CN108707678A - With the relevant PACSIN2 gene molecule markers of pig kind reproductive trait and application - Google Patents

With the relevant PACSIN2 gene molecule markers of pig kind reproductive trait and application Download PDF

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CN108707678A
CN108707678A CN201810644972.2A CN201810644972A CN108707678A CN 108707678 A CN108707678 A CN 108707678A CN 201810644972 A CN201810644972 A CN 201810644972A CN 108707678 A CN108707678 A CN 108707678A
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pacsin2
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郭晓令
徐宁迎
阮鹏
蔡薇
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Zhejiang University ZJU
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Abstract

The present invention relates to the relevant CTNNA2 gene molecule markers of pig kind reproductive trait and application.With the relevant CTNNA2 gene molecule markers of pig kind reproductive trait, nucleotide sequence is as shown in SEQ ID No.1.The present invention carries out GWAS analyses to the local pig breed in Zhejiang Province for the first time, to analyze relevance of the SNPs genetic markers with local pig breed reproductive trait, to obtain several most High relevancy sites, by reverse-locating acquisition and the relevant CTNNA2 gene molecule markers of pig kind reproductive trait, provide the foundation for local pig breed seed selection and breeding.

Description

With the relevant PACSIN2 gene molecule markers of pig kind reproductive trait and application
(1) technical field
The present invention relates to the relevant PACSIN2 gene molecule markers of pig kind reproductive trait and application.
(2) background technology
Zhejiang Province is located in the Yangtze River Delta south wing, is one of coastal area of southeastern China province.It goes up north as Shanghai, Jiangsu, goes down south For Fujian, the East Sea is faced in east, and west borders on Anhui, Jiangxi.Thing and north and south spacing are about 450 kilometers, and land area is only 10.55 ten thousand square kilometres, belong to the smaller city of Chinese area." seven mountains, one water, two points of fields " are that Zhejiang Province is said since ancient times Method, because of its mountainous region and hills area accounting 74.63%, Plain accounting 20.32%, water surface area is about 5.05%.
According to Historical Data Data About, because Zhejiang Province has a large population and a few land, it is few that ground area is minimal tilled in the more Plains in mountain, therefore peasant's majority passes through pig raising To increase household economy income and subsist；And the ecological condition in labour Zhejiang Province additional plentifully is preferable, pannage resource It is abundant, provide good condition for the development of pig breeding industry.According to《Chinese Application of Animal Genetic will pig will》[1]In record, at present Mainly there are seven main local varieties to be respectively distributed to Zhejiang Province's different zones, distribution from south to north is followed successively by green lake pig, Shengxian County Seven main local varieties of pig and Jiaxing Black Pig are spent in flower pig, Jinhua both ends crow, Ninghai Cha Lu pigs, Lanxi flower pig, Chunan.Each Kind suffers from oneself long cultivation history, and if Ninghai Chalu Black Pig possesses 300 years or more cultivation history, pig is spent in Lanxi Cultivation just has historical record when the Qing Dynasty, and the cultivation history of Shengxian County flower pig can trace back between Ming Dynasty's Wanli year year.Kind Partitioning standards be the division for mostling come from region, such as belong to the Jiaxing Black Pig of Taihu pigs system due to close to Taihu Lake basin； Spend pig in Chunan that Anhui Zhejiang pig system is belonged to due to close to Anhui；Though Jinhua both ends crow and Lanxi flower pig are all in Shaoxing Jinhua Area, but the body characteristics of pig inter-species are at a distance of apparent.Thus, it could be seen that the accuracy and reasonability that are divided according to the kind of region have It waits for further investigating.
Zhejiang Province's local pig breed lacks the market competitiveness, in the different degrees of threat for receiving extinction, conservation work The importance of work gradually by people, it is realized that still causing due to the time of not good system and development and soon to protect The work progress of kind is more slow.Up to the present, Jinhua Pigs, Shengxian County spend pig, Jiaxing in seven, Zhejiang Province local varieties Black pig and Chunan flower pig have more complete conservation system and measure.Wherein Jinhua Pigs and Jiaxing Black Pig are begun in the fifties Preservable measures are taken, conservation level locates leading state at home, and up to the present effect of breeds conservation is good, also there is new strain quilt It turns out successively.The present situation of Chalu Black Pig, green lake pig and Lanxi flower pig etc. pig kind elsewhere but allows of no optimist：Such as Chalu Black Pig There is no the cultivation of scale, mainly still cultivated by casual household, therefore manage, record, the progress of the work of breeding is simultaneously lack of standardization, leads Cause conservation work is difficult to carry out；Lanxi spends the conservation work of pig also not smooth, due to lacking the management of professional person and referring to It leads, the phenomenon that record such as pedigree data, means of production is chaotic, missing, inbreeding is also more serious；Green lake pig has been difficult mirror The pure of its fixed blood lineage, follow-up work are difficult to carry out.So the conservation work of Zhejiang Province's local pig breed is faced with many choose War.
(3) invention content
It is an object of the present invention to provide be related to and the relevant PACSIN2 gene molecule markers of pig kind reproductive trait and application.
The technical solution adopted by the present invention is：
With the relevant PACSIN2 gene molecule markers of pig kind reproductive trait, nucleotide sequence such as SEQ ID No.1 institutes Show.
Reproductive capacity character includes：The ovulation rate of sow, number born alive, piglet birth weight, number of nipples, is secreted at nest litter size Newborn power is bred as piglet number and weight of weaning litter etc..The characters such as litter size and birth weight, weaning pig weight, incubation piglet number suffer from More close relationship.In the production of Pig Industry industry, the reproductive performance of sow is the most important of influence pig farm economic benefit One of factor.
