CN104651356A - SNP (Single Nucleotide Polymorphism) marker related to farrowing traits of Erhualian sows and detection method and application of SNP marker - Google Patents

SNP (Single Nucleotide Polymorphism) marker related to farrowing traits of Erhualian sows and detection method and application of SNP marker Download PDF

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CN104651356A
CN104651356A CN201510113227.1A CN201510113227A CN104651356A CN 104651356 A CN104651356 A CN 104651356A CN 201510113227 A CN201510113227 A CN 201510113227A CN 104651356 A CN104651356 A CN 104651356A
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snp
marker
erhualian
snp marker
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CN104651356B (en
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李平华
贺丽春
黄瑞华
马翔
高硕�
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Nanjing Agricultural University
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Abstract

The invention discloses an SNP (Single Nucleotide Polymorphism) marker related to farrowing traits of Erhualian sows and a detection method and application of the SNP marker. A locus of the SNP marker is a nucleotide locus g.37502410 on a porcine chromosome 12 of a reference sequence of an international porcine genome version 10.2, is of A/C mutation and corresponds to a 630-th site of SEQ ID NO: 1, and the SNP marker is extremely remarkably related to the total litter size of the Erhualian sows. According to a primer pair for detecting the SNP marker disclosed by the invention, a forward primer is SEQ ID NO: 2, and a reverse primer is SEQ ID NO: 3. The SNP marker provided by the invention is related to the farrowing performance of the Erhualian sows, so that high-yielding Erhualian sow strains can be screened through identifying the SNP marker, and the obtained high-yielding Erhualian sow strains have important economic benefits and social values.

