CN107988391A - A kind of method for differentiating Jiang Shumin, Landrace based on SNP site - Google Patents
A kind of method for differentiating Jiang Shumin, Landrace based on SNP site Download PDFInfo
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Abstract
The present invention relates to a kind of method for differentiating Jiang Shumin, Landrace based on SNP site, using the difference of SNP site on Jiang Shumin, Landrace SSC1, Jiang Shumin, Landrace are differentiated, SNP titles are respectively：MARC0039661, INRA0001043, DRGA0000202, INRA0003745, INRA0003746, INRA0004022, CASI0011475, INRA0004282, DRGA0001542, INRA0004305, INRA0004312, INRA0004460, M1GA0001181, ALGA0010213, H3GA0004837, DRGA0002521, H3GA0004881, ASGA0095244, MARC0028771, ALGA0013070, amount to 20 SNP sites.Compared with prior art, the present invention by select 20 SNP sites, by the measure to SNP site it is marked down, fast, easily differentiate Jiang Shumin, Landrace.
Description
Technical field
The present invention relates to animal molecular biotechnology and Animal Genetics field, and SNP are based on more particularly, to one kind
Point differentiates Jiang Shumin, the method for Landrace.
Background technology
China is one of earliest country of raising pigs in the world, history for thousands of years, pig China be known as six domestic animals it
It is first.Due to the influence of natural environment, economic condition and folk culture, Chinese local pig breed aboundresources and with their own characteristics, be
Precious resources in world's pig kind gene pool.But so far, the SNP marker combination for cultivar identification and individual identification
SNP marker combination is also seldom.
With the application of pig high density SNP chip, the popularization of genome sequencing technology and development, and Genotyping, survey
The continuous decline of sequence cost, establishes individual tracking tracing technology and cultivar identification skill based on DNA marker or whole genome sequence
Art is possibly realized.
Jiang Shumin is one of excellent local pig breed resource in China, has resistance to crude feed, early sexual maturity, reproductive capacity height, color and luster
Red gorgeous, fresh and tender succulence, osteoderm ratio is relatively low, mouthfeel is relatively good.Duroc is one of large-scale pig kind, the U.S. is originated in, in China
In pig breeding market, Duroc is one of main male parent varieties in cross combination, to produce commodity lean meat pig.It is currently based on
Differentiate that the method for ginger Qu Haiyu duroc kinds is still not perfect on molecular level in the method in SNPs sites.
Chinese patent CN106520943A disclose it is a kind of with plus be the relevant SNP site of the Duroc thickness of backfat and its should
With being to be on an intragenic SNP of CACNA1E on No. 9 chromosomes of pig, the SNP site of the CACNA1E genes
ALGA0055091 (G/A), the individual which is AA have thinner back fat than the individual of GG type, on this basis,
ALGA0055091 can be used as a SNP marker, by the selection to genotype, can accelerate pair plus be the Duroc thickness of backfat
Selection, while accelerate improve plus be Duroc lean meat percentage genetic progress.
Chinese patent CN105603089A discloses one group and is used to differentiate the SNP marker of pig kind, mainly using purebred big
In vain, long white totally 200 individuals carry out full-length genome SNP 60K chips as research object to whole samples of above-mentioned 2 kinds
Type is sentenced in scanning；After carrying out Quality Control on request to all data, filter out and can be used for differentiating long white, the SNP marker site of great Bai,
By whole-genome association filter out 16 SNP sites be used for it is long in vain and Large White discriminating；Additionally by principal component point
Analysis and cluster analysis are verified that the rate of accuracy reached of 16 SNP sites shows to invent to 99% in other 500 individuals
16 SNP sites can be used for great Bai and long white discriminating.
Chinese patent CN106566887A discloses one group and is used to differentiate plus is Duroc, the SNP site of platform system Duroc,
These SNP sites are located at respectively：On SSC1,2,5,7,9,12,14,23, SNP titles are respectively：H3GA0021245、
ASGA0033017、ALGA0075620、ALGA0075780、INRA0025222、H3GA0006033、ASGA0024360、
ASGA0011065、ASGA0042109、ASGA0090983、ALGA0016497、M1GA0016745、ASGA0089906、
ALGA0040895、ALGA0075815、ALGA0099582、ALGA0066519、ALGA0075754、ALGA0075715、
SIRI0001491 amounts to 20 SNP sites.20 SNP sites of invention can be used in differentiating plus be Duroc, platform system Du Luo
Gram.
