CN106566887A - Group of SNP sites used for identifying Canada Duroc and Taiwan Duroc - Google Patents
Group of SNP sites used for identifying Canada Duroc and Taiwan Duroc Download PDFInfo
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- CN106566887A CN106566887A CN201610974894.3A CN201610974894A CN106566887A CN 106566887 A CN106566887 A CN 106566887A CN 201610974894 A CN201610974894 A CN 201610974894A CN 106566887 A CN106566887 A CN 106566887A
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Abstract
The invention discloses a group of SNP sites used for identifying Canada Duroc and Taiwan Duroc. The SNP sites are located at SSC1, 2, 5, 7, 9, 12, 14 and 23. The SNP names of the 20 SNP sites are H3GA0021245, ASGA0033017, ALGA0075620, ALGA0075780, INRA0025222, H3GA0006033, ASGA0024360, ASGA0011065, ASGA0042109, ASGA0090983, ALGA0016497, M1GA0016745, ASGA0089906, ALGA0040895, ALGA0075815, ALGA0099582, ALGA0066519, ALGA0075754, ALGA0075715, and SIRI0001491 respectively. The 20 SNP sites can be used for identifying the Canada Duroc and the Taiwan Duroc.
Description
Technical field
The present invention relates to animal molecular biotechnology and Animal Genetics field, to the effect that develop a set of molecule mark
Remember for plus be the discriminating of Duroc, platform system Duroc.
Background technology
China is one of earliest country of raising pigs in the world, history for thousand of years, pig China be described as six domestic animals it
It is first.Due to the impact of natural environment, economic condition and folk culture, where China, pig resources are abundant and differ from one another, and are
Precious resources in world's pig kind gene bank.But so far, the SNP marker for cultivar identification is combined and individual identification
SNP marker combination is also little.
With application, the popularization of genome sequencing technology and the development of pig high density SNP chip, and gene type, survey
The continuous decline of sequence cost, sets up and follows the trail of tracing technology and cultivar identification skill based on DNA marker or the individual of whole genome sequence
Art is possibly realized.
Plus be Duroc, platform system Duroc be the pig practitioner of China to the address from different regions Duroc, plus
It is that Duroc shows the Duroc from Canada, then from Taiwan, the Duroc of each strain has respective to platform system Duroc
Feature, such as plus be that Duroc more focuses on growth rate, meat.Platform system Duroc more focuses on build, with double flesh buttockss is
Main feature.But on market most of pig practitioner be difficult to judge this Duroc be on earth platform system or plus be, mainly
It is to learn it is what strain from buyer there.
The content of the invention
It is an object of the invention to provide a kind of cheap, quickly, the molecular engineering of aspect is used to differentiate platform system Duroc, adds
It is Duroc.
Applicant utilizes plus is the full-length genome 60K information of Duroc, platform system Duroc, through full-length genome association point
It is Duroc, the SNP site of platform system Duroc discriminating that analysis, screening finally pick out 20 to can be used to add.
The technical scheme that the present invention is provided is as follows：
The present invention provides one group and can be used to differentiate that it is Duroc, the SNP site of platform system Duroc to add.These SNP sites point
It is not located at：On SSC (pig chromosome, Sus scrofa chromosome) 1,2,5,7,9,12,14,23, SNP site is respectively：
H3GA0021245、ASGA0033017、ALGA0075620、ALGA0075780、INRA0025222、H3GA0006033、
ASGA0024360、ASGA0011065、ASGA0042109、ASGA0090983、ALGA0016497、M1GA0016745、
ASGA0089906、ALGA0040895、ALGA0075815、ALGA0099582、ALGA0066519、ALGA0075754、
ALGA0075715, SIRI0001491 amount to 20 SNP sites.The positional information of this 20 SNP sites such as following table.
Table 1:20 SNP sites position on chromosome.
Wherein, SNP is respectively：The A of H3GA0021245 positions or the A or C of C, ASGA0033017 position,
The C of ALGA0075620 positions or the A or G, H3GA0006033 of the A of A, ALGA0075780 position or G, INRA0025222 position
The G or A of the G or A, ASGA0042109 position of the A of position or the G of G, ASGA0024360 position or A, ASGA0011065 position,
The G of ASGA0090983 positions or the G or A, ASGA0089906 of the G of A, ALGA0016497 position or A, M1GA0016745 position
The G or A of the G or A, ALGA0099582 position of the G of position or the G of A, ALGA0040895 position or A, ALGA0075815 position,
The G of ALGA0066519 positions or the G or A, SIRI0001491 of the G of A, ALGA0075754 position or A, ALGA0075715 position
The A or C of position amounts to 20 SNP sites.
