CN103757006B - A SNP site relevant to litter size and primer thereof on No. 6 chromosomes of pig - Google Patents
A SNP site relevant to litter size and primer thereof on No. 6 chromosomes of pig Download PDFInfo
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Abstract
The present invention relates to the SNP site relevant to pig number born character, be specifically related to a SNP site relevant to litter size and primer thereof on No. 6 chromosomes of pig, belong to biological technical field.This SNP site is the Chr6:64826013 of genome version NCBI Build Sscrofa10.2；The allele in this site is T and C, has tri-kinds of genotype of C/C, T/C and T/T, this site and flanking sequence thereof as shown in SEQ ID NO:1.Expand this SNP site primer and extend primer be: Chr6 2 PCRU:5 ' GAC GGC CAA GCA GAA CAG 3 '；Chr6 2 PCRL:5 ' TTG GGG CAG ATT AAT ATT TCA A 3 '；Chr6 2 SNPU:5 ' ACT GAC TGA CTG ACT CTG ACA AGA ACG TGT CCA CCG AGC C 3 '.Litter size of pig with C/C genotype is higher than T/C and T/T genotype.The beneficial effects of the present invention is: use full-length genome weight sequence measurement, can screen the SNP site relevant to character or candidate gene quickly, in bulk, this site of Chr6:64826013 can be used for the litter size of the genetic breeding raising sow of pig as genetic marker.
Description
Technical field:
The present invention relates to the molecular marker relevant to pig number born character, be specifically related on No. 6 chromosomes of pig one
The SNP site relevant to litter size and primer thereof, belong to biological technical field.
Background technology:
The characters of number born of pig is the key component of pig reproductive trait, improves litter size of pig to improving pig industry
Overall economic benefit significant.But litter size belongs to the quantitative trait that heritability is the lowest, it is difficult to educate by routine
The technology of kind carries out genetic improvement.The Taihu pigs of China is well-known with high yield, and nest litter size is than other China of great majority
Nest litter size many 4-5 head of local pig breed and external pig kind (" Chinese pig breeds will " Zhang Zhongge edits, on
Sea Science Press, 1986).Erhualian is the one of Taihu pigs, is the pig kind that reproductive capacity is the highest in the world.
Polymorphic site relevant to high litter size in Taihu pigs, it is possible to as genetic marker for improving the farrowing of sow
Number.
Research worker uses the method for genome-wide screening and candidate gene to carry out characters of number born both at home and abroad
QTL location and the research of candidate gene.Li et al. (Li, K., J.Ren, et al.Anim Genet.2009.40 (6):
963-966) utilize and cover total relevant to litter size of pig of 183 microsatellite markers pair of 19 chromosomes of pig
Litter size, number born alive, produces dead young number and carries out QTL(Quantitative Trait Locus, Quantitative Trait Genes
Seat) location.They have studied the F of 299 durocs and China's Erhualian hybridization2In generation, 6,7,8
Located and total yield coefficient with on No. 15 chromosomes, the QTL that number born alive is relevant with producing dead young number.
(Rothischild, M., Jacobson, the D.et al.Proc Natl Acad Sci U S such as Rothschild
A.1996.93 (1): 201-205) by candidate gene approach, utilize two including Prunus mume in China mountain system Taihu pigs
Extreme mixing breed, finds a gene (ESR) at estrogen receptor seat on No. 1 chromosome and high litter size
Major gene resistance is chain.Analyzed by the RFLPs at female hormone receptor gene seat, it is believed that there is 3.7kb band
Homozygous sow (BB type) wants many 2.3 than when having homozygous sow (AA type) primiparity of 4.3kb band
(P < 0.01), every tire averagely 1.5 (P < 0.01) of fecund.Report the gene relevant to litter size also at present
Have OPN (US6410227B1), PRLR (Tomas, A., J.Casellas, et al.J Anim Sci.2006.84 (8):
1991-1998), FSH β (Zhao, Y.Li N, et al.Sci China C Life Sci.1998.41 (6): 664-668)
With RBP4 (Spotter, A., S.Muller, et al.Reprod Domest Anim.2009.44 (1): 100-105)
Deng.
Application QTL localization method can position region closely linked with character, however it is necessary that research several generations man
A lot of individualities of system, the cycle is long, wastes time and energy, and cannot complete at general laboratory, and some QTL
Position the most wide in range.Utilize candidate gene approach that character is studied, simple direct comparatively speaking, but utilize and wait
Select that gene approach mainly studies is the sudden change of exon region, and the sudden change much playing critical function is likely to
Intron or other functional area；Some complex character is affected by polygenes regulation and control；Can not detect all of
QTL, and some does not find the location of QTL with the gene of candidate gene approach research.