Description

A kind of SNP marker relevant to Erhualian sow litter trait and detection method thereof and application
Technical field
The invention belongs to technical field of molecular biology, relate to a kind of SN P relevant to Erhualian sow litter trait and mark and detection method and application.
Background technology
Litter size of pig is important economic characters, and the raising of litter size will increase the supply of commodity pork widely, produces bring huge economic benefit to Pig Industry.Along with China's sustain economic develops fast, people's living standard improves gradually, also increasing to the demand of pork.China can numerous sow amount of livestock on hand about 4,300 ten thousand in by the end of December, 2014, if average every young 1 of the tire fecund of sow, produces 2 tires and calculates, then can be whole industry every year and provide about 9,000 ten thousand pigs more by every sow every year.Therefore, people also more and more pay close attention to the litter size performance how improving pig.But litter size is the economic characters of complicated controlled by multiple genes, and heritability is low, improves litter size of pig by traditional selection and produce little effect, so the reproductive performance that the new molecule seed selection mark of development and utilization improves pig is extremely paid attention to.
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.According to contriver unit one belongs to the maximum base of painted face in Beijing opera swinery " Jiao Xi Erhualian Specialty Co-operative Organization " interior 177 painted faces in Beijing opera about 1000 nest farrowing data analysis, in painted face in Beijing opera colony there is remarkable separation in Farrowing Traits, and especially primiparity total yield coefficient and the number born alive variation coefficient reach 22.14% and 26.97% respectively; Multiparity is also respectively 19.87% and 22.14%.But cause the Genetic Mechanisms of litter size variation in Erhualian kind it be unclear that at present.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, the site of described SNP marker is g.37502410 nucleotide site on international pig genome 10.2 version reference sequences No. 12 karyomit(e)s, and it is A/C sudden change, described SNP marker and Erhualian sow nest produce total young number pole significant correlation.G.37502410 site has the genotypic painted face in Beijing opera of AA 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 CC.
Develop a method for molecule marker based on described SNP, 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.
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 630th, there is A/C polymorphism.
The molecule marker obtained according to the method described above.
Described molecule marker preferred sequence is as shown in SEQ ID NO:1, and described SNP site is positioned at the 630th, there is A/C 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 SNP marker of the present invention, comprise one section of sequence containing described SNP marker in pcr amplification Erhualian sow genome, check order to amplified production, the A/C in this site of interpretation is polymorphic.
The method of described detection SNP marker 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 polymorphic at the A/C of SEQ ID NO:1 the 630th.
Wherein, the pcr amplification 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 SEQ ID 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 59 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, molecule marker, primer.
Screen a method for high yield Erhualian sow strain, comprise the genotype detecting Erhualian sow g.37502410 nucleotide site, the AA type of seed selection g.37502410 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 the distribution situation of SNP marker Fst value on karyomit(e) between high yield with relative low yield painted face in Beijing opera colony.Wherein, 18 euchromosomes of pig and X chromosome message identification are in X-axis.
Fig. 2 be target area resurvey amalgamation result after sequence No. 12 karyomit(e)s on the distribution situation of SNP marker Fst value.Wherein X-axis is No. 12 karyomit(e)s.
Fig. 3 uses primer amplification of the present invention electrophorogram g.37502410.
Fig. 4 is the DNA sequencing results peaks figure of mutational site different genotype g.37502410.
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.Selection and use value comes the individuality of front 10% and rear 10%.Extract genomic dna
Gather the ear tissue sample of 36 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.
2, 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.
3, the calculating of high yield and relative low yield colony Fst value
Use the 60K SNP marker type data of Powermarker software package to somatotype individuality to process, calculate each SNP site genetic differentiation coefficient Fst value of Liang Ge colony.Result shows, and the point that on No. 12 karyomit(e)s, existence one is higher, this SNP marker is relevant to total yield coefficient proterties (Fig. 1) very likely.
4, resurvey sequence in target area
Within the scope of above-mentioned SNP marker upstream and downstream 300kb, screen 44 SNP (R2<0.8), somatotype is carried out to above-mentioned 36 Erhualian sows.Result successful analysis 43 mark, wherein 10 marks are without polymorphism.Have polymorphic site 33, merge with the result of 60K chip, re-start the Fst value of high and low product colony, g.37502410 result display vertex is still (Fig. 2).
Embodiment 2
The present embodiment is that the SNP site that obtains in embodiment 1 is g.37502410A/C in the intragroup checking of Erhualian sow.
1, Erhualian sow genomic dna is extracted
Gather and there is the ear tissue sample of 197 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 59 DEG C of 30s; Extend 72 DEG C of 45s; 35 circulations; Then 10min is extended.
Part PCR primer electrophoresis detection in 1.2% sepharose, the object clip size of amplification is 699bp, and electrophorogram is shown in Fig. 2, and Fig. 2 display can amplify target stripe.Remaining amplified production is checked order, the sequencing result genes involved fragment sequence comparison of pig in DNAman software and GenBank, analysis, g.37502410, the A/C genotype that interpretation is located, 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.37502410A/C 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.37502410A/C the AA genotype individuals in site is compared with CC type individuality: Litter size on average increases by 1.74.As can be seen here, in Erhualian kind, the AA type in Systematic Breeding g.37502410A/C site is individual, all progressively can improve the Litter size of Erhualian sow, reach the object improving Erhualian sow reproductive performance.
The association analysis of table 1, g.37502410A/C SNP site and Erhualian sow Litter size

Claims (10)

1. a SNP marker relevant to Erhualian sow litter trait, it is characterized in that, the site of described SNP marker is g.37502410 nucleotide site on international pig genome 10.2 version reference sequences No. 12 karyomit(e)s, and there is A/C 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 630th, there is A/C 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 630th, there is A/C 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, and it is characterized in that comprising one section of sequence containing SNP marker according to claim 1 in pcr amplification Erhualian sow genome, check order to amplified production, the A/C in this site of interpretation is polymorphic.
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 order-checking, analyze sequencing result, interpretation is in the A/C polymorphism of SEQ ID NO:1 the 630th.
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.37502410 nucleotide site, the AA type of seed selection g.37502410 nucleotide site is individual as boar.
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CN107299143A (en) * 2017-08-03 2017-10-27 南京农业大学 Pig No. 12 chromosome SNP markers related to Erhualian litter size and detection method
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CN108330199A (en) * 2018-03-30 2018-07-27 上杭傲农槐猪产业发展有限公司 Government's bank spends pig SNP site, SNP chip to be combined with its detection primer, detection kit and its application and germplasm identification method
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