20 SNP sites of the present invention can be used in differentiating that it is Duroc, platform system Duroc to add.
Description of the drawings
Fig. 1 is Duroc, the Duroc composition analysis result displaying of platform system to add.
X-axis：1 Y-axis of main constituent：Main constituent 2；
Specific embodiment
With reference to embodiment and compare accompanying drawing the present invention is described in further detail.
The present invention with plus be Duroc, platform system Duroc as research material, using Illumina 60K SNP chips to this
A little Duroc individualities carry out full-length genome gene type, analyze and filter out and as few as possible can be used in plus be Duroc, platform
It is the SNP marker combination of Duroc identification.
Experiment swinery：It is Duroc individuality, 18 caster bed system Durocs individualities that the material that the present invention is used adds from 94.
Pig full-length genome 60K SNP genotype detection：Each individuality one fritter ear tissue sample of collection from above-mentioned colony,
Genomic DNA is extracted with standard phenol chloroform method, DNA is dissolved in TE buffer.
Standard phenol-chloroform method extracts complete genome DNA, and which comprises the following steps that：
1st, ear sample is shredded, is put in 1.5mlEP pipes, add 350ul lysates, 20ul E.C. 3.4.21.64s and 0.9ul
RNaseA, mixes.
2nd, in hot couveuse, 55 DEG C overnight.(just having started to rock once every 30min)
3rd, EP pipes are taken out, equal-volume Tris balance phenol is added, is firmly rocked 3min；12000g, is centrifuged 10 minutes.
4th, gentle aspiration supernatant is into a new 1.5mlEP pipes.
5th, equal-volume phenol/chloroform is added in supernatant, firmly rock 2 minutes；12000g, is centrifuged 2 minutes.
6th, supernatant is drawn into another new 1.5mlEP pipes, add the sodium acetate solution and 2.5 times of volumes of 1/10 volume
Dehydrated alcohol, shakes up.
7th, 12000g, is centrifuged 1 minute, absorbs upper strata ethanol as far as possible.
8th, 1ml, 70% ethanol rinse DNA are added, is firmly shaken up, to remove the SDS and phenol of residual；
9th, 12000g, is centrifuged 1 minute, removes ethanol.
10th, EP pipes are upside down in absorbent paper, to blot ethanol.(9,10 can be repeated once)
11st, with the aseptic ddH2O of 65 DEG C of preheatings, 35ul dissolving DNAs, -20 DEG C of preservations.
Quality testing and concentration mensuration are carried out to the DNA for extracting with Nanodrop-1000 nucleic acid-proteins analyser,
In 1.8-2.0, it is qualified that A260/230 ratios are judged to A260/280 ratios in 1.7-1.9.Qualified DNA sample unification is diluted to
50ng/ μ L, using Illumina Infinium SNP typing platforms, order Porcine SNP60DNA Analysis Kit cores
Piece, is carried out chip hybridization according to the operation instruction and normal process of Illumina Infinium and is scanned with result, passed through
GenomeStudio softwares read genotype data.Quality control is carried out to the genotype data for obtaining with PLINK v1.07, is picked
Except recall rate<99.7%th, secondary gene frequency (minor allele frequency, MAF)<0.01 deviates Hardy's Wenbo
Lattice balance (Hardy-Weinberg Equilibrium, HWE) P≤10-6SNP marker, exclude recall rate<90%th, family Meng
Individuality of the Dare error rate higher than 0.1, finally has 48165 SNP and 112 individualities for data analysiss.
Full-length genome association (GWAS) analysis, using plink softwares to plus be that Duroc and platform system Duroc carry out Case-
Control is analyzed, plus is that Duroc is Case, and platform system Duroc is Control.Determine that adding be Du using Bonferroni methods
There is the SNP site of significant difference in Luo Ke, Taiwan Duroc pigs, genomic level remarkable threshold is 0.05 divided by effective SNP
Bit number of points, i.e. 0.05/48165=1.04e-6；GWAS results show that the SNP site of top20 is located at respectively：SSC (dye by pig
Body) on 1,2,5,7,9,12,13,14,23, for plus be Duroc, Taiwan Duroc pigs discriminating.20 SNP sites are adding
Be Duroc, the genotype distribution in platform system Duroc it is as shown in table 1.It is Duroc that the representative of J beginnings adds, the representative of T beginnings
Platform system Duroc.With SNP site：As a example by H3GA0021245, plus be AA in Duroc individuality ratio it is very high, and in platform system
The ratio highest of CC in Duroc colony.Each SNP site plus be Duroc and platform system Duroc main genotypes not
Equally, therefore by the combination of 20 points, the purpose for distinguishing plus be Duroc and platform system Duroc can just be reached.