The reproductive trait of sow includes nest litter size, newborn piglet weight and weaning pig weight etc., median fovea litter size It is the important indicator for weighing sow economic characters with number born alive.There is research to indicate, two characters of nest litter size and number born alive There is correlation between the reproductive traits such as same weigth at birth, weight of weaning litter, the young number number of wean, related coefficient is respectively 0.93, 0.61 and 0.70.Therefore the improvement of reproductive trait is always that in these years China and America and Europe etc. are national for pig breeding research work Emphasis and the target assaulted the main target.
It has been investigated that PACSIN2 genes of the present invention are related to reproductive capacity character nest litter size (LS).Nest litter size：Packet Include the practical normal living young number, dead piglet number and deformity piglet number living of sow newborn pig, wherein dead piglet include normal tire, The mummification of fetus and monster.Nest litter size is the important indicator for the fertility for reflecting pig kind.Influence nest litter size because being known as Heredity, ovulation, feeding management, nutrition, parity etc., the litter size of the first tire of sow is minimum under normal circumstances, then continues to increase straight Reach production peak value to the 6th tire or so, then force of labor is begun to decline.The upper limit of number born of sow is determined by the number of eggs ovulated of sow Fixed, others are also influenced by embryo survival and uterine capacity, and last actual litter size is still by the phase of this three Mutual relation influences.
The invention further relates to application of the molecular labeling in local pig breed breeding.It can be by regulating and controlling PACSIN2 bases Because of expression quantity, to regulate and control to pig kind reproductive trait.
The local pig breed is one of following：Pig, Jinhua Pigs, Chunan is spent to spend pig in Shengxian County.
According to statistics, the production of one annual of China sow in recent years young sum living only about 15, it is American-European to compare identical index Equal western developed countries can reach 20~26 or so, in contrast one annual number born alive ratio of European and American developed countries sow China will be higher by 33.3%~73.3%, and gap is quite big.But every parity average litter size of many local pig breeds and production are lived Young quantity is low unlike European and American developed countries, and the reason of leading to this gap is optimization and the pipe of sow breeding flow system Reason such as shortens the weaned piglet date and can reach wean standard, so as to shorten sows in lactation；Shorten sows in lactation knot Period of the beam to heat again；The success rate of artificial insemination is improved, reduce does not lead to waste of time etc. because having fertilization.Such as Every sow of fruit can produce a piglet more, then the whole nation can have more millions of of column market pig every year；If every 2 to 3 Year can a voluminous parity, that also will be very huge for the income that economy-zone is come.It can be raised less due to improving yield Sow can save millions of ton of feed.The reproductive trait of sow is affected by many factors, other than environmental factor, It influences maximum to be exactly the genetic aspect of itself.Present breeder both domestic and external is by finding something lost associated with reproductive trait Label and other higher characters of associated genetic force are passed, and reproductive ability is improved with indirect selections by directly selecting Energy.Deeply and reinforce the research to pig reproductive trait, has ten to the economic benefit for improving fertility of sow and increasing pig raising Divide important meaning, also lays the foundation to accelerate the improvement of boar and cultivating work.
The local pig breed in China is various in style and possesses many excellent Specific characters, especially Zhejiang Native Pig Breeds Inferred, Reproductive capacity is high, sex premature, delicious meat and premunition is strong.Zhejiang Province's local pig breed includes Jinhua Pigs, Shengxian County flower pig, Jiaxing Black Pig is spent in pig, Chunan flower pig, Chalu Black Pig, green lake pig and Lanxi.Reproductive trait for the breeding work of local pig breed very It is important, but since reproductive trait belongs to more complicated character, reported according to current research, early application microsatellite equimolecular Major gene resistance of the label detection Zhejiang Province's local pig breed on reproductive trait, because its quantity is few, covering surface is small to be not enough in full base Because screening and explaining the genetic mechanism of the character in the range of group.The genetic force of reproductive trait is relatively low, utilizes conventional breeding side Method selection and breeding difficulty is larger, and makes slow progress.With molecular breeding technology development with it is universal, differentiate the major gene resistance of reproductive trait Or correlated inheritance label, breeding cycle can be shortened by marking supplementary breeding technology, can effectively accelerate breeding process.It utilizes SNP biochip technologies and whole-genome association (GWAS) technology can use lower cost and higher accuracy rate to sieve The genetic marker strong with reproductive trait relevance is selected, is the function in later stage to further filter out corresponding candidate gene The market pig kind of verification and seed selection and breeding, culture more prolificacy lays the first stone.
The beneficial effects are mainly as follows：The present invention carries out GWAS analyses to the local pig breed in Zhejiang Province for the first time, Relevance of the SNPs genetic markers with local pig breed reproductive trait is analyzed, to obtain several most High relevancy sites, is passed through Acquisition and the relevant PACSIN2 gene molecule markers of pig kind reproductive trait are reverse-located, is provided for local pig breed seed selection and breeding Basis.
(4) it illustrates
Fig. 1 is that pig SNPs distributions are spent in Shengxian County；
Fig. 2 is Jinhua Pigs SNPs distributions；
Fig. 3 is that pig SNPs distributions are spent in Chunan；
Fig. 4 is that META analyzes SNPs distributions.
(5) specific implementation mode
With reference to specific embodiment, the present invention is described further, but protection scope of the present invention is not limited in This：
Embodiment 1：
One, materials and methods
1, experimental animal
Sample used by experiment is the group of 3 pig kinds respectively：Pig is spent in 114 Shengxian County, comes from the Shaoxin City Sheng seeds of flowering plants Pig Co., Ltd；185 Jinhua Pigs come from Jinhua two Tou Wu boars Co., Ltd of agriculture of family and the Jinhua institute of agricultural sciences；31 pure Peace flower pig, comes from Chunan County Maoshan Mountain Chunan flower pig farm, these three groups are all in production sow.