Along with development and the maturation of technology, genome and gene annotation are more and more perfect.Fast due to sequencing technologies
Speed development, the reduction of order-checking cost, it is possible to utilize genome sequencing or transcript profile to check order to trait related
Cause or mutational site carry out batch and screen.The present invention selects Erhualian (one of Taihu pigs), hides pig, bar
Horse perfume (or spice) pig, Laiwu Pigs, 5 Chinese native pig breeds such as the southern regions of the Yunnan Province microtia pig and wild boar have carried out full-length genome and have resurveyed
Sequence.Wish therefrom to filter out the SNPs(single nucleotide polymorphisms relevant to high litter size, single
Nucleotide polymorphisms) site as genetic marker for the genetic breeding of pig, to improve the litter size of sow.
Summary of the invention:
It is an object of the invention to provide on No. 6 chromosomes of pig a SNP site relevant to litter size and draw
Thing.
The present invention have selected Erhualian (one of Taihu pigs), hides pig, BaMa miniature pig, Laiwu Pigs, and Yunnan
South 5 Chinese native pig breeds of microtia pig and wild boar have carried out full-length genome and have resurveyed sequence.The sequence of resurveying of 6 pig kinds
Number of individuals is respectively 11,11,9,10,10 and 10.Weight sequencing data is with reference to base
Because group (NCBI Build Sscrofa 10.2) is compared, SAMTools software is utilized to carry out SNPs site
Extraction.Inventor compares Erhualian and other 5 pig kinds, finds a SNP on No. 6 chromosomes
(Chr6:64826013 of genome version NCBI Build Sscrofa10.2) may be with the farrowing of pig in site
Number is relevant.The allele in this site is T and C, has tri-kinds of genotype of C/C, T/C and T/T.This site
And flanking sequence (SEQ ID NO:1) is:
After screening this site, inventor comprises the nucleotide in this site with the DNA of pig for template amplification
Sequence fragment also checks order, and verifies this site and correlation analysis.The individuality that wherein inventor selects
It is the F2 offspring of white Duroc × Erhualian (one of Taihu pigs).Found that farrow with pig in this site
Number has significant correlation.
The beneficial effects of the present invention is: use full-length genome weight sequence measurement, it is possible to quickly, screen in bulk
The SNP site relevant to character or candidate gene, the Chr6 of genome version NCBI Build Sscrofa 10.2:
64826013 these sites can be used for the litter size of the genetic breeding raising sow of pig as genetic marker.
Accompanying drawing illustrates:
Fig. 1: white Duroc × painted face in Beijing opera F23 kinds of Chr6:64826013 site gene in godmother's pig resource population
The litter size of type compares that (* represents when two kinds of genotype litter sizes compare, 0.01≤P≤0.05；* table
Show P ＜ 0.01).
Specific embodiments:
(1) the population distribution feature of SNP site
The present invention have selected Erhualian (one of Taihu pigs), hides pig, BaMa miniature pig, Laiwu Pigs, and Yunnan
South 5 Chinese native pig breeds of microtia pig and wild boar have carried out full-length genome and have resurveyed sequence.The sequence of resurveying of 6 pig kinds
Number of individuals is respectively 11,11,9,10,10 and 10.Weight sequencing data is with reference to base
Because group (NCBI Build Sscrofa 10.2) is compared, SAMTools software is utilized to carry out SNPs site
Extraction.Inventor compares Erhualian and other 5 pig kinds, finds a SNP on No. 6 chromosomes
(Chr6:64826013 of genome version NCBI Build Sscrofa 10.2) may be with the farrowing of pig in site
Number is relevant.From the point of view of the analysis result of sequence of resurveying, this site equipotential in other 4 Chinese native pig breeds and wild boar
The frequency averaging of gene T is 100%, and is 100% in the frequency of Erhualian allelic C.
