CN108130375A - A kind of method for differentiating Jinhua Pigs, Landrace based on SNP site - Google Patents
A kind of method for differentiating Jinhua Pigs, Landrace based on SNP site Download PDFInfo
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Abstract
The present invention relates to a kind of methods for differentiating Jinhua Pigs, Landrace based on SNP site, using the difference of SNP site on Jinhua Pigs, Landrace SSC1, Jinhua Pigs, Landrace are differentiated, SNP titles are respectively：MARC0039661, ASGA0001510, INRA0001043, DRGA0000202, MARC0041365, DRGA0000334, INRA0003745, INRA0003746, INRA0004022, CASI0011475, INRA0004282, DRGA0001542, DRGA0001542, INRA0004305, INRA0004312, ALGA0006239, INRA0004460, MARC0046211, MARC0036323, M1GA0001181, altogether 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 Jinhua Pigs, Landrace.
Description
Technical field
The present invention relates to animal molecular biotechnology and Animal Genetics fields, and SNP are based on more particularly, to one kind
The method that point differentiates Jinhua Pigs, 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 is resourceful and with their own characteristics, is
Precious resources in world's pig kind gene pool.But so far, for the combination of the SNP marker of cultivar identification and individual identification
SNP marker combination is also seldom.
With the application of pig high density SNP chip, the universal and development of genome sequencing technology and Genotyping, survey
Individual tracking tracing technology and cultivar identification skill based on DNA marker or whole genome sequence are established in the continuous decline of sequence cost
Art is possibly realized.
Jinhua Pigs, Landrace be the pig raising practitioner in China to the address from different regions Landrace, Jinhua Pigs have
Ripe early, meat is good, the excellent performances such as breeding potential height.Because its back leg thin skin bone is thin, delicious meat, fat content is high between meat, is
The optimum feed stock of cured ham.In western pig breeds, Large White is referred to as " omnipotent pig kind ".Some boar dorsal muscles and rear quarters muscle are non-
Chang Fada is had a preference for, and there is the address of double-muscling pig in the country.
Chinese patent CN106520943A disclose it is a kind of with plus be the relevant SNP site of the long white thickness of backfat and its application,
It is the intragenic SNP of CACNA1E being located on No. 9 chromosomes of pig about one, the SNP site of the CACNA1E genes is
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 long white thickness of backfat
Selection, while accelerate to improve plus be the genetic progress of long white lean meat percentage.
Chinese patent CN105603089A discloses one group for differentiating 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 as required to all data, filter out and can be used for differentiating long white, great Bai SNP marker site,
By whole-genome association filter out 16 SNP sites for it is long in vain and the discriminating of Large White；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 disclose one group for differentiate plus be it is long in vain, the white SNP site of platform system head, these
SNP site is 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 that length is white, platform system head is white.
Invention content
The purpose of the present invention is just to provide for a kind of method for differentiating Jinhua Pigs, Landrace based on SNP site.
The present invention by whole-genome association, is screened most using the full-length genome 60K information of Jinhua Pigs, Landrace
20 SNP sites that Jinhua Pigs, Landrace can be used for differentiate are picked out afterwards.
The purpose of the present invention can be achieved through the following technical solutions：
A kind of method for differentiating Jinhua Pigs, Landrace based on SNP site, using Jinhua Pigs, Landrace SSC, ((pig is dyed
Body, Sus scrofa chromosome)) difference of SNP site on 1, Jinhua Pigs, Landrace are differentiated, SNP titles point
It is not：MARC0039661、ASGA0001510、INRA0001043、DRGA0000202、MARC0041365、DRGA0000334、
INRA0003745、INRA0003746、INRA0004022、CASI0011475、INRA0004282、DRGA0001542、
DRGA0001542、INRA0004305、INRA0004312、ALGA0006239、INRA0004460、MARC0046211、
MARC0036323, M1GA0001181, altogether 20 SNP sites.
The difference of SNP site on Jinhua Pigs, Landrace SSC1, specially：
The C of the MARC0039661 positions or A of A, ASGA0001510 position or the C or T of G, INRA0001043 position,
The G of the DRGA0000202 positions or G of T, MARC0041365 position or the T or C, INRA0003745 of A, DRGA0000334 position
The C or A of the G of position or the A or G, CASI0011475 position of the C of A, INRA0003746 position or T, INRA0004022 position,
The T of the INRA0004282 positions or G of C, DRGA0001542 position or the G or A, INRA0004305 of A, DRGA0001542 position
The T or C of the T of position or the G or T, INRA0004460 position of the G of C, INRA0004312 position or A, ALGA0006239 position,
The G of the MARC0046211 positions or A of A, MARC0036323 position or the T or C of C, M1GA0001181 position.