2, the extraction of DNA and pig 50K SNP chip genotype sentence type
The blood cake card sample of three groups is collected in respectively：Flower pig is collected on June 24th, 2017 for Shengxian County；Jinhua Pigs acquire On June 28th, 2017 and 29 days；Flower pig is collected on June 15th, 2017 in Chunan.Take droplet of blood in blood from the ear vein of pig On spot card, bloodstain preserves the black circles of layer full of the dry blood cake among blood cake card, be placed on after dripping off at shady and cool ventilation dry to Discoloration, writes sample number clearly on card, closes blood cake card levels, collects blood cake card room temperature and transports to company's progress DNA extractions It is detected with chip.Final upper array experiment needs the genomic DNA of general 300ng, and transport when at least needs the dry of 1 microgram Dry genomic DNA.Genomic DNA after extraction requires DNA to be detected by agarose gel electrophoresis, there is clearly band, Length is more than 10kb, does not degrade significantly, the OD260/280 of DNA sample should be between 1.7-2.1.By the DNA of quality inspection qualification Sample carries out genotyping using the GGP Porcine50K SNP chips of Illumina platforms.
3, phenotypic data
The data of 6 reproductive traits of three pig kinds come from Shaoxin City Sheng seeds of flowering plants pigs Co., Ltd, the agriculture two of Jinhua man The data record of black boar Co., Ltd, the Jinhua institute of agricultural sciences and Chunan County Maoshan Mountain Chunan flower pig farm, this 6 reproductive trait difference It is that litter size (LS), number born alive (LSA), production male earner number (NM), the female young number (NF) of production, born weight (BW), piglet are averaged day It increases weight (ADG).
4, statistical analysis software
EXCEL：One of microsoft office office software, for recording phenotypic data namely three pig kinds of statistical analysis 6 reproductive trait data, do some simple data scrubbing, arrangement and calculating；
R：It is a kind of to be used for statistical analysis software, the language of drawing and operating environment.R is a kind of one based on GNU systems Freely, free, open source software is one for counting the excellent tool calculated with statistical cartography.This experiment GWAS analyzes main flow and is realized in R language environments.Official's network address of R：https://www.r-project.org/；
Rstudio：A kind of Integrated Development Environment done exclusively for R, the institute that R may be implemented are functional and accomplish that function is excellent Change, editor and preservation are convenient, and operation interface is made to become friendly easy.Official's network address of Rstudio：https:// www.rstudio.com/。
5, statistical analysis
Initial data is arranged into format, Rstudio is read in, with R language to the SNPs and individual of sample in initial data Quality Control is carried out, ineligible label is screened out.Data after Quality Control are calculated using General linear mixed model each Relevance between SNP and reproductive trait, analysis model are：
Y=X β+Z μ+e
Wherein, y is corresponding reproductive trait phenotypic number, and X and Z are corresponding fixed effect and the association square of stochastic effects Battle array, β are the fixed effect vector of mean value, gender and batch, and μ is the substitution effect of the SNP surveyed, and e is residual error.
With the GenABEL packets in R language[55], do following work：1. chip is sentenced type by the data entry requirement according to packet Data result is organized into corresponding format, generates genotype partial data, then by three pig kinds, 6 reproductive abilities from each pig farm The phenotypic data of shape reads in and is organized into phenotype partial data, and two parts data are combined to the file for generating " geno.raw " format It preserves；2. being loaded into GenABEL packets in R, make character overview rough estimates, generates file record；3. carrying out the first inferior quality control System, the index for screening out label are：Minimum gene frequency (MAF)s <0.05, SNP marker recall rate (call rate of SNPs)<0.95, individual of sample recall rate (call rate of individuals)s <0.95, the coefficient of consanguinity (IBS)s >0.95, Excessively high heterozygosity and less than hardy weinberg equilibrium value (HWE, the FDR&lt after correction;0.2)；4. individual of sample is carried out parent Edge coefficient clusters, the high individual of removal coefficient of consanguinity value；5. pair remaining individual of sample and genetic marker make the second inferior quality control System, generation the result is that be ultimately used to analysis sample and label；6. carrying out character description, result and the sites SNPs point are generated Butut；7. making GWAS analyses, determining conspicuousness threshold value and generate Manhattan point diagram and Q-Q figures, output is all to be higher than conspicuousness threshold The site of value and its information；8. choose the strong site of each character conspicuousness obtains its details in websites such as NCBI.
Make independent GWAS and three group of three groups respectively based on GWAS's with the GenABEL packets in R language META is analyzed.In GWAS analyses, Bonferroni is used to correct multiple check[56]Determine the conspicuousness threshold value of association analysis, The wherein effective SNP site quantity in Chromosome level remarkable threshold=1/；Genomic level remarkable threshold=0.05/ is SNP effective Point quantity.Since Bonferroni corrections are very much stringent, therefore also use more loose FDR correction multiple checks[57-58]Come Determine conspicuousness threshold value.The method of correction is as follows：By the correspondence p-value of SNP marker according to p1≤p2≤…≤pkSequence row Row, wherein k is effective SNP number；Search out the condition of satisfaction：piThe maximum p-value of≤i/k*0.05, wherein i are comparisons I-th of sample serial number；This maximum p-value finally obtained is the conspicuousness threshold value of FDR corrections.
6, candidate gene search
According to the result output of GWAS analyses and the strongest SNP site of reproductive trait relevance, then the name according to SNP site Claim and location information is in Ensembl (http://www.ensembl.org/Sus_scrofa/Info/Index) and NCBI (http://www.ncbi.nlm.n-ih.gov/) on pig genome database in it is corresponding with reference to where finding these SNPs or Person is most similar gene, and reference gene annotates obtain whether may be character candidate gene.
Two, result and analysis
1, reproductive trait describes
Spend pig, Jinhua Pigs and Chunan that the character initial data of pig and genotype data is spent to arrange format and typing Shengxian County Rstudio is merged into " geno.raw " formatted file, and first round quality control is carried out to data using the GenABEL packets of R language System, it is 113,182 and 28 to obtain effective number of individuals respectively；Then shape is made respectively to three pig kinds and META analyses Description generates record file；As a result the effective Shengxian County flower SNP number of pig obtained is 22 661, Jinhua Pigs 34 430, Chunan Flower pig 19 899, it is 38 881 that META, which analyzes effective SNP number, and specific character description data are shown in Table 1.