(2) qualification of SNP site
At design of primers website design SNAPSHOT primer, including a pair pcr amplification primer thing
(Chr6-2-PCRU:5 '-GAC GGC CAA GCA GAA CAG-3 '；Chr6-2-PCRL:5 '-TTG
GGG CAG ATT AAT ATT TCA A-3 ') and extension primer (Chr6-2-SNPU:5 '-ACT GAC
TGA CTG ACT CTG ACA AGA ACG TGT CCA CCG AGC C-3 ').This site and other
Totally 24,11 sites (12 to) primer respectively takes 1 μ l and is mixed into new multiple PCR primer pond.First carry out
12 weight PCR reactions, reaction system agents useful for same is: multiple PCR primer pond (6.25 μMs of each) 8 μ l, dNTP
(10mM each)8μl、10×PCR Buffer II116μl、MgCl2(25mM Stock)234μl、Fast Start
Taq (5U/ μ l) 24 μ l and ddH2O460 μ l, by above reagent mixed liquor 8.5 μ l and 1.5 μ l DNA (50ng/ μ l)
The 10 μ l systems that are mixed into carry out 12 weight pcr amplification reactions.Amplification reaction condition is: 94 DEG C of 4min；94 DEG C of 30s,
55 DEG C of 30s, 72 DEG C of 1min, totally 40 circulations.Next step carries out PCR reaction purification, and required reagent is:
Exo I (10U/ μ l) 60 μ l, SAP (1U/ μ l) 130 μ l, 10 × SAP Buffer35 μ l and ddH2O125 μ l,
The PCR primer of each sample adds after 3.5 μ l above-mentioned purification mixed liquor is centrifuged and reacts by following procedure:
37 DEG C of 40min, 96 DEG C of 10min.Then carrying out single base extension, required reagent is: SNAPSHOT
(6.25 μMs of each, 12 extension primers are each for Multiplex ready reaction Mix100 μ l, extension primer pond
Take 1 μ l mixing) 8 μ l, 5 × Sequencing Buffer200 μ l and ddH2O300 μ l, by above reagent mixed liquor
The purified product of 6 μ l and 4 μ l is mixed into 10 μ l systems and carries out extension.Extension condition is: 96 DEG C of 10s,
50 DEG C of 5s, 60 DEG C of 30s, totally 25 circulations.Then carrying out the purification of extension product, required reagent is:
SAP (1U/ μ l) 120 μ l, 10 × SAP Buffer70 μ l and ddH2O140 μ l, at the extension of each sample
Product adds after above-mentioned 3.3 μ l purification mixed liquors are centrifuged and react by following procedure: 37 DEG C of 40min, 75 DEG C
20min, 4 DEG C save backup.Each sample take the above-mentioned SNAPSHOT product after purification of 5-4 μ l and
High-purity Methanamide (Hi-Di Formamide) of 5-6 μ l is mixed into after 10 μ l systems are centrifuged and is splined on ABI3730XL
Sequenator carries out gene type, uses GeneMarker software analysis genotyping result.
(note: the reaction reagent mixed liquor consumption of above 4 steps is amount of reagent needed for 100 samples, from single alkali
Base extension starts, and needs lucifuge to carry out.)
(3) white Duroc × painted face in Beijing opera reproductive performance hybridization resource population builds
Follow-up confirmatory experiment used resource group's individual sample and trait data thereof are given birth to by Agricultural University Of Jiangxi animal
Thing technology National Key Laboratory cultivation base provides.
In December, 1998, will purchase from Erhualian conservation field, 3, Jiangsu Province on Agricultural University Of Jiangxi's scientific research pig farm
The Erhualian sow bought carries out the intersection breeding of blood relationship between field.January calendar year 2001 according to parent's Farrowing Traits, from 3
The pure breeding offspring of head boar and 11 sows have selected 17 Erhualian sows mother for generations as sources group
This.2 high-quality white Duroc boars that Sygen PIC company is given are as the male parent for generations of Resource family.
The F that these 2 white Durocs and 17 Erhualian hybridization are produced1Breed for individuality, it is to avoid Quan Tong
Born of the same parents' copulation, and every boar generally with same head insemination of sows, to obtain the F of large sample2Family half sibs.2003
January in year, March and June, project team is respectively by the 1st batch and the 2nd crowd of F2Sow is sent to Jiangxi Province Yichun City poultry
Herd seed multiplication farm (59), state-run Red Star kind pig farm, Jiangxi Province (52) and quaternionic breeding pig farm, Shangyou County, Jiangxi
(118) are for the mensuration of sow reproductive trait.
(4) SNP site is at hybridization resource population F2The gene type of godmother's swinery body
According to the method described in above-mentioned steps (2), with 192 white Durocs × Erhualian hybridization resource population F2
Godmother pig individuality DNA is the genotype of this SNP site of template detection.F2For 183 individualities in resource population individuality
Success typing, 3 kinds of genotype C/C, the number of individuals of T/C and T/T is 82,87 and 14 respectively.