The content of the invention
It is an object of the present invention to overcome the above-mentioned drawbacks of the prior art and provide one kind based on SNP site mirror
Other Jiang Shumin, the method for Landrace.
The present invention is using Jiang Shumin, the full-length genome 60K information of Landrace, by whole-genome association, screening
Finally pick out 20 SNP sites that can be used for Jiang Shumin, Landrace to differentiate.
The purpose of the present invention can be achieved through the following technical solutions：
A kind of method for differentiating Jiang Shumin, Landrace based on SNP site, using Jiang Shumin, Landrace SSC, (pig contaminates
Colour solid, Sus scrofa chromosome) difference of SNP site on 1, Jiang Shumin, Landrace are differentiated, SNP titles
Respectively：MARC0039661、INRA0001043、DRGA0000202、INRA0003745、INRA0003746、
INRA0004022、CASI0011475、INRA0004282、DRGA0001542、INRA0004305、INRA0004312、
INRA0004460、M1GA0001181、ALGA0010213、H3GA0004837、DRGA0002521、H3GA0004881、
ASGA0095244, MARC0028771, ALGA0013070, amount to 20 SNP sites.
The difference of SNP site on Jiang Shumin, Landrace SSC1, is specially：
The A of the MARC0039661 positions or T of C, INRA0001043 position or the G or T of C, DRGA0000202 position,
The A of the INRA0003745 positions or T of G, INRA0003746 position or the A or G, CASI0011475 of C, INRA0004022 position
The T or C of the A of position or the G or A, INRA0004305 position of the T of C, INRA0004282 position or C, DRGA0001542 position,
The G of the INRA0004312 positions or T of A, INRA0004460 position or the T or C, ALGA0010213 of C, M1GA0001181 position
The T or C of the C of position or the T or C, H3GA0004881 position of the G of A, H3GA0004837 position or T, DRGA0002521 position,
The T of the ASGA0095244 positions or G of C, MARC0028771 position or the T or C of A, ALGA0013070 position, amount to 20 SNP
Site.
The positional information of this 20 SNP sites such as table 1 below.
The position of 1 20 SNP sites of table on chromosome
More than 10 have difference in 20 SNP sites, then can identify Jiang Shumin, Landrace.
SNP site method known to discriminating, can design corresponding primer for one section of gene order where the site,
Again by the method for quantitative fluorescent PCR, the fragment is expanded, then determine to be somebody's turn to do by amplification (wave crest of different bases is different)
SNP site, can use conventional biology techniques means.
SNP titles be respectively MARC0039661, INRA0001043, DRGA0000202, INRA0003745,
INRA0003746、INRA0004022、CASI0011475、INRA0004282、DRGA0001542、INRA0004305、
INRA0004312、INRA0004460、M1GA0001181、ALGA0010213、H3GA0004837、DRGA0002521、
The SNP site of H3GA0004881, ASGA0095244, MARC0028771, ALGA0013070, the primer sequence of corresponding design is such as
Under：
Landrace and Jiang Shumin are carried out using The R Project for Statistical Computing it is main into
Analysis, wherein abscissa represents principal component 1, and ordinate represents principal component 2, and principal component 1 represents same respectively with principal component 2
The point of the different genotype of SNP site, wherein abscissa more than 0 is Landrace colony, and point of the abscissa less than 0 is ginger Qu Haiqun
Body.
Compared with prior art, the present invention by select 20 SNP sites, by the measure to SNP site it is marked down,
Fast, easily differentiate Jiang Shumin, Landrace.
Brief description of the drawings
Fig. 1 is Jiang Shumin, Landrace composition analysis result is shown.
X-axis：1 Y-axis of principal component：Principal component 2
Embodiment
The present invention is described in detail with specific embodiment below in conjunction with the accompanying drawings.
Embodiment
The present invention is using Jiang Shumin, Landrace as research material, using Illumina 60K SNP chips to these pigs
Body carries out full-length genome Genotyping, analyzes and filters out and as few as possible can be used in Jiang Shumin, the SNP of Landrace identification
Mark combination.