Table 1：Spend the reproductive trait description of pig, Jinhua Pigs and Chunan flower pig in Shengxian County
Note：NA indicates shortage of data
2, quality control
After first round Quality Control, the ibs functions in operation R language GenABEL packets calculate between each pig kind individual The coefficient of consanguinity, and individual of sample is clustered according to the coefficient of consanguinity using kmean functions, weeds out excessively high of the coefficient of consanguinity Body.Make the second wheel Quality Control：1. screening out the excessively high individual of sample of the coefficient of consanguinity, wherein flower pig in Shengxian County independently analyzes 25, and Jinhua Pigs are only Vertical analysis 44, Chunan flower pig independently analyze 10；2. the SNP marker that minimum gene frequency is less than 0.05 is screened out, wherein Shengxian County flower pig independently analyzes 25, and Jinhua Pigs independently analyze 6 570, and Chunan flower pig independently analyzes 4 236, META analyses 882；3. screening out the site that genetic marker recall rate is less than 0.95, wherein flower pig in Shengxian County independently analyzes 23, and Jinhua Pigs are independent Analysis 158, Chunan flower pig independently analyze 323, and META analyzes 124；4. screening out flat less than the Kazakhstan enlightening Weinberg after correction Weighing apparatus value (HWE, FDR<0.2) genetic marker, wherein Shengxian County flower pig independently analyze 92, and Jinhua Pigs independently analyze 554, Chunan Flower pig independently analyzes 38, and META analyzes 11 581.
After the quality control of two-wheeled, the GWAS analyses of SXHZ independences are finally obtained：88 individuals and 22 521 SNPs, wherein the sites SNPs are up to 2 093 on No. 1 chromosome, the sites SNPs are minimum on No. 12 chromosomes, only 465； The GWAS analyses of JHZ independences：138 individuals and 27 183 SNPs, wherein the sites SNPs are up to 2 454 on No. 1 chromosome, The sites SNPs are minimum on No. 18 chromosomes, only 577；The GWAS analyses of CAHZ independences：18 individuals and 15 345 SNPs, In on No. 1 chromosome the sites SNPs be up to 1 392, the sites SNPs are minimum on X chromosome, only 257；META is analyzed： 221 individuals and 2 6358 SNPs, wherein SNPs is up to 2 528 on No. 1 chromosome, the sites SNPs on No. 18 chromosomes At least, only 535.The numbered positions information of corresponding SNPs, is fabricated to the distribution map of SNPs as shown in figures 1-4.
3, whole-genome association
Shengxian County after two-wheeled Quality Control is spent to 22 521 SNPs of pig independence GWAS analyses, the GWAS analyses of Jinhua Pigs independence 27 183 SNPs, Chunan spend 15 345 SNPs of pig independence GWAS analyses and 26 358 SNPs for META analyses to protect Deposit, in GenABEL packets Generalized Linear Mixed Models and corresponding function, calculate each SNP site and reproductive trait Corresponding relevance P values, the conspicuousness threshold value and FDR correction multiple checks determined according to Bonferroni correction multiple checks are true Fixed conspicuousness threshold value, obtains final the selection result, and makees Manhattan point diagram and Q-Q figures are associated with character SNPs is presented Property and other information, being searched on the websites Ensembl and NCBI further according to name location information of the SNP site filtered out etc. can The candidate gene of energy.
Spend pig independence GWAS analysis results in 3.1 Shengxian County
Shengxian County is spent in 6 reproductive traits of pig, and LS has 16 SNPs to reach the FDR correction levels of signifiance, and character LSA has 28 SNPs reaches the FDR correction levels of signifiance, and character NM has 33 SNPs to reach the FDR correction levels of signifiance, and character NF has 33 SNPs Reach the FDR correction levels of signifiance, character BW there are 15 SNPs to reach the FDR correction levels of signifiance, and character ADG there are 35 SNPs to reach FDR corrects the level of signifiance.The Name & Location information in the strongest sites SNPs of conspicuousness is compareed, and passes through Ensembl and NCBI Website search candidate gene primarily determines the candidate gene point corresponding to character LS, LSA, NM, NF, BW, ADG of Shengxian County flower pig It is not SEMA4D, EYA4, ZC3H12D, BANP, DIP2B and TUSC3.
3.2 Jinhua Pigs independence GWAS analysis results
In the reproductive trait of Jinhua Pigs, LS has 33 SNPs to reach the FDR correction levels of signifiance, and character LSA has 35 SNPs Reach the FDR correction levels of signifiance, character NM there are 23 SNPs to reach the FDR correction levels of signifiance, and character NF there are 33 SNPs to reach FDR corrects the level of signifiance.The Name & Location information in the strongest sites SNPs of conspicuousness is compareed, and passes through Ensembl and NCBI Website search candidate gene primarily determines that the candidate gene corresponding to character LS, LSA, NM, NF of Jinhua Pigs is respectively SPINK14, SPINK14, GRIP1 and PPP3CA.Spend pig independence GWAS analysis results in 3.3 Chunan
Chunan is spent in the reproductive trait of pig, and LS has 22 SNPs to reach the FDR correction levels of signifiance, and character LSA has 18 SNPs reaches the FDR correction levels of signifiance, and character NM has 14 SNPs to reach the FDR correction levels of signifiance, and character NF has 8 SNPs to reach The level of signifiance is corrected to FDR, character BW there are 7 SNPs to reach the FDR correction levels of signifiance.Compare the strongest sites SNPs of conspicuousness Name & Location information, and by Ensembl and NCBI website search candidate genes, primarily determine the character of Chunan flower pig Candidate gene corresponding to LS, LSA, NM, NF, BW is RAD51AP2, RAD51AP2, TRIM21, OLFM3 and PBX1 respectively.
