CN107858441A - To pig up to the related SNP marker of 100kg body weight age in days characters and its application - Google Patents
To pig up to the related SNP marker of 100kg body weight age in days characters and its application Download PDFInfo
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- CN107858441A CN107858441A CN201711122294.5A CN201711122294A CN107858441A CN 107858441 A CN107858441 A CN 107858441A CN 201711122294 A CN201711122294 A CN 201711122294A CN 107858441 A CN107858441 A CN 107858441A
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/124—Animal traits, i.e. production traits, including athletic performance or the like
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/172—Haplotypes
Abstract
The present invention, which provides, a kind of reaches the related SNP marker of 100kg body weight age in days characters and its application with pig.The duroc colony for having Important Economic performance inventory to 3702 by the GBS technologies of optimization carries out GWAS researchs, and a SNP (chr8 for influenceing pig and reaching 100kg body weight ages in days is obtained by the analysis on GWAS results:140618337, genome version EnsemblSscrofa 10.2) site, SNP frequency analyses are carried out in Chinese native pig breed and market pig kind to this site, it was found that there is significant difference in its SNP frequency distribution in local pig breed and market pig kind, T is advantage allele in market pig, and C is advantage allele in Native Pig.Commodity growth speed of pigs is higher than local pig breed, shows that this SNP site can be applied to the seed selection of excellent pig kind as molecular labeling.
Description
Technical field
The present invention relates to molecular genetics field, specifically, is related to a kind of related up to 100kg body weight age in days characters to pig
SNP marker and its application.
Background technology
China is a pig big country, and the market demand of pork yield and quality increasingly increases, and improves pork yield, improves
Pork carcase quality, turn into the work that breeding scientist constantly explores for a long time.The breeding work of early stage focuses primarily upon pig
Phenotypic Selection, with the continuous propulsion of genome work and the extensive exploitation of genetic marker, be increasingly becoming can for molecule selection
Lean on and effective system of selection.
SNP (single nucleotide polymorphism, SNP) mark is third generation molecule mark
Note, refers to there is the mutation of single base on genomic dna sequence and a kind of caused polymorphism, this mutation include single base
Transversion, conversion, insertion and missing.The SNP amounts of having the advantages that are big, high-frequency, low mutation rate, are widely used in gene component
Analysis, biological information automatic detection, simple and complex disease genetic research, herding breeding mark and global racial inheritance etc.
Research.Molecular marker assisted selection breeding, it is that objective trait is selected on a molecular scale, can not be affected by environment,
Selected by genetic background, Linkage drag is reduced, so as to accelerate breeding process and precision.
Whole-genome association (Genome-wide association studies, GWAS) is livestock and poultry economic characters
Genetic improvement and the important method of mechanism parsing.With the development of two generation sequencing technologies, full-length genome resurveys sequence and simplifies gene
Group sequencing technologies turn into the powerful of high flux SNP partings, and GBS (Genotyping-by-sequencing) is simplified gene
The classical representative of group sequencing, it is a kind of efficient full-length genome SNP classifying methods, Direct Identification SNP can be gone forward side by side from colony
Row parting, tens of thousands of SNP parting information not waited to hundreds of thousands can be obtained with relatively low cost, have been widely used in animals and plants
(De in the researchs such as molecular markers development, population genetic analysis, whole-genome association and genome selection and use
Donato et al., 2013;Elshire et al., 2011;He et al., 2014).
Pig is directly related to the growth performance of pig up to 100kg body weight age in days, and therefore, that studies pig reaches 100kg body weight ages in days,
There is important Research Significance in breeding.
GWAS researchs are carried out to swinery body using the GBS technologies of optimization, helping to be quickly found out influences pig and reach 100kg body weight
The significant molecular labeling of age in days, favourable theoretical foundation is provided for the marker assisted selection breeding of pig.
The content of the invention
Up to the related SNP marker of 100kg body weight age in days characters and its answered to pig it is an object of the invention to provide a kind of
With.
In order to realize the object of the invention, inventor to 3702 there is Important Economic performance to remember by the GBS technologies of optimization
The duroc colony of record carries out GWAS researchs, and obtaining an influence pig by the analysis on GWAS results reaches 100kg body weight days
SNP (the chr8 in age:140618337, genome version Ensembl Sscrofa 10.2) site, to this site on Chinese ground
SNP frequency analyses are carried out in square pig kind and market pig kind, it is found that its SNP frequency distribution exists in local pig breed and market pig kind
Significant difference, T is advantage allele in market pig, and C is advantage allele in Native Pig.Commodity growth speed of pigs is higher than
Local pig breed, show that this SNP site can be applied to the seed selection of excellent pig kind as molecular labeling.
