CN104878110B - A kind of analysis method of animal economic characters chondriogen effect - Google Patents
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Abstract
The present invention relates to the technical field of animal Analysis on Economic Traits, more particularly to a kind of analysis method of animal economic characters chondriogen effect, including the reciprocal effects between mitochondrial genomes haplotype effect, the gene effect of single polymorphic site and single polymorphic site.The present invention uses DNA to mix pond and the PCR amplification sequencings substituted with reference to Allele-specific PCR (AS PCR) in art methods to each laboratory sample (individual) is sequenced, targetedly detect the genotype of each polymorphic site, save each laboratory sample is entered in current methods performing PCR amplification sequencing repeat, improve experiment detection efficiency, experimental expenses is reduced, establishes the detection method that mitochondrial genomes haplotype is quick, easy.
Description
Technical field
The present invention relates to animal economic characters technical field, more particularly to a kind of animal economic characters chondriogen effect
Analysis method.
Background technology
Mitochondria is the power factory of zooblast, and more than 90% energy is supplied by mitochondria in body.Line grain
Body DNA (mitochondrial DNA, hereinafter referred to as mtDNA) is the unique long-term, dna extranuclear gene that is stabilized in animal body
Group.In human diseases, have now been found that hundreds of disease is polymorphic relevant with mtDNA, mtDNA is polymorphic to cause electron transport chain complex
Combined oxidative phosphorylation de and then initiation mitochondrial function defect turn into the cause of the numerous diseases of induction.In addition to disease, motion is resistance to
The characters such as power, fat deposition, life-span are all closely related with mtDNA types.In terms of agricultural animal economic characters, exist at present
Report mtDNA gene effects in the research of the livestock and poultry such as ox, sheep, pig, chicken, duck successively, for example, the output of milk of milk cow, butterfat production,
Somatic number character, the growth of beef cattle and Meat Quality, the anti-Marek's disease character of chicken, the Carcass Traits of duck, 21 ages in days of pig
Weanling weight, daily gain character, the characters of number born of sheep etc..
Although carry out chondriogen effect analysis method using mtDNA polymorphic sites or mitochondrial genomes haplotype to exist
It has been reported that but these methods are not from the angle systems of mitochondrial genomes point in different plant species, different economic characters
Analyse chondriogen effect.Simply by the method for single or several mtDNA polymorphic sites, whole chondriogens are not accounted for
The effect of group polymorphic site;And with the analysis method of mitochondrial genomes haplotype do not account for each polymorphic site effect and
Reciprocal effects between polymorphic site.At present, the method for detecting mitochondrial genomes haplotype is covered using mitochondrial genomes
The PCR sequencing technologies of primer, i.e., all samples (individual) are carried out one by one chondriogen set of segmentation primer PCR amplification and
The sequencing of PCR primer, this method are time-consuming, laborious, it is necessary to which substantial amounts of PCR amplifications and PCR primer sequencing repeat.
The content of the invention
The technical problems to be solved by the invention are the deficiency for overcoming above-mentioned prior art, there is provided a kind of animal economy
The analysis method of plastochondria gene effect, it establishes quick, the easy detection method of mitochondrial genomes haplotype, save
Enter to each laboratory sample performing PCR amplification sequencing in current methods to repeat, improve experiment detection efficiency, reduce
Experimental expenses.
The major technique side that a kind of analysis method of animal economic characters chondriogen effect provided by the invention uses
Case is:Comprise the following steps:
(1) using the DNA sample mixed in equal amounts of the Animal resources group of extraction as DNA profiling, then using covering mitochondria
The special primer of genome enters performing PCR amplification, sequencing, obtains Animal resources group's mitochondrial genomes polymorphism information;
(2) Animal resources group's mitochondrial genomes polymorphism information is directed to, each polymorphic site is entered using AS-PCR methods
Row genotype identification, obtain the mitochondrial genomes haplotype of resource population individual;
(3) each polymorphic site genotype and the relevance of haplotype and economic characters are analyzed respectively by animal model, is obtained
Obtain the hereditary effect of polymorphic site and haplotype;
(4) associating to the combined pattern that the polymorphic site that notable hereditary effect be present is formed and economic characters is passed through
Analysis, obtain the reciprocal effects between polymorphic site.