3.4META analysis result
In 6 reproductive traits of META analyses, LS has 51 SNPs to reach the FDR correction levels of signifiance, has 1 SNP to reach Bonferroni corrects the chromosome level of signifiance, and character LSA has 44 SNPs to reach the FDR correction levels of signifiance, has 1 SNP to reach The chromosome level of signifiance is corrected to Bonferroni, character NM there are 36 SNPs to reach the FDR correction levels of signifiance, and character NF has 81 A SNPs reaches the FDR correction levels of signifiance, has 4 SNPs to reach the Bonferroni correction chromosome levels of signifiance, and character BW has 70 SNPs reach the FDR correction levels of signifiance, have 2 SNPs to reach the Bonferroni correction chromosome levels of signifiance, character ADG There are 55 SNPs to reach the FDR correction levels of signifiance, there are 8 SNPs to reach the Bonferroni correction chromosome levels of signifiance.Control The Name & Location information in the strongest sites SNPs of conspicuousness, and by Ensembl and NCBI website search candidate genes, tentatively Determine the corresponding candidate gene of character LS, LSA, NM, NF, BW, ADG be respectively PACSIN2, PACSIN2, ATP8A2, ZNF32, CTNNA2 and FAT1.
Three, it discusses
This research has been independent GWAS to 6 kinds of reproductive traits of Shengxian County flower pig, Jinhua Pigs and Chunan 3 groups of flower pig and has been analyzed With the META analyses based on GWAS, wherein in the independent GWAS analyses of Shengxian County flower pig, determined using FDR correction multiple checks aobvious Work property threshold value obtains 160 SNPs and reaches the level of signifiance altogether；In the independent GWAS analyses of Jinhua pig groups, corrected using FDR more Determining conspicuousness threshold value is examined again, is obtained 124 SNPs altogether and is reached the level of signifiance；Spend the independent GWAS analyses of pig groups in Chunan In, the conspicuousness threshold value determined using FDR correction multiple checks is obtained 69 SNPs and reaches the level of signifiance altogether, but due to Chunan Flower pig sample size is too small, and in conjunction with QQ-plot figure interpretations of result, accuracy is not high so do not use；And the META analyses of 3 pig kinds In, it has obtained 337 SNPs and has been corrected significantly in FDR, 16 SNPs are notable in Bonferroni correction Chromosome levels.
It is because META have character that META analyses based on GWAS have obtained more sites SNPs than independent GWAS The SNP site for the different groups of phase same-action merges, and expands sample size, increases the reliability of GWAS analyses, closes And sample is also possible to find the new sites SNPs.It is generally acknowledged that about the female young number (NF) of reproductive trait production male earner number (NM) and production Determined completely by sex chromosome, but also there is researcher to propose in fertilization process in recent years, egg cell and sperm for Mutated-genotype is the viewpoint by skewed popularity, therefore discusses that influences of the SNPs to NM and NF still has the certain significance in our current research 's.
It is analyzed according to META, the candidate gene positioned by the sites SNPs of reproductive trait LS, LSA, NM, NF, BW and ADG Respectively：PACSIN2, PACSIN2, ATP8A2, ZNF32, CTNNA2 and FAT1.PACSIN2 is located at the 5 853 of No. 5 chromosome 377bp can regulate and control metalloproteinases and ADAM13 disintegrins at 5 985 174bp, and characterizing gene sequence is shown in SEQ ID NO.1 can be used as PACSIN2 gene molecule markers.From gene annotation and online each document, have no the gene of positioning with The related association of the reproductive trait of research and report.
Each reproductive trait of sow is all protected from environmental to some extent.Consistent growing environment, identical feeding are provided Material, feeding amount, take identical wean number of days, enlarged sample amount these can increase the reliability of research so that analysis knot Fruit is more accurate.There is differences for reproductive trait between the kind of Discrepancy Description existing for the phenotypic data of different cultivars, different Kind positioning conspicuousness site differ illustrate kind between there is differences on gene.For this 3 pig kinds, 6 reproductive trait GWAS analysis and research it can be found that influence some factors of these characters, be the breeding work that we promote pig reproductive trait Bring help.