Test swinery：The material that the present invention uses is from 20 Landrace individuals, 11 Jiang Shumin individuals.
Pig full-length genome 60K SNP genotype detections：A fritter ear tissue sample is gathered from each individual in above-mentioned colony,
Genomic DNA is extracted with standard phenol chloroform method, DNA is dissolved in TE buffer solutions.With Nanodrop-1000 nucleic acid-proteins point
Analyzer carries out quality testing and concentration mensuration to the DNA extracted, and A260/280 ratios are in 1.8-2.0, A260/230 ratios
It is determined as qualification in 1.7-1.9.Qualified DNA sample is uniformly diluted to 50ng/ μ L, utilizes Illumina Infinium SNP
Parting platform, orders Porcine SNP60DNA Analysis Kit chips, is said according to the use of Illumina Infinium
Bright and normal process carries out chip hybridization and is scanned with result, and genotype data is read by GenomeStudio softwares.Use PLINK
V1.07 carries out quality control to the genotype data of acquisition, rejects recall rate ＜ 99.7%, secondary gene frequency (minor
Allele frequency, MAF) ＜ 0.01 or deviate Hardy Weinberg equilibrium (Hardy-Weinberg Equilibrium,
HWE)P≤10-6SNP marker, exclude recall rate ＜ 90%, family Mendel error rate be higher than 0.1 individual, finally have 620
A SNP and 31 individual is used for data analysis.
Full-length genome association (GWAS) analysis, carries out Case-Control using plink softwares to Jiang Shumin, Landrace
Analysis, Landrace Case, Jiang Shumin Control.Determine to deposit in Jiang Shumin, Landrace using Bonferroni methods
In the SNP site of significant difference, genomic level remarkable threshold is 0.05 divided by effective SNP site quantity, i.e., and 0.05/48165
=1.04e-6；GWAS is the results show that the SNP site of top20 is located at respectively：On SSC (pig chromosome) 1, for Jiang Shumin, length
The discriminating of white pig.Genotype distribution of 20 SNP sites in Jiang Shumin, Landrace is as shown in table 2.The representative ginger of J beginnings
The representative length of Qu Hai, L beginning is white.By taking SNP site MARC0039661 as an example, the ratio of CC is very high in long white individual, and in ginger
The ratio highest of AA in Qu Hai colonies.Each SNP site is different in the main genotypes of Landrace and Jiang Shumin, therefore
By the combination of 20 points, can achieve the purpose that to distinguish Jiang Shumin and Landrace.
2 20 SNP of table genotype situations in Jiang Shumin, Landrace
In order to examine 20 SNP sites to differentiate the accuracy of Jiang Shumin, Landrace, the present invention is with this 20 SNP
O'clock verified in 20 long white, 11 Jiang Qu seas individuals.Mainly use R software (full name：The R Project for
Statistical Computing) principal component analysis is carried out to Landrace and Jiang Shumin, with reference to statistical principal component analysis
Method, and practical problem, principal component 1 and principal component 2 represent the different genotype of same SNP site respectively.
The present embodiment uses Principal Component Analysis, Principal Component Analysis be intended to investigate in statistics it is related between multiple variables
A kind of multivariate statistical method of property.How research discloses the internal structure between multiple variables by a few principal component, i.e.,
A few principal component is exported from original variable, them is retained the information of original variable as much as possible, and it is mutual to each other
It is uncorrelated.Processing usually mathematically is exactly that original P index is made linear combination, as new overall target.Classical way
For：Represented with the variance of F1 (first linear combination of selection, i.e. first overall target), i.e. Var (F1) is bigger, represents
The F1 chosen in all linear combination should be variance maximum, therefore F1 is referred to as first principal component.If first principal component
It is not enough to represent the information of original P index, considers further that choosing F2 selects second linear combination, it is original in order to effectively reflect
Information, the existing information of F1 avoid the need for appearing in F2 again, are exactly to require Cov (F1, F2)=0 with mathematical linguistics expression, then
Be Second principal component, into F2, and so on can construct the three, the 4th ..., the P principal component, each point generation in figure
The information of 1 pig of table, 20 SNP.
