CN104726577A - SNP (single nucleotide polymorphisms) marker correlated with farrowing characters of Erhualian sows and detection method thereof - Google Patents
SNP (single nucleotide polymorphisms) marker correlated with farrowing characters of Erhualian sows and detection method thereof Download PDFInfo
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Abstract
The invention discloses an SNP (single nucleotide polymorphisms) marker correlated with farrowing characters of Erhualian sows and a detection method thereof. The SNP marker is on a nucleotide sequence of an autism susceptibility gene AUTS2 on a pig chromosome 3. A site of the SNP marker is g.14734925 nucleotide site on a pig chromosome 3 on a reference sequence of an international pig genome version 10.2 and has G/T polymorphism. The SNP marker is extremely significantly correlated with the total litter size of the Erhualian sows. The invention discloses a primer pair used for detecting the SNP marker, wherein the primer pair comprises a forward primer and a reverse primer; the sequence of the forward primer is SEQ ID NO:2; the sequence of the reverse primer is SEQ ID NO:3. The SNP marker provided by the invention is correlated with the farrowing characters of the Erhualian sows, so that high-yield Erhualian sow strains can be screened by identifying the SNP marker. The obtained high-yield Erhualian sow strains have important economic benefits and social values.
Description
Technical field
The invention belongs to technical field of molecular biology, relate to a kind of SNP marker relevant to Erhualian sow litter trait and detection method thereof.
Background technology
Litter size is the important indicator of reflection fertility of sow, pig farm production level and economic benefits, and the height of litter size is directly connected to quantity and pork feed rate that every sow provides growing and fattening pigs.The numerous sow amount of livestock on hand of China's energy will at 4,300 ten thousand in by the end of December, 2014, if average every young 1 of the tire fecund of sow, produce 2 tires by every sow every year to calculate, then can be whole industry every year and provide about 9,000 ten thousand pigs more, this can play very large promoter action to the pig industry of China.Along with China's sustain economic develops fast, people's living standard improves gradually, also increasing to the demand of pork, and therefore, people also more and more pay close attention to the litter size performance how improving pig.But because traditional selection produces little effect to litter size raising, therefore resolve the Genetic Mechanisms of litter size variation, the Farrowing Traits that the gene that development and utilization is new or molecule seed selection mark improve pig is significant.
Painted face in Beijing opera is the very outstanding national Genetic Resources of Domestic Animal protection kind of China's Taihu Lake basin Farrowing Traits, has the good reputation of " king of world's pig kind farrowing ", the valuable source of Ye Shi China pig industry Sustainable development.Although for many years domestic existing a large amount of research institution utilizes painted face in Beijing opera to differentiate the Genetic Mechanisms of Erhualian kind prolificacy, but be limited to the restriction of the many factors such as research method, means, material and the complicacy of reproductive trait own, Erhualian kind prolificacy genetic mechanism does not obtain disclosing fully and effective utilization.
Along with plum mountain pig exports to abroad, its prolificacy protogene has been carried out the research of system science by external many mechanisms and has effectively been utilized, improve the reproductivity of its bacon hogs kind, very high from the general reproductivity of pig kind of France and Denmark's introduction in recent years, our Native Pig High Yielding Heterosis is weakened gradually, this is a serious threat, is that compatriots have in the face of and need the reality of seeking countermeasure badly.Differentiate and be separated not yet by the High Yielding Heterosis gene of Erhualian kind exported, the metastable yielding Populations of performance, the High Yielding Heterosis consolidating these local pig breeds of Taihu Lake basin are very urgent.
From international pig QTL database website (http://www.animalgenome.org/cgi ?bin/QTLdb/SS/index), do not navigate to except on 10, No. 11 karyomit(e)s and sex chromosome the QTL affecting total yield coefficient at present pig, other euchromosome navigates to all the QTL affecting total yield coefficient, but major part is the QTL utilizing microsatellite marker to locate, fiducial interval many 10 ?20cM, real major gene and crucial variant sites thereof cannot be determined, be therefore difficult to directly apply to boar selection and improvement.
Summary of the invention
The object of the invention is to for prior art not enough, the low heritability of litter size, provides the SNP marker relevant to sow Litter size.
Another object of the present invention is the primer that is provided for detecting above-mentioned SNP marker and detection method.
Another object of the present invention is the purposes providing above-mentioned SNP marker.