Sequence table
<110>Zhejiang University
<120>With the relevant PACSIN2 gene molecule markers of pig kind reproductive trait and application
<160> 1
<170> SIPOSequenceListing 1.0
<210> 1
<211> 9903
<212> DNA
<213>Unknown (Unknown)
<400> 1
ggggcgctct gggctggcgg cagaagcggc agcggctggg tagggcaggg ctgggtaacg 60
cggccagagc gagggcggga gccgggccgg agccggagtc ggagccgggg caggagtcac 120
cgtcgcggct ggagcggagt gagcggcgtg ttgagaggcg agcggcggcc gaggtgaggg 180
gcccaccgcg acggttgggg cgccgcggac ggacgcgggg cgctggtcgg cggccgggcc 240
cgagccctgt caggccgccg cggcgcggcc gcgctccgcg cccgagggca gcctcagggg 300
ccgcgccggc ggcgcgcgaa cttcctgtcg ctgtgggagg gggtgtgttc aggggccact 360
gcgttcaggg gacgtcgggg gggccgaggg agggcgcccg agggcgcgtc gcggggcgtc 420
cggagggcgg gtggggtgct tgcgggaggc gggggccggg cgtgcggggt tggggcggcg 480
gcggcgccgc ggaggagcgg acgagttctc gagtgagggc ttctggaggg agaagttggg 540
gagcggggcc cgcggggtca gagggctgct gcggaagggc aggtgggagc cctgaggaga 600
gacctagcga ggggaggcgg ggaagtcgag gggtgccggg gttccctggg ggaagcgcgg 660
gcaggcgcgg gaggctgggg gagccgcgtg ggagccgagg ggccgggtaa gcgccggcga 720
gaggagggca gggctgggtc cgagggtggc ctggaggggc ggaggcggcc cgagcagccc 780
ggacacatat gcggatgcgc tcatttgggg ccctttgatg accgtcgtcc atttccttcc 840
ttcccaccct cccctccctc tccaggctca atgttgtagg tgaggcgggg gcggggaggg 900
gggtgggggg tggccagccc cttttgcgag caggtcctgg ggctggggac gcaggccgga 960
gaggctggtc gcccctggga gttttcccag attgtcgttt ggagcaacgt gagcgccctt 1020
cctcccgtag ggttccgagc ctgccggggc atccggagag gcctggagcg gagagggggt 1080
gctttctgct gctcagtttc agtggctcag ttgggttttt agctccagga gctgaaaacg 1140
ctggttttct gttttagacg gaggtggtcg gggggcgagc agcgctgcct cctggggatc 1200
ccacggagct gcagcctttg aggatgctgc tcttgggttg ggtgcctgag ggaaggtggc 1260
cttcaggtgg ggcgtgtgtg tccctgggtc ttgatttctc tcttttacct caactgtcct 1320
gtgtttttgt ggttaaggag ggctggctgc tcagagtctc cacgactact cattacactg 1380
tttaccaaac actccctggc tgtcctgatg aaaatcagga gaccagccca gagaatttaa 1440
acctaggttg caagcggtga gctcacaaaa atgccttcct ttctctgcag ttgcttcctc 1500
tccagttatc ccactgtgct gaagttctgt tttaactctc ccaggattgt caggttggag 1560
ccagggcaag ggaaccaacc cttcttcccc ttcttccctg aaggttatta ctattatttt 1620
ttaaatgtta tggctgcacc tgcagcaaat ggaggttccc aggctggggg ctgaatcgga 1680
gctgcagctg ccagcctaca ccacagccac agcaatgctg gatccttaac tcactgagct 1740
aggccaggaa tcgaacccac atcctcatgg atactagtca ggttcattac tgctgatcca 1800
cagcagaaac tctcattctg tgaaagttct tattctactt gattcccagt cccgcctgga 1860
gcctctccat agaggcattg aatgggagcc agtgcaagtg gggtttctct ggattcacat 1920
gggaaacaat aatctgtgtg catttaaact taattctaga gtttcacagt ctccttaatg 1980
aggttctgtt agttgagata tgagcccact gcatcaaaaa cttttctgtc gtgtgttttc 2040
cttctgacaa ttgtcttgaa gctttaaaga aattggccgt taaactggtg atatttagta 2100
ctttggaaag taatgtagca caggagtgga tgagcgacta ggtctgcact cttaatccac 2160
tttttttgga gaagagtaaa aactcatttg gatggaaatg tcattctcag ctcatgcttt 2220
tggggaactg gaactttatt acttttagtt tcaaattata agatgtaggt cataatattt 2280
aaacagtcta aaagtatgca tttgtaaaaa atagtatctg gggtttgaac acagcttgct 2340
gctgttggct ttcccccgtc ctggatgccc tgtctagatt tttgatggcc aggcagtttc 2400
tgggatggga gctgaaggac atttgtcctt aattttctca tttctttatt cacttggaag 2460
tctgtgcaga ccaagttaag gacatgatgc tcagatttcc cttctggtct ggtcatcagt 2520
tgattatagg atattatgga atatcaaaaa gatgacacag atgtcttagt aatagtaaca 2580
gcgccttgtc tctagagatc acaatagcat ttagcaagcg ctctccccct cacctaaacc 2640
tcgcatctgg cttggcctgc cttatctgcc atcacattgt acccgtggct ttgtggaggc 2700
caccctgtag attatttggg taatgaccac attcacgtga gcgatagtgc tggctcagtt 2760
tttttccaat taggttgttt ggaagtgcag ctgcatgcct gaaggcagca cagccatgcc 2820
ttagttacga agtcagtttg cattccacag gtggagacct ttccttatgg acctggaatg 2880
attcttcaca tacctgaaag catgtcagtg cctgaaacct gtttcctgat aggcctagtg 2940
gtggtccctg ggatggctgt gtaggaattc cgtcagattt ttagttttca gatgattgtg 3000
ctatactgac tagagacaat cttaaaaaga agagttttca aagtattttg tacaatgcaa 3060
cattcttggc gtatgtatat ttccaaaggt aactatttga gggacagtgg ccatctaaga 3120
gcacaagttt tgatattttg attaaaaaca caaatgacaa aaactcctta gttaaattat 3180
gttaacttgt atttattccc atgattgtat gtttatctgt ttgcttaata aaacagagca 3240
ccatgtagtt tagttttctt gtttcctaga ataaaatctt tattttcaac attaaagcac 3300
catgtgggta tttcttgaca ttaggcactg aaagaataag atatgagaat atagaaatga 3360
atagaatgct gtctaagtga tcaaagacct cagcaagaag gctttaagag agaaaaataa 3420
