 | Two major markers for increasing number of pork ribs and application thereof in pig breeding |
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CN104232630A (en) * | 2012-12-04 | 2014-12-24 | 江西农业大学 | Two major markers for increasing number of pork ribs and application thereof in pig breeding |
KR101312480B1 (en) * | 2012-12-31 | 2013-10-01 | 대한민국(농촌진흥청장) | Novel snp marker for discriminating number of rib of pig and use thereof |
Non-Patent Citations (1)
Title |
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"猪3、4和7号染色体QTL定位及六个候选基因的分离、鉴定";左波;《中国优秀硕士论文全文数据库 农业科技辑》;20050315(第1期);图2、图9、正文第45页 * |
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