A kind of SNP marker relevant to Erhualian sow litter trait, described SNP marker is positioned on the nucleotide sequence of the autism susceptibility Gene A UTS2 on pig No. 3 karyomit(e)s, the site of described SNP marker is g.14734925 nucleotide site on international pig genome 10.2 version reference sequences pig No. 3 karyomit(e)s, and there is G/T polymorphism, described SNP marker and Erhualian sow nest produce total young number pole significant correlation.G.14734925 site has the genotypic painted face in Beijing opera of TT individual sow Litter size and is significantly higher than and has the individual sow Litter size of the genotypic painted face in Beijing opera of GG.
A kind of method developing molecule marker based on SNP of the present invention, sequence based on the nucleotide sequence containing described SNP marker, design primer pair, carries out pcr amplification with Erhualian sow genomic dna for template, makes described SNP marker be converted into molecule marker.
Wherein, described primer pair sequence preference is upstream primer: SEQ ID NO:2, downstream primer: SEQ ID NO:3; Described molecule labelled series is preferred as shown in SEQ ID NO:1 further, and described SNP site is positioned at the 535th, there is G/T polymorphism.
The molecule marker obtained according to the method described above.
Described molecule marker is preferably as shown in SEQ ID NO:1, and described SNP site is positioned at the 535th, there is G/T polymorphism.
For detecting a primer pair for SNP marker of the present invention, upstream primer is: SEQ ID NO:2, and downstream primer is: SEQ ID NO:3.
Detect a method for described SNP marker, comprise one section of sequence containing described SNP marker in pcr amplification Erhualian sow genome, amplified production is checked order, the G/T polymorphism in this site of interpretation.
The method of the described SNP marker of detection of the present invention, preferably includes following steps:
(1) get the ear tissue sample of an Erhualian sow and extract STb gene;
(2) use the Erhualian sow genomic dna extracted to be template, use the primer described in claim 5 to carry out pcr amplification;
(3) amplified production checks order, and analyze sequencing result, interpretation is in the G/T polymorphism of SEQ ID NO:1 the 535th.
Pcr amplification further preferred reaction system described in step (2) is each 1.25 μ L of the primer shown in DNA profiling 2.5 μ L, SEQ ID NO:2 and SEQID NO:3, PCR Mix reagent 25 μ L, distilled water 20 μ L; Wherein said DNA profiling concentration is 30ng/ μ L, and the concentration of described primer is 10mol/L, and described PCR Mix reagent is the P394961L model reagent of Nanjing Ou Ke Bioisystech Co., Ltd; The response procedures of pcr amplification is: denaturation 96 DEG C of 2min; Sex change 96 DEG C of 20s; Anneal 55 DEG C of 30s, extends 72 DEG C of 45s, 35 circulations; Extend 72 DEG C of 10min.
The application in screening high yield Erhualian sow strain of SNP marker of the present invention, described molecule marker, primer pair.
Screen a method for high yield Erhualian sow strain, comprise the genotype detecting Erhualian sow g.14734925 nucleotide site, the TT type of seed selection g.14734925 nucleotide site is individual as boar.
Beneficial effect:
SNP marker provided by the invention is relevant to the Farrowing Traits of Erhualian sow, and therefore, can be tested and appraised this SNP marker to screen the Erhualian sow strain of high yield, the Erhualian sow high-yielding strain of gained has important economic benefit and social value.
Accompanying drawing explanation
Fig. 1 is GWAS positioning result schematic diagram karyomit(e) affecting pigsty total yield coefficient.Be the GWAS positioning result of 177 purebred Erhualian sow colonies.Wherein, 18 euchromosomes of pig and X chromosome message identification in X-axis, SNP and Litter size dependency ?log10 (P) value press the position display Y-axis of SNP in genome.What blue line represented is karyomit(e) conspicuous level threshold value, the threshold value of genome conspicuous level that what red line represented is.
Fig. 2 is the electrophorogram using primer amplification AUTS2 gene of the present invention.
Fig. 3 is the DNA sequencing results peaks figure of the mutational site different genotype of AUTS2 gene.
Embodiment
Following examples for illustration of the present invention, but are not used for limiting the scope of the invention.When not deviating from the present invention's spirit and essence, the amendment do the inventive method, step or condition or replacement, all belong to scope of the present invention.
Embodiment 1
1, laboratory animal source
Changzhou Jiao Xi Erhualian Specialty Co-operative Organization.