The location information of this 20 SNP sites such as following table.
Table 1:The position of 20 SNP sites on chromosome
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 segment is expanded, then determine to be somebody's turn to do by amplification (wave crest of different bases is different)
Conventional biology techniques means may be used in SNP site.The primer sequence of design is corresponded to for this 20 SNP sites below：
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 Jinhua Pigs, Landrace.
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
Specific embodiment
The present invention is described in detail with specific embodiment below in conjunction with the accompanying drawings.
The present invention is using Jinhua Pigs, Landrace as research material, using Illumina 60K SNP chips to these pigs individual
Carry out full-length genome Genotyping, analyze and filter out it is as few as possible can be used in Jinhua Pigs, Landrace identification SNP marker
Combination.
Test swinery：The material that the present invention uses is from 20 long white individual, 17 Jinhua Pigs individuals.
Pig full-length genome 60K SNP genotype detections：A fritter ear tissue sample is acquired from each individual in above-mentioned group,
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 is ordered 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%th, 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%th, family Mendel error rate is higher than 0.1 individual, finally there is 740
SNP and 37 individual is used for data analysis.
Full-length genome association (GWAS) analysis carries out Case-Control using plink softwares to Jinhua Pigs and Landrace
Analysis, Landrace Case, Jinhua Pigs Control.Determine exist in Jinhua Pigs, Landrace pig using Bonferroni methods
The SNP site of significant difference, genomic level remarkable threshold is 0.05 divided by effective SNP site quantity, i.e. 0.05/740=
6.75e-5；GWAS is the results show that the SNP site of top20 is located at respectively：On SSC1 (pig chromosome), for Jinhua Pigs, Landrace
Discriminating.Genotype distribution of 20 SNP sites in Jinhua Pigs, Landrace is as shown in table 2.The representative Jinhua Pigs of JH beginnings, L
The representative Landrace of beginning.
By taking SNP site INRA0001043 as an example, the ratio of TT is very high in Jinhua Pigs individual, and the CC in Chang Bai groups
Ratio highest.Each SNP site is different in the main genotypes of Jinhua Pigs and Landrace, therefore passes through the group of 20 points
It closes, can achieve the purpose that distinguish Jinhua Pigs and Landrace.
2 20 SNP of table are in Jinhua Pigs and long white middle genotype situation
Principal component analysis：
In order to which 20 SNP sites is examined to differentiate the accuracy of Jinhua Pigs, Landrace, this 20 SNP sites of the invention
It is verified in 20 long white, 17 Jinhua Pigs individuals.Mainly use the soft (full name of R：The R Project for
Statistical Computing) principal component analysis is carried out to long white and Jinhua Pigs, with reference to statistical Principal Component Analysis,
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 made to retain the information of original variable as much as possible, and to each other mutually
It is uncorrelated.Processing usually mathematically is exactly that original P index is made linear combination, as new overall target.Classical way
For：It is 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 are exactly to require Cov (F1, F2)=0 with mathematical linguistics expression, then there is no need to appear in F2 again
Be Second principal component, into F2, and so on can construct third, the the 4th ... ..., the P principal component is each put in figure and represents 1
The information of 20 SNP of head pig.
The results are shown in Figure 1, can be learnt by Fig. 1：20 SNP sites can separate Jinhua Pigs, Landrace.Figure
In, each point represents the information of this 20 SNP sites of 1 pig, these points differentiated by whole-genome association
Information, for point of the abscissa more than 0 for Chang Bai groups, point of the abscissa less than 0 is Jinhua pig groups.Verification result shows to lead to
Cross the discriminating that 20 SNP sites that whole-genome association differentiates can be used for Jinhua Pigs, Landrace.
Above-mentioned is to be intended to facilitate those of ordinary skill in the art to understand and use hair to the description of embodiment
It is bright.Person skilled in the art obviously easily can make various modifications, and described herein to these embodiments
General Principle is applied in other embodiment without having to go through creative labor.Therefore, the present invention is not limited to above-described embodiment,
Those skilled in the art's announcement according to the present invention, improvement and modification made without departing from the scope of the present invention all should be in this hairs
Within bright protection domain.
