To pig up to the related SNP marker of 100 kg body weight ages in days and its application
Technical field
The present invention relates to molecular genetics field, more particularly to pig up to the related molecule mark of 100 kg body weight ages in days
Note, in particular it relates to educated to pig up to 100 kg body weight ages in days related SNP marker, its application and the molecular labeling
Application in kind.
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, help quickly to look for
To significant molecular labeling of the pig up to 100kg body weight ages in days is influenceed, favourable reason is provided for the marker assisted selection breeding of pig
By foundation.
The content of the invention
First purpose of the present invention is to provide to pig up to the related SNP marker of 100 kg body weight ages in days.
Second object of the present invention is to provide the application of the SNP marker.
The purpose of the present invention is achieved through the following technical solutions:
Determine and record the important economical trait of 3702 durocs, using the GBS technologies of optimization to duroc body
GWAS researchs are carried out, one has been obtained and has reached the significantly correlated SNP marker of 100kg body weight ages in days, the SNP marker with pig
Positioned at genome version Ensembl Sscrofa 10.2 chr1:177334696 sites.Count the SNP site and resurvey sequence
Local pig breed (Jinhua Pigs, Wuzhi Mountain pig, Luchuan pig, plum mountain pig, BaMa miniature pig, Rongchang Pig, Laiwu Pigs, Erhualian, the river bend
Pig and people pig) with market pig kind (duroc, Yorkshire and DLY pig) in SNP frequencies, find its SNP frequency distribution
Significant difference in local pig breed and market pig kind be present, G is advantage allele in market pig, and A is advantage etc. in Native Pig
Position gene.
Specifically, the SNP marker is located at the 101st bit base in the nucleotide sequence shown in SEQ ID NO.1.
Thus, obtained it is a kind of to pig up to the SNP marker that 100 kg body weight ages in days are related, in the colony that the speed of growth is slow
In, by selecting the individual with market pig kind iso-allele G, the speed of growth of colony can be improved.
Further, the application the invention provides the SNP marker in the marker assisted selection breeding of pig.
The application is embodied as a kind of method for carrying out assistant breeding to pig using the SNP marker, can wrap
Include following steps:
(1) genotype of the sample pig in the SNP marker is detected;
(2) sample pig of the selection with advantage allele genotype carries out the seed selection of advantage strain.
Preferably, the pig that Select gene type is G/G carries out seed selection.
Wherein, the advantage strain is mainly shown as that the speed of growth is fast.
Further, the step (1) can use direct Sequencing, or first expand the fragment containing the SNP site and detect again
Mode carry out, for example, design primer, amplified from the sequence shown in SEQ ID No.1 containing the SNP marker
Fragment, then detect the allele on the site.
Present invention also offers application of the SNP marker in the fast pig kind of the identification speed of growth.
On the other hand, the protection of the present invention is fallen within for expanding the primer pair containing SNP site fragment of the present invention
Scope.The primer pair is act as:The fragment containing the SNP site is amplified from the sequence shown in SEQ ID No.1.
The beneficial effects of the present invention are:There is Important Economic performance inventory to 3702 by the GBS technologies of optimization
Duroc colony carry out GWAS researchs, by the analysis to GWAS results obtain one with pig reach 100kg body weight ages in days it is notable
Related SNP (chr1:177334696) site, SNP frequencies are carried out in Chinese native pig breed and market pig kind to this site
Analysis, it is found that its SNP frequency distribution has significant difference in local pig breed and market pig kind, G is advantage equipotential in market pig
Gene, A is advantage allele in Native Pig.Commodity growth speed of pigs is higher than local pig breed, illustrates that this SNP site can be made
It is applied to the seed selection of excellent pig kind for molecular labeling.In the slow colony of the speed of growth, pass through selection and the same equipotential of market pig kind
Gene G individual, the growth speed of colony can be improved.The present invention by detect SNP marker can early stage, it is quick, low into
Originally growth speed of pigs effectively, is predicted, is had broad application prospects in terms of improving breeding pig, and excellent economy can be obtained
Value.
Brief description of the drawings
Fig. 1 is the Manhattan figure that pig reaches 100kg body weight age in days GWAS results.
Embodiment
Following examples further illustrate present disclosure, but should not be construed as limiting the invention.Without departing substantially from
In the case of of the invention spirit and essence, the modifications or substitutions made to the inventive method, step or condition belong to the present invention
Scope.
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 this research.Up to 100kg body weight age in days (Age to
100kg live weight, AGE) carried out according to pig farm internal specification.
2. test method
2.1 100kg body weight ages in days:When pig body weight reaches 30 ± 5kg, i.e., empty material prepares to begin to survey (to begin to survey under the previous day
Noon cleaning hopper is surplus to expect to morning on the same day), sky material weighs the body weight of pig with weighing instrument after 12 hours, be designated as body weight;By 2-3
The raising of individual month, when pig body weight reaches 100 ± 5kg, proceed by whole survey;Survey noon before that day starts to stop expecting eventually, sky material
The body weight of pig is weighed after 10 hours, is designated as surveying body weight eventually;According to the body weight and age in days when beginning to survey and surveying eventually, calculating reaches 100kg
Age in days.Because updating formula there are certain requirements to surveying body weight eventually, therefore during follow-up data processing, body weight will be surveyed eventually<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, select EcoRI-MspI double digestions 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, Quality Control is carried out 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 potentially associated 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 with 3702 Duroc colony position objects 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
(chr1:177334696) site, as shown in Figure 1.
SNP marker (the chr1 of embodiment 2:177334696) frequency distribution in different cultivars pig
1 test material
Local pig breed:6 Laiwu Pigs, 5 Erhualians, 6 river bend pigs, 6 people pigs, 5 Jinhua Pigs, 6 Wuzhi Mountain
Pig, 6 Luchuan pigs, 14 plum mountain pigs, 9 Rongchang Pigs and 6 BaMa miniature pigs.Market pig kind includes:16 durocs, 8
Yorkshire and 36 DLY pigs.
2 test methods
2.1 the extraction of genomic DNA
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 tube, add 20 μ l Proteinase Ks, are mixed;
(2) 20mg or so ear tissue sample is taken to be put into above-mentioned solution, 55 DEG C of digestion 8h;
(3) 3 μ l RNase A are added into the tissue fluid digested, 30min, purpose are placed in 37 DEG C of thermostat water baths
It is the RNA in degraded tissue solution;
(4) 200 μ l AL solution are added into 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 the 1.5ml centrifuge tubes of the number of finishing, room temperature places 2min, makes
The ethanol remained in pipe 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(chr1:177334696) frequency distribution in each breeding pig full-length genome weight sequencing data
Send each breeding pig genomic DNA to sequencing, statistics SNP (chr1:177334696) in above local pig breed and commodity
Frequency distribution in pig kind weight sequencing data.
3 results and analysis
SNP(chr1:177334696) 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.G is advantage allele in market pig, and A is advantage in Native Pig
Allele.
SNP (the chr1 of table 1:177334696) 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 100 kg body weight ages in days are related, it is slow in the speed of growth
In colony, pass through Select gene group version Ensembl Sscrofa 10.2 chr1:177334696 allele G individual
Breeding is carried out, the speed of growth of breeding population can be improved.
Although above with general explanation, embodiment and experiment, the present invention is described in detail,
But some modifications on the basis of the present invention, can be made to it or are improved, this is apparent to those skilled in the art
's.Therefore, these modifications or improvements without departing from theon the basis of the spirit of the present invention, are belonged to claimed
Scope.
Sequence table
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