Calculate the breeding value of 177 Erhualian sows, computation model is Y (nest produces total young number)=parity (parity)+farm (field)+year (year)+season (season)+age (Farrowing age)+sire (with joining boar)+permanent effect (permanent effects of sow)+additive effect (individual additive effect)+e (residual error)
Comprising fixing Xiao Ying ?parity, Farrowing field/year/season, covariant Liang ?age of Farrowing, random Xiao Ying ?with join boar, permanent Xiao Ying ?sow, individual additive inheritance value.23 individualities that selection and use value is higher and lower 25 individualities of breeding value.
2, genomic dna is extracted
Gather the ear tissue sample of 48 sows, be positioned over 70% alcohol is housed centrifuge tube Nei , ?20 DEG C of Refrigerator stores for subsequent use.
Use traditional phenol/chloroform method to extract ear tissue genomic dna, required reagent comprises:
Lysate laboratory is equipped with
Proteinase K (German MERCK bio tech ltd)
The saturated phenol of Tris (Suo Laibao bio tech ltd, Beijing)
The saturated phenol of Tris: chloroform: primary isoamyl alcohol (25:24:1) (Suo Laibao bio tech ltd, Beijing)
Chloroform (Jiangsu Yonghua Fine Chemical Co., Ltd.)
Dehydrated alcohol (Guangdong Guanghua Science and Technology Co., Ltd.)
3M sodium acetate (Suo Laibao bio tech ltd, Beijing)
Concrete steps are as described below:
(1) get soya bean size and organize sample, shred as far as possible and put into 2ml centrifuge tube;
(2) lysate (oneself is equipped with) 800 μ L are added, and Proteinase K 30 μ L (0mg/ml);
(3) sample is placed in 55 DEG C of thermostat container overnight incubation, to inorganization block in pipe;
(4) add Tris saturated phenol 800 μ L, slightly mix 10min, 4 DEG C of centrifugal 12min of 12000r/min;
(5) get on 650 μ L and reset and add the saturated phenol of Tris: chloroform: primary isoamyl alcohol (25:24:1) 800 μ L, mix and shake 10min, 4 DEG C of centrifugal 12min of 12000r/min;
(6) get 550 μ L supernatants, add chloroform 800 μ L, mix and shake 10min, 4 DEG C of centrifugal 12min of 12000r/min; Following steps change the centrifuge tube of 1.5ml
(7) get 450 μ L supernatants, add dehydrated alcohol 800 μ L, 3M sodium acetate 40 μ L, mix and shake 6min, 4 DEG C of centrifugal 8min of 1000r/min;
(8) abandon supernatant and leave DNA precipitation group, add 1000 μ L 70% ethanol (oneself is equipped with), mix and shake 5min, 4 DEG C of centrifugal 5min of 1000r/min, abandon supernatant (as needs can repeat once);
(9) centrifuge tube is put into stink cupboard, dry up to pipe without droplet;
(10) sample adds 100 μ L ultrapure waters, and slight piping and druming is dissolved to DNA, through Nanodrop ?after 100 spectrophotometer Detection job and concentration by same for the concentration 50ng/ of being diluted to μ L Yu ?save backup at 20 DEG C.
3, pig full-length genome 60,000 (60K) SNP genotype detection
The DNA of above-mentioned individuality carries out pig full-length genome 60KSNP (Illumina, the U.S.) genotype according to company standard flow process and judges on Illumina Beadstation platform.Utilize PLINK (1.9) to carry out quality control to all sample 60K chip datas, reject recall rate lower than 0.95, family Mendelian error rate higher than 0.05 individuality; The SNP marker that minimum gene frequency is less than 0.05.
4, full-length genome association (GWAS) is analyzed
Use PLINK (1.9) software to carry out GWAS analysis to the 60K SNP marker type data of somatotype individuality and Litter size phenotypic data, adopt Bonferroni correction method to control multiple check, genome significance threshold value is defined as 0.05/ reference numerals.The result display of GWAS, on pig No. 3 karyomit(e)s, existence 1 and nest produce the SNP site (Fig. 1) of total young number significant correlation.
Embodiment 2
The present embodiment is that the SNP site that obtains in embodiment 1 is g.14734925G/T in the intragroup checking of Erhualian sow.
1, Erhualian sow genomic dna is extracted
Gather and there is the ear tissue sample of 132 purebred Erhualian sows of accurate Litter size record, be positioned over 70% alcohol is housed centrifuge tube Nei , ?20 DEG C of Refrigerator stores for subsequent use.Utilize aforesaid method to extract ear tissue genomic dna, after quality, Concentration Testing by concentration dilution to 30ng/ μ L Yu ?save backup at 20 DEG C.