In consideration of it, the present invention provides and a kind of the related SNP marker of 100kg body weight age in days characters, the SNP is reached with pig
Molecular labeling is located on No. 8 chromosomes of pig, and as shown in SEQ ID NO.1, the bit base of sequence the 101st is its nucleotide sequence
SNP site, the growth speed of pigs that base is T at this is higher than the growth speed of pigs that base at this is C.
The present invention also provides application of the described SNP marker in the marker assisted selection breeding of pig.
Foregoing application comprises the following steps:
(1) genotype of the sample pig in the SNP site is detected;
(2) sample pig of the selection with advantage allele genotype carries out the seed selection of advantage strain.
Wherein, base is T at the SNP site of the advantage allele.In the slow colony of the speed of growth, pass through selection
With market pig kind iso-allele T individual, the speed of growth of colony can be improved.
The step (1) uses direct Sequencing, or first expands the side that the DNA fragmentation containing the SNP marker detects again
Formula is carried out.For example, being target sequence according to the DNA fragmentation containing the SNP site, primer is designed, from shown in SEQ ID No.1
The DNA fragmentation containing the SNP marker is amplified in sequence, then detects the allele on the site.
Present invention also offers the SNP marker in the fast market pig/Native pig breeds of the identification speed of growth
Using.
On the other hand, for expanding the primer pair of the DNA fragmentation containing SNP site of the present invention, containing the primer pair
Detection reagent or kit fall within protection scope of the present invention.
The present invention also provides the SNP marker, primer pair or states detection reagent or kit and given birth in identification or seed selection
Application in long fireballing excellent pig kind.
The present invention also provides the SNP marker, primer pair or states detection reagent or kit is reaching 100kg with pig
Application in the related Genotyping detection of body weight age in days character.
The present invention also provides the SNP marker, primer pair or states detection reagent or kit in pig full-length genome
Application in SNP Genotypings.
The beneficial effects of the present invention are:
By determining and recording the important economical trait of duroc, using the GBS technologies of optimization to 3702 Durocs
Pig body carries out GWAS researchs, has obtained one and has reached the significantly correlated SNP (chr8 of 100kg body weight ages in days with pig:140618337) position
Point.Count the SNP site and resurvey local pig breed (Wuzhi Mountain pig, Luchuan pig, plum mountain pig, BaMa miniature pig, Rongchang Pig, the Lay of sequence
Overgrown with weeds pig, Erhualian, river bend pig and people pig) with market pig kind (duroc, Yorkshire and DLY pig) in SNP frequency
Rate, it is found that its SNP frequency distribution has significant difference in local pig breed and market pig kind, T is advantage equipotential base in market pig
Cause, C is advantage allele in Native Pig.Commodity growth speed of pigs is higher than local pig breed, shows that this SNP site can conduct
Molecular labeling is applied to the seed selection of the fast excellent pig kind of the speed of growth.In the slow colony of the speed of growth, pass through selection and commodity
Pig kind phase iso-allele T individual, the speed of growth of colony can be improved.The present invention can by detecting SNP marker
In early days, quickly, low cost, effectively predict growth speed of pigs, had broad application prospects in terms of improving breeding pig, and can
Obtain excellent economic value.
Brief description of the drawings
Fig. 1 is the Manhattan figure that pig reaches 100kg body weight age in days GWAS results in the embodiment of the present invention 1.
Embodiment
Following examples are used to illustrate the present invention, but are not limited to the scope of the present invention.Unless otherwise specified, embodiment
According to conventional laboratory conditions, as Sambrook equimoleculars Cloning: A Laboratory Manual (Sambrook J&Russell DW,
Molecular Cloning:A Laboratory Manual, 2001), or the condition according to manufacturer's specification suggestion.
The pig economic characters whole-genome association of embodiment 1
1. test material
Using the purebred colony of duroc as research object, 33,960 to be born in August, 2007 in January, 2016 are collected
The production performance of body (12,987 boars and 20,973 sows) is recorded for the present invention.Surveyed up to 100kg body weight ages in days performance
It is fixed to be carried out in strict accordance with pig farm internal specification.
2. test method
2.1 determine up to 100kg body weight age in days
When pig body weight reaches 100 ± 5kg, detection is proceeded by, detection noon before that day starts to stop expecting, sky material 10 is small
When after weigh the body weight of pig, be designated as body weight and record to reach 100kg age in days indexs.Because updating formula has necessarily to surveying body weight eventually
It is required that therefore follow-up data handle when, will eventually survey body weight<75kg or>140kg individual record is set as missing values.
The 2.2 pig full-length genome SNP classifying methods based on GBS technologies
By simulating digestion pig genome, 36 kinds of common II type restriction enzymes and 24 kinds of double digestion groups are predicted
Close the digestion effect in pig genome;According to research purpose and colony's feature, EcoR I and the double digestions of Msp I is selected to combine and be used for
The GBS of pig builds storehouse, and GBS experiments and analysis process are optimized, and establishes the pig full-length genome SNP based on GBS technologies
Classifying method.By the way that 3757 durocs are carried out with GBS sequencings, 102 identified, 254 SNP cover the whole base of pig
Because of group.