ggatggaaaa ttttctctaa cttcagaagg cacatgtgca gtggtttgta ttaacatact 3480
ccatggctat gtgagattta tgtgactttt ttcctacttg gagtggaagg agcatggatg 3540
gagactagga gccccggctc tgtccagccc tttcctcagt cacataactt aaggtctcag 3600
ttttcatgtt tgtaaaagta gggccttaga ggtccttaac cttgtgagaa tctgatagca 3660
attagagctg tcttcccaga aagcgcactt ggggacagca tcagaggctg gaccccagac 3720
tagtaacgcc cggctcatcc catctcttag ctccctctgg cctctgttag tctgtaatcc 3780
tattttcttg gtcgtctttg agctaataat aataatgatg actacattta tagaagacac 3840
atcccaaagc attttcacct gtcctttttg gtcctcaaaa acatttctga ggggtgtgag 3900
tggtgatgga tggagaaagg ggtaccaggc ctgccgccat tttaggaggg ttacacagcc 3960
agcagcctgt cctgggatca gcatcagggc tcctggtcgc cagcttgggg tttttccatt 4020
aggttttgct tccttggtgg ttgtcattat gagttatgtt tggcagtgta aatatcccag 4080
aatgtgtcac ttgcagagga aatatttgtt catctactga aaggactgtt ttttgtctga 4140
atttggatca ctgaacacct ttctgcctgt caaaaggtta cttactttgt ttttgttatt 4200
tctttgtgcc atacttttca tagagaaacg tttgtggggc atgggtgttt tgagcagact 4260
tattgaatgt ttatcgatta accagtacat tgagatgatt gcttttcagt tgcttggcgc 4320
ttgagaaact tgtgaaataa atgctaagtg aaattccaaa tgtttgactt gttctatcaa 4380
atatgtcctc acagacgaga ctttccctgc agcctaaggg gcccctccct gggcccagag 4440
ccaccgggtg ggtttgagag ttgggtgtgg tttgtgccaa tgaccatgac tgtctaacag 4500
tggcttcttg tggccttctg gccagattct gactatttgg gggacttccc ccccagttta 4560
ttcacagagt atagagtatt agttatatga caggcttgta gatgcaagag tactaaactg 4620
taaagcctca cagattttac atgctttgtt actgatggaa agaatcgttg taataaagat 4680
gttttgaata atcagacatg gaggtaatga aatggtatac ggtaggtgtc actcagaggt 4740
ggtgtatgtt gtgtctgatc ctggtaagga gactggctga catcattcac tctccaggca 4800
tgggaaaggg tatttgctca ttgcacggtg cctttcttga gaacactgga gaggaggagg 4860
ctgacgtgca cagcctcact gacactgaac ataaaccctg atgtcatgtg tcagcttccc 4920
taggcaaatt gctcaccaga gagaggactt ggtagaggct aaaggcaggc agtgaaggct 4980
gagcatgaag cagtaggaaa tcatcaaaat gagaagtctg gtcaggtgat gaggctgtca 5040
gaggtcaagg cccaggttga agtgtaaact ccaggcctcg gccaccatgc aggagtggca 5100
tccaggtaac tatataacct gccacaacgc ctccttcatt atctctgcta gtatttatgg 5160
gcccttctct gaccaggaaa cttgcatcgc taggctcttt tattccagtg gcctgttgtc 5220
tgtgatttaa atattgatag agtggcagag ctgtcagtag tcagctgggg aactccatta 5280
ggctgctgtg ttgaagtact tgctttttat ttaagtttca ctcccagggc tgagtgtttg 5340
gagggagtgt atgtgggtga gcagaagtgg gcaagggggg tcaaagggag ccttcctggc 5400
cactgtgtac gcagcgcccc tgacgcttgg ctctactcac agttctggga tcccaagatt 5460
atggtgactc ttagtcagga ggcgggttct tagaagcatt cccatcttgt gacagtagca 5520
gataggcgtg tgtgcgaagt taggggcaga caggagggcg ggtctgactg ccctcaggac 5580
actgcagaga gctgaccttc agggatgtga ctttagagtg atttgtcact ttccaggtgc 5640
tctccaggtg gagatgactg gaaggggcgt ctcaggcaga ggcgcggagt tgtaaggaat 5700
gtggggctgt gagaggggcc tcacagtgga gggctggatg actgggtggg caggcttcag 5760
gttgtcaggt ttggacttcc tcttggagga tgaagttcaa cggggagtca tttctgggtg 5820
gtacacacag caggtggaag ctctgcacag aagtgagagg tcagggatgc agagggagga 5880
gggatacttc aggtggctca tttcagcaaa ggttacctat gtcactggaa gctcaaggat 5940
aactggggac atccttagga agcagtgcta aactctaatg agaggggctt ccagaatggg 6000
cctggcatca gtcttagttt ctttgcctgt gtttatattt ttacttgata atacagcagc 6060
tgcctgggtt ctgcttctct ttccatatgg cttgtgctca caaatccagg cagttagagt 6120
atgtcatttt cactgccagt tcctgcagaa aaaaagggaa tagtgaagta aggtgtagga 6180
ggttacatgg tttgggagcc atgcagccct gtgtttgagt tccagctcca ctactaggtc 6240
accgtgctct tccttggaca aacgcttcaa catttccaaa accaggacac tgacagcccc 6300
cttctcatat gtctgagtga gggaagtgtg agggaatgga ccacagacgc agagagctca 6360
gcacttgtgc ctggtccatg gtgttggctc ataacttcag catcacagtg cagtgtcttc 6420
tgaagagaat ttgctaagtg aaatatacct ttaaagggtt caaactgatg ttctattgtc 6480
caattctatt caaaatcctt ctaagtcgtg ttactctttt ctgagcctat gcgtattcag 6540
tatacttgga tcttttcctt ggtgcctcag ggtcacagag atgctgttgg ggttgttgac 6600
gtgaatgagg cttctgacct tgcatggaat accctctcat cctgccactt acaagccctg 6660
tcttgtctct ccactgctta ttctctctgg gttttgaggg cagtcctgcc acacagaggg 6720
cttgctcctg tctgggttgg cagttctgtg cttgagttga atattacgta ggttatagaa 6780
agcctgaccc tggggtgaat ggatattgtg actagactta gcgactcaga attggaagga 6840
accatgtgtg atggtgacag tggcttgtac tcaggtaagg aaaaatacga agccttgaaa 6900
aggcaaatta tagcgataca tacactcatc acgtgtaaaa tattaaaata atacacggtg 6960
actatggtag ttaaggctgc agaattatgg aaagtttctc cttcatttcc aaattgttcc 7020
attacccttt tacttgtatt taattttatt tatttaattt taattaatta attaattaat 7080
tggccatccc catggcaagg gaaagtttcc aggccaggaa ccgaaccccc accacagcag 7140