The analysis method of a kind of animal economic characters chondriogen effect provided by the invention, using following attached technology
Scheme:
It is design that in the step 1 mitochondrial genomes of Animal resources group are specifically covered with the method that primer is expanded
The PCR primer of the species specific 16 pairs of coverings mitochondrial genomes of thing, every section of expanding fragment length 1.2kb, adjacent segment have 100bp
Overlapping region, each section of PCR fragment amplification program conventionally carry out.
In the step 1 mitochondrial genomes of Animal resources group are specifically covered with method that primer is sequenced to use
The method of PCR primer direct Sequencing.
It is allele specific primer PCR method to the method for the genotype identification of individual polymorphic site in the step 2.
The allele specific primer PCR method is to lack 3 ' → 5 ' exonuclease enzyme activity using Taq archaeal dna polymerases
Property the characteristics of, the mispairing of the end of PCR primer 3 ' under certain condition causes the drastically reduction of amplified production, so as to for different
Known mutations design appropriate primer, and the purpose for distinguishing saltant type and wild type gene is directly reached by PCR method.
The animal model that the analysis method of polymorphic site and haplotype hereditary effect uses in the step 3 is united for SAS9.0
The LSM processes in analysis software generalized linear model are counted, model includes polymorphic site or haplotype effect, paternal effect, Nian Ji
Effect and environmental error.
The method of reciprocal effects is by analyzing combined pattern and economic characters between 4 analysis polymorphic sites in the step
Relevance obtain polymorphic site between reciprocal effects.
The combined pattern refers to the presence significantly heredity effect obtained according to the allele specific primer PCR method
The genotype that the polymorphic site answered is formed.
The gene effect of the combined pattern uses animal model as SAS9.0 statistical analysis software generalized linear models
Analyzed.
The method that Animal resources group DNA is extracted in step 1, comprises the following steps:
A, 500ul suspension is added into the anticoagulation of 200 μ L Animal resources groups, after mixing, Proteinase K is added, makes
The concentration of Proteinase K is 100ng/mL, and 4h is incubated at a temperature of 55 DEG C;
B, isometric Tris- saturations phenol, the chloroform and isoamyl of volume ratio 24: 1 are sequentially added into above-mentioned solution
Alcohol, extract 2 times;
C, a certain amount of liquid phase is taken, the absolute ethyl alcohol of 1/10 volume 3M sodium acetate solution and 2.5 times of volumes is added to it,
At -20 DEG C, 30min is stood, then under the conditions of 12000g, centrifuges 10min, precipitation is dissolved standby with appropriate ultra-pure water after drying
With.
The suspension includes 1% lauryl sodium sulfate, 400mmol sodium chloride, 5mmol EDTA and 20mmol
Tris-cl solution.
The pH of the Tris-cl solution is 8.0.
The beneficial effect of the analysis method of the animal economic characters chondriogen effect of the present invention is:
1) present invention mixes pond sequencing using DNA and substitutes prior art side with reference to Allele-specific PCR (AS-PCR)
Sequencing is expanded to the PCR of each laboratory sample (individual) in method, targetedly detects the genotype of each polymorphic site, is saved
Enter to each laboratory sample performing PCR amplification sequencing in current methods to repeat, improve experiment detection efficiency, reduce
Experimental expenses, establish the detection method that mitochondrial genomes haplotype is quick, easy.
2) present invention had both included mitochondrial genomes haplotype effect and the gene effect of each polymorphic site, in addition to
A kind of reciprocal effects between single polymorphic site, there is provided analysis side of brand-new animal economic characters chondriogen effect
Method, it is capable of the chondriogen effect of systematically analyzing animal economic characters.
Embodiment
The present invention is described in further detail with reference to embodiments.
The analysis method of the animal economic characters chondriogen effect of the present invention comprises the following steps:
First, the present embodiment is pig resource population from experimental animal, wherein, sow 113, litter size is recorded as 365.