2, the amplification of object fragment PCR and order-checking
Be template with the DNA extracted, according to designed primer, carry out pcr amplification: get each 1.25 μ L of primer shown in DNA profiling 2.5 μ L, SEQ IDNO:2 and SEQ ID NO:3, PCR Mix reagent 25 μ L, distilled water 20 μ L; PCR amplification system is set: denaturation 96 DEG C of 2min; Sex change 96 DEG C of 20s; Anneal 55 DEG C of 30s; Extend 72 DEG C of 45s; 35 circulations; Then 10min is extended.
PCR primer is electrophoresis detection in 1.2% sepharose, the object clip size of amplification is 512bp, electrophorogram is shown in Fig. 2, remaining amplified production is checked order, the sequencing result genes involved fragment sequence comparison of pig in DNAman software and GenBank, analysis, interpretation genotype g.14734925G/T, then utilizes SAS software to carry out the influential effect analysis of genotype to phenotype.Analytical model is Y
ijklm=u+G
j+ B
k+ P
l+ e
ijklm
Wherein: Y
ijkmfor the litter size of pig; G
jrepresent the genotype fixed effect of a jth SNP; B
kit is a kth batch fixed effect; P
lbe the stochastic effect of parity, the litter size record of different parity is as repeating data process; e
ijklmfor residual error.
The P value of significance corrects through the stochastic sampling of 10000 times.
Table 1 gives the g.14734925G/T influential effect of mutational site to Litter size in purebred painted face in Beijing opera colony.As shown in Table 1, in purebred Erhualian, g.14734925G/T the TT genotype individuals in site is compared with GG type individuality: Litter size on average increases by 1.66.As can be seen here, in Erhualian kind, the TT type in Systematic Breeding g.14734925G/T site all progressively can improve the Litter size of Erhualian sow, reaches the object improving Erhualian sow reproductive performance.
The association analysis of table 1, g.14734925G/T SNP site and Erhualian sow Litter size
Claims (10)
1. a SNP marker relevant to Erhualian sow litter trait, it is characterized in that described SNP marker is positioned on the nucleotide sequence of the autism susceptibility Gene A UTS2 on pig No. 3 karyomit(e)s, the site of described SNP marker is g.14734925 nucleotide site on international pig genome 10.2 version reference sequences pig No. 3 karyomit(e)s, and there is G/T polymorphism, described SNP marker and Erhualian sow nest produce total young number pole significant correlation.
2. develop the method for molecule marker based on SNP according to claim 1 for one kind, it is characterized in that sequence based on the nucleotide sequence containing SNP marker according to claim 1, design primer pair, carry out pcr amplification with Erhualian sow genomic dna for template, make SNP marker according to claim 1 be converted into molecule marker.
3. method according to claim 21, is characterized in that described primer pair sequence is upstream primer: SEQ ID NO:2, downstream primer: SEQ ID NO:3; Described molecule labelled series is as shown in SEQ ID NO:1, and described SNP site is positioned at the 535th, there is G/T polymorphism.
4. according to the molecule marker that the method for Claims 2 or 3 obtains.
5. molecule marker according to claim 4, it is characterized in that molecule labelled series is as shown in SEQ ID NO:1, described SNP site is positioned at the 535th, there is G/T polymorphism.
6. require a primer pair for the SNP marker described in 1 for test right, it is characterized in that upstream primer is: SEQ ID NO:2, downstream primer is: SEQ ID NO:3.
7. test right requires a method for the SNP marker described in 1, it is characterized in that comprising one section of sequence containing SNP marker according to claim 1 in pcr amplification Erhualian sow genome, checks order to amplified production, the G/T polymorphism in this site of interpretation.
8. method according to claim 7, is characterized in that comprising the following steps:
(1) get the ear tissue sample of an Erhualian sow and extract STb gene;
(2) use the Erhualian sow genomic dna extracted to be template, use the primer described in claim 5 to carry out pcr amplification;
(3) amplified production checks order, and analyze sequencing result, interpretation is in the G/T polymorphism of SEQ ID NO:1 the 535th.
9. the application in screening high yield Erhualian sow strain of the molecule marker described in SNP marker according to claim 1, claim 4 or 5, primer according to claim 6.
10. screen a method for high yield Erhualian sow strain, it is characterized in that comprising the genotype detecting Erhualian sow g.14734925 nucleotide site, the TT type of seed selection g.14734925 nucleotide site is individual as boar.
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