Principal component analysiss：
In order to check 20 SNP sites to differentiate plus be the accuracy of Duroc, platform system Duroc, we are with this 20
SNP site is at 94 plus is Duroc, verified in 18 caster bed system Durocs individualities.Mainly soft using R is Du Luo to adding
Gram and platform system Duroc carry out principal component analysiss (Fig. 1) and can be learnt by figure：20 SNP sites can be Duroc, platform by adding
It is that Duroc is separated.Wherein point of the abscissa more than 0 is Duroc colony to add, and point of the abscissa less than 0 is platform system Du Luo
Gram colony.It is Duroc, platform that the result shows that 20 SNP sites differentiated by whole-genome association can be used to add
It is the discriminating of Duroc.
1,20 SNP of table plus genotype situation in being Duroc and platform system Duroc.
Claims (3)
1. one group is used to differentiating plus is Duroc, the SNP site of platform system Duroc, and these SNP sites are located at respectively：SSC1、2、
5th, on 7,9,12,14,23, SNP site is respectively：H3GA0021245、ASGA0033017、ALGA0075620、
ALGA0075780、INRA0025222、H3GA0006033、ASGA0024360、ASGA0011065、ASGA0042109、
ASGA0090983、ALGA0016497、M1GA0016745、ASGA0089906、ALGA0040895、ALGA0075815、
ALGA0099582, ALGA0066519, ALGA0075754, ALGA0075715, SIRI0001491 amount to 20 SNP sites.
2. one group as claimed in claim 1 is used to differentiating plus is Duroc, the SNP site of platform system Duroc, and SNP is respectively：
The C or A of the A of H3GA0021245 positions or the A of C, ASGA0033017 position or C, ALGA0075620 position,
The A of ALGA0075780 positions or the A or G, ASGA0024360 of the A of G, INRA0025222 position or G, H3GA0006033 position
The G or A of the G or A, ASGA0090983 position of the G of position or the G of A, ASGA0011065 position or A, ASGA0042109 position,
The G of ALGA0016497 positions or the G or A, ALGA0040895 of the G of A, M1GA0016745 position or A, ASGA0089906 position
The G or A of the G or A, ALGA0066519 position of the G of position or the G of A, ALGA0075815 position or A, ALGA0099582 position,
The A or C of the G of ALGA0075754 positions or the G of A, ALGA0075715 position or A, SIRI0001491 position amounts to 20 SNP
Site.
3. the application of one group of SNP site as claimed in claim 1 or 2, which is used to differentiate plus is Duroc, platform system Duroc.
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Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN107988391A (en) * | 2017-12-26 | 2018-05-04 | 福建傲农生物科技集团股份有限公司 | A kind of method for differentiating Jiang Shumin, Landrace based on SNP site |
| CN108060236A (en) * | 2017-12-26 | 2018-05-22 | 福建傲农生物科技集团股份有限公司 | A kind of method based on SNP site discriminating Jinhua Pigs, Large White |
Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN105256035A (en) * | 2015-10-26 | 2016-01-20 | 浙江省农业科学院 | Molecular marker for identifying genetic backgrounds of Jinhua pigs and Duroc pigs and application thereof |
| 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 |
| CN105671192A (en) * | 2016-04-13 | 2016-06-15 | 上海市农业科学院 | DNA bar code establishing method for pork tracing and tracing method |
-
2016
- 2016-11-07 CN CN201610974894.3A patent/CN106566887A/en active Pending
Patent Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN105256035A (en) * | 2015-10-26 | 2016-01-20 | 浙江省农业科学院 | Molecular marker for identifying genetic backgrounds of Jinhua pigs and Duroc pigs and application thereof |
| 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 |
| CN105671192A (en) * | 2016-04-13 | 2016-06-15 | 上海市农业科学院 | DNA bar code establishing method for pork tracing and tracing method |
Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN107988391A (en) * | 2017-12-26 | 2018-05-04 | 福建傲农生物科技集团股份有限公司 | A kind of method for differentiating Jiang Shumin, Landrace based on SNP site |
| CN108060236A (en) * | 2017-12-26 | 2018-05-22 | 福建傲农生物科技集团股份有限公司 | A kind of method based on SNP site discriminating Jinhua Pigs, Large White |
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Application publication date: 20170419 |