Pig resource population DNA extracting method:500ul suspension is added into the anticoagulation of 200 μ L Animal resources groups, is mixed
Afterwards, Proteinase K is added, the concentration for making Proteinase K is 100ng/mL, and 4h is incubated at a temperature of 55 DEG C;State then up molten
Isometric Tris- saturations phenol, the chloroform and isoamyl alcohol of volume ratio 24: 1 are sequentially added in liquid, is extracted 2 times;Finally, take
A certain amount of liquid phase, the absolute ethyl alcohol of 1/10 volume 3M sodium acetate solution and 2.5 times of volumes is added to it, it is quiet at -20 DEG C
30min is put, then under the conditions of 12000g, centrifuges 10min, precipitation is dissolved standby with appropriate ultra-pure water after drying.
2nd, pig resource population DNA equivalent mixes pond and is expanded and be sequenced
The concentration of each DNA sample is determined, is that 100ng/ μ L form the mixed pond (mixing of DNA according to each DNA sample concentration
DNA sample quantity is up to 20), the present embodiment establishes 6 DNA ponds;Utilize 16 pairs of mitochondrial genomes specific PCR primers
(primer information is shown in Table 1) mixes pond to DNA and is expanded and be sequenced respectively, detects pig resource population mitochondrial genomes more than 9 altogether
State site (is shown in Table 2).
The porcine mtdna genome specific PCR primer information of table 1
The pig resource population mitochondrial genomes polymorphism information of table 2
3rd, analyzed using AS-PCR and obtain mitochondrial genomes haplotype
According to the information of above-mentioned 9 polymorphic sites detected, AS-PCR special primers (primer information is shown in Table 3) are designed,
Then the genotype identification of 9 polymorphic sites is carried out to each individual respectively, obtains pig resource population mitochondrial genomes 10 altogether
Haplotype (is shown in Table 4).
The AS-PCR primer information of table 3
The pig resource population mitochondrial genomes haplotype of table 4 and its characters of number born effect
Wherein, a, b, c represent the different levels of signifiance (P < 0.05) respectively.
4th, using the LSM processes in SAS9.0 statistical analysis softwares linear model (GLM), analyze each polymorphic site and
Haplotype effect, model are as follows:
yijmnk=μ+ai+bj+cm+dn+eijmnk
Wherein, yijmnkFor trait phenotypes value, μ is community average, aiFor polymorphic site effect or haplotype effect, bjFor
Paternal effect, cmFor parity effect, dnFor season in year effect, eijmnkFor environmental error.
By the linear model analysis (the results are shown in Table 4) of haplotype, it is found that haplotype CATATCTAG litter size is significantly high
In haplotype TATGTTCGG, CACGTTTAG, CATGCTTAA and CGTGCTTAA (P < 0.05), haplotype CGTATCTAG and
CGTACTTAG litter size is significantly higher than haplotype CATGCTTAA and CGTGCTTAA (P < 0.05), the maximum gene of haplotype
Effect reaches 1.97 (haplotype CATATCTAG is compared with haplotype CATGCTTAA).
By the linear model analysis (the results are shown in Table 5) of single polymorphic site, A13751G/ND5 and A15141G/ is found
There is notable gene effect (P < 0.05) in ND6 litter size, the maximum gene effect of single polymorphic site reaches 1.33
(A15141G/ND6)。
The pig number born character mitochondrial genomes polymorphic site effect of table 5
Wherein, a, b represent the different levels of signifiance (P < 0.05) respectively.
By the linear model analysis (the results are shown in Table 6) of A13751G/ND5 and A15141G/ND6 combined patterns, find
AG litter size is significantly higher than GA (P < 0.05), and gene effect reaches 1.70, is higher by 0.43 respectively than Single locus effect
(A13751G/ND5) and 0.33 (A15141G/ND6), illustrate that A13751G/ND5 and A15141G/ND6 sites have cumulative effect
Should.
The reciprocal effects in the pig number born character A13751G-A15141G sites of table 6
Wherein a, b, c represent the different levels of signifiance (P < 0.05) respectively.