Claims (6)
1. a kind of method for differentiating Jinhua Pigs, Landrace based on SNP site, utilizes SNP site on Jinhua Pigs, Landrace SSC1
Difference differentiates Jinhua Pigs, Landrace SNP titles are respectively：MARC0039661、ASGA0001510、
INRA0001043、DRGA0000202、MARC0041365、DRGA0000334、INRA0003745、INRA0003746、
INRA0004022、CASI0011475、INRA0004282、DRGA0001542、DRGA0001542、INRA0004305、
INRA0004312, ALGA0006239, INRA0004460, MARC0046211, MARC0036323, M1GA0001181, altogether
20 SNP sites.
2. the method according to claim 1 for differentiating Jinhua Pigs, Landrace based on SNP site, which is characterized in that Jinhua
The difference of SNP site on pig, Landrace SSC1, specially：
The C of the MARC0039661 positions or A of A, ASGA0001510 position or the C or T of G, INRA0001043 position,
The G of the DRGA0000202 positions or G of T, MARC0041365 position or the T or C, INRA0003745 of A, DRGA0000334 position
The C or A of the G of position or the A or G, CASI0011475 position of the C of A, INRA0003746 position or T, INRA0004022 position,
The T of the INRA0004282 positions or G of C, DRGA0001542 position or the G or A, INRA0004305 of A, DRGA0001542 position
The T or C of the T of position or the G or T, INRA0004460 position of the G of C, INRA0004312 position or A, ALGA0006239 position,
The G of the MARC0046211 positions or A of A, MARC0036323 position or the T or C of C, M1GA0001181 position.
3. the method according to claim 1 for differentiating Jinhua Pigs, Landrace based on SNP site, which is characterized in that 20
10 or more have difference in SNP site, then can identify Jinhua Pigs, Landrace.
4. the method according to claim 1 for differentiating Jinhua Pigs, Landrace based on SNP site, which is characterized in that differentiate
The SNP site method known is：Corresponding primer is designed, then pass through fluorescent quantitation for one section of gene order where the site
The method of PCR expands the segment, then determines the SNP site by amplification.
5. the method according to claim 4 for differentiating Jinhua Pigs, Landrace based on SNP site, which is characterized in that SNP
Title is respectively：MARC0039661、ASGA0001510、INRA0001043、DRGA0000202、MARC0041365、
DRGA0000334、INRA0003745、INRA0003746、INRA0004022、CASI0011475、INRA0004282、
DRGA0001542、DRGA0001542、INRA0004305、INRA0004312、ALGA0006239、INRA0004460、
The SNP site of MARC0046211, MARC0036323, M1GA0001181, the primer sequence of corresponding design are as follows：
6. the method according to claim 1 for differentiating Jinhua Pigs, Landrace based on SNP site, which is characterized in that use
The R Project for Statistical Computing carry out principal component analysis to long white and Jinhua Pigs, wherein horizontal seat
Mark represents principal component 1, and ordinate represents principal component 2, and principal component 1 represents the different bases of same SNP site from principal component 2 respectively
Because of type, point of the abscissa more than 0 is Landrace group, and point of the abscissa less than 0 is Jinhua pig groups.
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Citations (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN102816837A (en) * | 2012-05-23 | 2012-12-12 | 中国农业大学 | Method for identifying Chinese and foreign pig breeds |
| CN104293963A (en) * | 2014-10-21 | 2015-01-21 | 中国农业科学院北京畜牧兽医研究所 | Method for identifying inbred line of Gottingen strain by use of 145 SNPs |
| CN105603089A (en) * | 2016-02-03 | 2016-05-25 | 漳州傲农现代农业开发有限公司 | SNP (single-nucleotide polymorphism) marker set for identifying pig breeds and application thereof |
| CN105256035B (en) * | 2015-10-26 | 2018-08-10 | 浙江省农业科学院 | Molecular labeling for differentiating Jinhua both ends crow and duroc genetic background and its application |
-
2017
- 2017-12-04 CN CN201711260611.XA patent/CN108130375A/en active Pending
Patent Citations (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN102816837A (en) * | 2012-05-23 | 2012-12-12 | 中国农业大学 | Method for identifying Chinese and foreign pig breeds |
| CN104293963A (en) * | 2014-10-21 | 2015-01-21 | 中国农业科学院北京畜牧兽医研究所 | Method for identifying inbred line of Gottingen strain by use of 145 SNPs |
| CN105256035B (en) * | 2015-10-26 | 2018-08-10 | 浙江省农业科学院 | Molecular labeling for differentiating Jinhua both ends crow and duroc genetic background and its application |
| CN105603089A (en) * | 2016-02-03 | 2016-05-25 | 漳州傲农现代农业开发有限公司 | SNP (single-nucleotide polymorphism) marker set for identifying pig breeds and application thereof |
Non-Patent Citations (1)
| Title |
|---|
| HUASHUI AI等: "Genetic diversity, linkage disequilibrium and selection signatures in Chinese and Western pigs revealed by genome-wide SNP markers", 《PLOS ONE》 * |
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Application publication date: 20180608 |