tgacaatact gaatccttaa cctgctgcac taccaaggat atccaccttt tacttttaga 7200
attaatattt aagtaataac tgtgatgaaa ataaacatat ataaaaacag ctttgttttt 7260
aagcattttc attttacggg gacttttccc atagccctca ttttgtttgc agaacagtct 7320
tgttggtttg ctcccttctt tcactgttca gaggaggata agaaggagga ctggagggtt 7380
ggtggttttg cctgaggctg gccagccagg accccatgtg ggcctcagcc caagtcccag 7440
gctcccagag agcatagtta gggggcctcc gctggggcct gcagggtggt ctttatcatg 7500
cagaataaac tgtgtctagt gctttgaagt ttccttcgca taaatgaaat tttattattg 7560
taaagtgata ctgaaaccat agtttgtgaa cgttttcata ttttaaacta catttatgtt 7620
ccatcgtatc caattatgtt gtcgccaact gcgtgtgcca agtctgtgag ttgcggtcgt 7680
cagaggaacc acagagcagg ctccgtacct cacgtggacc tccaggcctg ctattagtgg 7740
gtttggtagc tggctgactg ctgtaggatg gagctggcct acctgggccc tgtttagctt 7800
ggacatgctg atgttttaat tgaggaggcc attgtgccct ttgtgccagt gaagatgtcg 7860
tcagctaagg agcctgggaa gccagtgagg aagccggctg aggggagggt ggatcagggt 7920
ggggtcgccg tctgggacag acaggcctct ggatgttggg gtttctgagg gaccatacaa 7980
gaagctctac actcctgctt attaattctt gcaacaaaat agagttaact ccagagttct 8040
cttcgtggca cagtggaaac ggatccgact aggaactgtg aggttgtggg ttcgatccct 8100
gggcttgccc agtgggttaa ggatccggct ttgcagtgag ctgaggtgta ggtcgcagat 8160
gtggctctga tctggtgttg ctgtggttct ggtgtcggct gacagcaaca gctctgatta 8220
gacctctagg ctgggaacct ccatatgccg aaggtgtggc cctaaaagga caaaagacaa 8280
aaagaaaaaa aaaaaagtag agttaactcc actttactca tgagtaaacc aagctctgag 8340
agatgaaatg accttcacag ggtcactggc agagcagacc ctcagcctgc ctctgaagct 8400
atgctcactt cacttatttt gctgtattga ataagtggat tctgagtcat ttgccctcaa 8460
atatgaagaa aaattttaag ttaatcttcc ttccccacct cccagaaacc tagaaaagag 8520
gcaagttatg tggtcttttt aagacagggt ccatgcctac aactaactta agataatcta 8580
aaagtttgca ataatttatg cattgggaaa gataagggca caaaaggaaa aggcttctaa 8640
acagctctgc tgtgactcca gagctcctgg cttaagtggt gggagtgctc ttgcctagcc 8700
tttcactagc tacatttttt tttgcttttt agggccgtgg aatacaatga tttccaaaca 8760
gaaatcatgg cacatggaag ttcccagggt aggggtcaaa ttggagctac agctgccggc 8820
ccacgccata gccacagcaa ctcaggatcg tagccttgtt ggagacctgc accacagctc 8880
atggcaatgc tggatcctta acccatggag tgaggccagg gatcaaatcc aagtccacat 8940
ggatactagt tggattcgtt ttgctgtgcc acagcgggaa ctcctagcta tattcgaaaa 9000
gctgccgtgt tattgaaaaa gcacttactt aggggagaag aaatgacatt tctgtaaagc 9060
attcattttg cactatgtaa aattgtgaaa gggcttcatg ttttgttgat attatgatat 9120
caaatgaaga tcatttgtgc aaataaatta gagcagatgt ttgtttttat gcttgtaatt 9180
gtcattttgt gtcaaaaacc tttttttttt tgctttcttg tcttataggt cttttaaaaa 9240
ttgaagatac aacgtagaaa atagagtttt ttgaataaaa aactctttgt gttttaccct 9300
ctacatgtat agagttttta atgttatctt agaagcagta gctgccacct acttactgag 9360
tgctttattc taagcttcag aaaagagaac ggccttgcct ctgtctgtcc tcacagcaac 9420
actaaggctc tgaggttact agtttgaaca tgagggtact gcagggagtg agatcatgtg 9480
cttagtccac ggtcatcaag attgtaaata ggggagagaa tttgaagcct gcactggctg 9540
catgggcctg tctccttttc atcaatctac actcttacaa ttgtattatt aagattctct 9600
gaaatattgt atcaaaaatt tcccatattt ttatcattgt ctttaaaaag ttttttttag 9660
gagttccctt ggtggcacag tggttaacaa atccgactag gaaccatgag gttgcgagtt 9720
ccatccctga cctcgctcag tgggttaaag atccagcgtt gctgtgagct gtggtgcagg 9780
ccgcagacac gggtcggatc tggcgaatct ggcgttgctg tggctgtggc ataggctggt 9840
ggctacagct ctgattcaac ccttagcctg ggaacctcta tgctgcgggt gtggccctta 9900
gaa 9903

Claims (3)

1. with the relevant PACSIN2 gene molecule markers of pig kind reproductive trait, nucleotide sequence is as shown in SEQ ID No.1.
2. application of the molecular labeling described in claim 1 in local pig breed breeding.
3. application as claimed in claim 3, it is characterised in that the local pig breed is one of following：Shengxian County spend pig, Jinhua Pigs, Spend pig in Chunan.
CN201810644972.2A 2018-06-21 2018-06-21 With the relevant PACSIN2 gene molecule markers of pig kind reproductive trait and application Pending CN108707678A (en)

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Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN114304057A (en) * 2021-12-23 2022-04-12 深圳市金新农科技股份有限公司 Molecular breeding method aiming at body size characters and application thereof

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN114304057A (en) * 2021-12-23 2022-04-12 深圳市金新农科技股份有限公司 Molecular breeding method aiming at body size characters and application thereof
CN114304057B (en) * 2021-12-23 2022-11-22 深圳市金新农科技股份有限公司 Molecular breeding method aiming at body size character and application thereof

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