Although above-mentioned the embodiment of the present invention is described in conjunction with the embodiments, not the present invention is protected
The limitation of scope, one of ordinary skill in the art should be understood that on the basis of technical scheme, those skilled in the art
Various modifications or deformation that creative work can make need not be paid still within protection scope of the present invention.
Claims (5)
1. a kind of analysis method of animal economic characters chondriogen effect, it is characterised in that the animal is pig, the warp
Ji character is characters of number born;Comprise the following steps:
(1) using the DNA sample mixed in equal amounts of the Animal resources group of extraction as DNA profiling, then using covering chondriogen
The special primer of group enters performing PCR amplification, sequencing, obtains Animal resources group's mitochondrial genomes polymorphism information;
The Animal resources group mitochondrial genomes polymorphism information is:Polymorphic site C2512T, A11586G, C11982T,
A13751G, C14119T, C14326T, C14397T, A14871G and A15141G;
The sequence of the special primer is:Sequence 1-2, sequence 3-4, sequence 5-6, sequence 7-8, sequence in sequence table
9-10, sequence 11-12, sequence 13-14, sequence 15-16, sequence 17-18,19-20, sequence 21-22, sequence 23-
24th, sequence 25-26, sequence 27-28, sequence 29-30, sequence 31-32;
(2) Animal resources group's mitochondrial genomes polymorphism information is directed to, base is carried out to each polymorphic site using AS-PCR methods
Because type is identified, the mitochondrial genomes haplotype of resource population individual is obtained;Primer sequence in the AS-PCR methods is:Sequence
Sequence 33-35, sequence 36-38, sequence 39-41, sequence 42-44, sequence 45-47, sequence 48-50, sequence in table
51-53, sequence 54-56, sequence 57-59;
(3) each polymorphic site genotype is analyzed by the LSM processes in SAS9.0 statistical analysis software generalized linear models respectively
With haplotype and the relevance of economic characters, the hereditary effect of acquisition polymorphic site and haplotype;
The haplotype is:CGTATCTAA、TGTATCTAG、CATATCTAG、CGTATCTAG、CGTACTTAG、CATGCTTAA、
CGTGCTTAA、CATGTTCAG、TATGTTCGG、CACGTTTAG;Wherein haplotype CATATCTAG litter size is significantly higher than list
Times type TATGTTCGG, CACGTTTAG, CATGCTTAA and CGTGCTTAA, haplotype CGTATCTAG and CGTACTTAG farrowing
Number is significantly higher than haplotype CATGCTTAA and CGTGCTTAA;
(4) associating point to the combined pattern that the polymorphic site that notable hereditary effect be present is formed and economic characters is passed through
Analysis, obtain the reciprocal effects between polymorphic site;
The polymorphic site in the presence of notable hereditary effect is:A13751G/ND5 and A15141G/ND6;
The combined pattern is:AA、AG、GA、GG;Wherein AG litter size is significantly higher than GA, the interaction effect between polymorphic site
It should be A13751G/ND5 and A15141G/ND6 sites and additive effect be present.
2. the analysis method of animal economic characters chondriogen effect according to claim 1, it is characterised in that:It is described
In step 1 mitochondrial genomes of Animal resources group are specifically covered with method that primer is expanded for shown in implementation sequence 1-32
The species specific 16 pairs of coverings mitochondrial genomes of thing PCR primers, every section of expanding fragment length 1.2kb, adjacent segment has
100bp overlapping region, each section of PCR fragment amplification program are conventionally carried out.
3. the analysis method of animal economic characters chondriogen effect according to claim 1, it is characterised in that:It is described
It is direct using PCR primer that in step 1 mitochondrial genomes of Animal resources group are specifically covered with the method that primer is sequenced
The method of sequencing.
4. the analysis method of animal economic characters chondriogen effect according to claim 1, it is characterised in that:It is described
The gene that the polymorphic site for the notable hereditary effect of presence that combined pattern refers to be obtained according to the AS-PCR methods is formed
Type.
5. the analysis method of animal economic characters chondriogen effect according to claim 4, it is characterised in that:It is described
The gene effect of combined pattern is analyzed using SAS9.0 statistical analysis software generalized linear models.
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