The results are shown in Figure 1, can be learnt by Fig. 1：20 SNP sites can separate Jiang Shumin, Landrace.Figure
In, each point represents the information of this 20 SNP sites of 1 pig, these points differentiated by whole-genome association
Information, wherein point of the abscissa more than 0 be Chang Bai colonies, and the point that abscissa is less than 0 is Jiang Quhai.Verification result shows to pass through
20 SNP sites that whole-genome association differentiates can be used for the discriminating of Jiang Shumin, Landrace.
The above-mentioned description to embodiment is understood that for ease of those skilled in the art and using invention.
Person skilled in the art obviously easily can make these embodiments various modifications, and described herein general
Principle is applied in other embodiment without by performing creative labour.Therefore, the invention is not restricted to above-described embodiment, ability
Field technique personnel disclose according to the present invention, do not depart from improvement that scope made and modification all should be the present invention's
Within protection domain.
Claims (6)
- A kind of 1. method for differentiating Jiang Shumin, Landrace based on SNP site, it is characterised in that utilize Jiang Shumin, Landrace The difference of the upper SNP sites of SSC1, differentiates Jiang Shumin, Landrace, and SNP titles are respectively：MARC0039661、 INRA0001043、DRGA0000202、INRA0003745、INRA0003746、INRA0004022、CASI0011475、 INRA0004282、DRGA0001542、INRA0004305、INRA0004312、INRA0004460、M1GA0001181、 ALGA0010213、H3GA0004837、DRGA0002521、H3GA0004881、ASGA0095244、MARC0028771、 ALGA0013070, amounts to 20 SNP sites.
- A kind of 2. method for differentiating Jiang Shumin, Landrace based on SNP site according to claim 1, it is characterised in that The difference of SNP site on Jiang Shumin, Landrace SSC1, is specially：The A of the MARC0039661 positions or T of C, INRA0001043 position or the G or T of C, DRGA0000202 position, The A of the INRA0003745 positions or T of G, INRA0003746 position or the A or G, CASI0011475 of C, INRA0004022 position The T or C of the A of position or the G or A, INRA0004305 position of the T of C, INRA0004282 position or C, DRGA0001542 position, The G of the INRA0004312 positions or T of A, INRA0004460 position or the T or C, ALGA0010213 of C, M1GA0001181 position The T or C of the C of position or the T or C, H3GA0004881 position of the G of A, H3GA0004837 position or T, DRGA0002521 position, The T of the ASGA0095244 positions or G of C, MARC0028771 position or the T or C of A, ALGA0013070 position, amount to 20 SNP Site.
- A kind of 3. method for differentiating Jiang Shumin, Landrace based on SNP site according to claim 1, it is characterised in that More than 10 have difference in 20 SNP sites, then can identify Jiang Shumin, Landrace.
- A kind of 4. method for differentiating Jiang Shumin, Landrace based on SNP site according to claim 1, it is characterised in that SNP site method is known to discriminating：Corresponding primer is designed for one section of gene order where the site, then passes through fluorescence The method of quantitative PCR, expands the fragment, then determines the SNP site by amplification.
- A kind of 5. method for differentiating Jiang Shumin, Landrace based on SNP site according to claim 4, it is characterised in that SNP titles be respectively MARC0039661, INRA0001043, DRGA0000202, INRA0003745, INRA0003746, INRA0004022、CASI0011475、INRA0004282、DRGA0001542、INRA0004305、INRA0004312、 INRA0004460、M1GA0001181、ALGA0010213、H3GA0004837、DRGA0002521、H3GA0004881、 The SNP site of ASGA0095244, MARC0028771, ALGA0013070, the primer sequence of corresponding design are as follows：
- A kind of 6. method for differentiating Jiang Shumin, Landrace based on SNP site according to claim 1, it is characterised in that Principal component analysis is carried out to Landrace and Jiang Shumin using The R Project for Statistical Computing, Wherein abscissa represents principal component 1, and ordinate represents principal component 2, and principal component 1 represents same SNP site respectively with principal component 2 Different genotype, wherein point of the abscissa more than 0 be Chang Bai colonies, and the point that abscissa is less than 0 is Jiang Qu seas colony.
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2017
- 2017-12-26 CN CN201711433725.XA patent/CN107988391A/en active Pending
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| CN101828539A (en) * | 2010-05-19 | 2010-09-15 | 扬州大学 | Method for breeding Sujiang pig variety |
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