2.3 whole-genome association
Whole-genome association has been carried out up to 100kg body weight age in days (AGE) to duroc colony.
2.4 SNP Quality Controls
In order to obtain reliable GWAS results, the present invention carries out Quality Control using following condition:(1)MAF≥0.05;(2)HWE
≥10E-6;(3) each SNP two kinds of homozygotic individual numbers are >=30.
2.5 with the significantly correlated SNP site of economic characters
The detection in the notable site of genomic level, Bonferroni corrections, independent marking number are carried out using independent marking number
Calculating using PLINK indep-pairwise orders obtain, obtain the p of the level of signifiance of Bonferroni genomic levels 5%
It is worth for 0.05/14,084=3.55 × 10-6, and the p value threshold value of potential association is 1.0/14,084=7.10 × 105。
According to the standard, the 5% genome water for reaching Bonferroni corrections up to 100kg body weight ages in days with pig is obtained
Put down significant SNP site (P<10-5.45)。
3. result and analysis
102,254 SNP pairs obtained is sequenced using the GBS of optimization using 3702 Duroc colonies as object by the present invention
Pig has carried out GWAS analyses up to 100kg body weight age in days, it is determined that one reaches the significantly correlated SNP of 100kg body weight ages in days with pig
(chr8:140618337) site, as shown in Figure 1.
The SNP is located on No. 8 chromosomes of pig, the nucleotide sequence such as SEQ containing each 100bp bases of SNP site and its both sides
Shown in ID NO.1, the growth speed of pigs that base is T at the SNP site is higher than the growth speed of pigs that base at this is C.
SNP marker (the chr8 of embodiment 2:140618337) frequency distribution in different cultivars pig
1. test material
Local pig breed includes:6 Laiwu Pigs, 5 Erhualians, 6 river bend pigs, 6 people pigs, 6 Wuzhi Mountain pigs, 6
Luchuan pig, 14 plum mountain pigs, 9 Rongchang Pigs and 6 BaMa miniature pigs.Market pig kind includes:16 durocs, 8 Yorkshires
Pig and 36 DLY pigs.
2. test method
The extraction of 2.1 genomic DNAs
Genomic DNA is extracted using the GIAamp DNA Mini kits of QIAGEN companies, concrete operation step is as follows:
(1) 180 μ l ATL buffer solutions are added into 1.5ml centrifuge tubes, add 20 μ l Proteinase Ks, are mixed;
(2) about 20mg pig ear tissue samples are taken to be put into above-mentioned solution, 55 DEG C of digestion 8h;
(3) the μ l of 25mg/ml RNase A 3 are added into the tissue fluid digested, are placed in 37 DEG C of thermostat water baths
30min, it is therefore an objective to the RNA in tissue solution of degrading;
(4) 200 μ l AL solution are added into above-mentioned solution again, vortex vibration is put into 70 DEG C of water-baths after mixing to be digested
10min;Treat that centrifuge tube recovers to room temperature, add 200 μ l absolute ethyl alcohols, be vortexed again for concussion and mix;
(5) above-mentioned solution is all added in DNA adsorption columns, after room temperature places 2min, 13000rpm centrifugations 1min;
(6) after centrifugation terminates, filter liquor is abandoned, and adsorption column is put into another new 2ml collecting pipe, adds 500 μ l
PW1 solution, 13000rpm centrifugations 1min;
(7) centrifuge after terminating, then adsorption column put into another new 2ml collecting pipe, add 500 μ l PW2 solution,
13000rpm centrifuges 3min;
(8) solution in collecting pipe is outwelled, the liquid of the collecting pipe mouth of pipe is cleaned with paper handkerchief, adsorption column is placed on collection again
Guan Zhong, 13000rpm centrifuge 2min;
(9) lid of DNA adsorption columns is opened, be put into numbered 1.5ml centrifuge tubes, room temperature places 2min, makes pipe
The ethanol of middle residual is evaporated completely;
(10) to adsorption column center add 120-150 μ l AE buffer solutions, room temperature place 2min after, 13000rpm from
Heart 1min, resulting solution are genomic DNA.Genomic DNA is used after the detection of 1% agarose gel electrophoresis is qualified
NanoDrop quantitative concentrations;Concentration is uniformly diluted to 50ng/ μ l again, for testing in next step.
2.2SNP(chr8:140618337) frequency in each breeding pig full-length genome weight sequencing data
Send each breeding pig genomic DNA to sequencing, statistics SNP (chr8:140618337) in above local pig breed and commodity
Frequency distribution in pig kind weight sequencing data.
3. result and analysis
SNP(chr8:140618337) such as institute of table 1 of the SNP frequency distribution result in different places pig kind and market pig kind
Show significant difference be present in local pig breed and market pig kind.T is advantage allele in market pig, and C is advantage in Native Pig
Allele.
SNP (the chr8 of table 1:140618337) the SNP frequencies in different places pig kind and market pig kind
Thus, obtained it is a kind of to pig up to the SNP marker that 100kg body weight age in days characters are related, it is slow in the speed of growth
Colony in, by select with market pig kind iso-allele T individual, the speed of growth of colony can be improved.
Although above the present invention is described in detail with a general description of the specific embodiments,
On the basis of the present invention, it can be modified or improved, this will be apparent to those skilled in the art.Cause
This, these modifications or improvements, belong to the scope of protection of present invention without departing from theon the basis of the spirit of the present invention.
Sequence table
<110>China Agricultural University
<120>To pig up to the related SNP marker of 100kg body weight age in days characters and its application
<130> KHP171115719.3
<160> 1
<170> SIPOSequenceListing 1.0
<210> 1
<211> 201
<212> DNA
<213>Pig (Sus scrofa)
<220>
<221> misc_feature
<222> (101)..(101)
<223>N=c or t
<400> 1
tatgctacct ccagactcat ttatctaaac acatctctac tcaaattcaa caagtccaaa 60
actaactcat catctttctt ctaggaccag attctctaat nttagtatta acaccaacat 120
ttactcagtt ccccaaatta gaaatgtgat agcccagaat tcctgtcgtg gctcagtggt 180
tactgaatcc gactaggaac c 201
Claims (10)
1. to pig up to the related SNP marker of 100kg body weight age in days characters, it is characterised in that the SNP marker is located at
On No. 8 chromosomes of pig, its nucleotide sequence is as shown in SEQ ID NO.1, and the bit base of sequence the 101st is SNP site, alkali at this
The growth speed of pigs that base is T is higher than the growth speed of pigs that base at this is C.
2. application of the SNP marker in the marker assisted selection breeding of pig described in claim 1.
3. application according to claim 2, it is characterised in that comprise the following steps:
(1) genotype of the sample pig in the SNP site is detected;
(2) sample pig of the selection with advantage allele genotype carries out the seed selection of advantage strain.
4. application according to claim 3, it is characterised in that base is T at the SNP site of the advantage allele.
5. according to the application described in any one of claim 2~4, it is characterised in that the step (1) uses direct Sequencing, or
The mode that the DNA fragmentation containing the SNP marker detects again is first expanded to carry out.
6. for expanding the primer pair of SNP marker described in claim 1, it is characterised in that for from SEQ ID No.1 institutes
Amplification obtains the DNA fragmentation containing the SNP marker in the sequence shown.
7. detection reagent or kit containing primer pair described in claim 6.
8. SNP marker described in claim 1, primer pair described in claim 6 or detection reagent described in claim 7 or
Application of the kit in the fast excellent pig kind of identification or the seed selection speed of growth.
9. SNP marker described in claim 1, primer pair described in claim 6 or detection reagent described in claim 7 or
Application of the kit in the Genotyping detection related up to 100kg body weight age in days characters to pig.
10. SNP marker described in claim 1, primer pair described in claim 6 or detection reagent described in claim 7 or
Application of the kit in pig full-length genome SNP Genotypings.
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CN109371143A (en) * | 2018-12-16 | 2019-02-22 | 华中农业大学 | SNP marker associated with pig growth traits |
CN109385481A (en) * | 2018-10-10 | 2019-02-26 | 江苏农牧科技职业学院 | Application and its selection of serpinA3 the and vitronectin gene in Soviet Union's ginger boar breeding |
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CN107267627A (en) * | 2017-07-12 | 2017-10-20 | 南京农业大学 | The preparation and application of the Six1 gene molecule marker related to pig production character |
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CN104404133A (en) * | 2014-10-20 | 2015-03-11 | 中国农业大学 | SNP marker associated with pig growth rate, and applications thereof |
CN107151690A (en) * | 2016-03-02 | 2017-09-12 | 中国农业科学院北京畜牧兽医研究所 | A kind of molecular labeling for detecting pig up to 100kg body weight ages in days and its application |
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Cited By (4)
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CN109385481A (en) * | 2018-10-10 | 2019-02-26 | 江苏农牧科技职业学院 | Application and its selection of serpinA3 the and vitronectin gene in Soviet Union's ginger boar breeding |
CN109385481B (en) * | 2018-10-10 | 2021-07-23 | 江苏农牧科技职业学院 | Application of serpinA3 and vitronectin genes in Sujiang boar breeding and breeding method thereof |
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