(5) SNP site regulating effect to characters of number born
At F2For in resource population individuality, the average litter size with C/C genotype individuals is 11.436, standard deviation
It is 0.884；Average litter size with T/C genotype individuals is 10.5272, and standard deviation is 0.8816；With
The average litter size of T/T genotype individuals is 9.9822, and standard deviation is 1.1389.
The present invention uses general linear model (GLM) to analyze SNP site to pig total yield coefficient, product son alive
The impact of number.All statistical analysis uses SAS software to carry out.Model is as follows:
Yijklm=u+Ai+Gj+Bk+Pl+eijklm
Wherein YijklmFor pig total yield coefficient or number born alive, u is colony's average, AiFor the additivity effect that i-th is individual
Should, GjFor the fixed effect of jth SNP site genotype, BkFor batch effect (k=1,2,3,4), Pl be with
Machine effect (l=1,2,3).
Analysis result finds that this SNP site of Chr6:64826013 has significant correlation (such as Fig. 1 with litter size
Shown in).F with C/C genotype2The litter size of godmother pig is more than the sow with T/C genotype
0.9088(P=0.0278)；F although with C/C genotype2The litter size of godmother pig with T/T gene
The sow of type does not has significant difference, but with the F of C/C genotype2The litter size ratio of godmother pig is with T/C
The sow of genotype averagely many 1.4538.As can be seen from Figure 1, the number born of sow with T/T genotype is minimum.
C is the useful allele improving litter size of pig.
Finding out with litter size correlation analysis from SNP site, this SNP site of Chr6:64826013 can
It is applied to molecular marker assisted selection (MAS) as molecular marker and improves the litter size of sow.
SEQUENCE LISTING
<110>Chinese Academy of Sciences Kunming Institute of Botany
Agricultural University Of Jiangxi
<120>SNP site relevant to litter size and primer thereof on No. 6 chromosomes of pig
<130> 7
<160> 1
<170> PatentIn
version 3.5
<210> 1
<211> 601
<212> DNA
<213> Sus scrofa
<400> 1
ccggggcgac ggccctgcct tgcactgagc atgcccagga ggggcttctg ctgtgtccgg 60
gctatggaag ctgacagcca atcagggcgg ttcaaactat gtgacctcgc ccgtcaagct 120
gtccggggct aggatgcgcg gcccgtccca gccgggccgg gctgggccgg ggaggatggg 180
ggcgctgggg ggggcggtgt gcctgggggg caaagggctg gagccgggtg ggcagaggag 240
tcggacggcc aagcagaaca gggcaaaaga aggggctgac aagaacgtgt ccaccgagcc 300
tttccccata atccccaagt gattgaaata ttaatctgcc ccaaggcgct gcagctgaca 360
gagagctgct gcacagacag caagtggcat tttattaaaa aataaaggaa aacggcccct 420
ccccttcact tgacctttct tttcggggaa ggagctttct ccaaagaaaa gaaagtactc 480
gacagtctgg ccactgagcc caaggtggcc ctggaggggg ccccgcccca gccgacaggc 540
acctggccgg ggggcgtggc cctgggcatc ccgcctgtcc ctcccacact cggagtggaa 600
g
601
SEQUENCE LISTING
<110>Kunming Institute of Zoology, Chinese Academy of Sciences
Agricultural University Of Jiangxi
<120>SNP site relevant to litter size and primer thereof on No. 6 chromosomes of pig
<130> 7
<160> 3
<170> PatentIn
version 3.5
<210> 1
<211> 18
<212> DNA
<213> Sus scrofa
<400> 1
gacggccaag cagaacag
18
<210> 2
<211> 22
<212> DNA
<213> Sus scrofa
<400> 2
ttggggcaga ttaatatttc aa
22
<210> 3
<211> 40
<212> DNA
<213> Sus scrofa
<400> 3
actgactgac tgactctgac aagaacgtgt ccaccgagcc
40
Claims (1)
1. one kind is detected on No. 6 chromosomes of pig the primer of a SNP site relevant to litter size detection pig
Application in litter size, it is characterised in that: described primer includes pcr amplification primer thing and extends primer, its
The nucleotide sequence of middle pcr amplification primer thing is as follows: Chr6-2-PCRU:5 '-GAC GGC CAA GCA
GAA CAG-3’；Chr6-2-PCRL:5 '-TTG GGG CAG ATT AAT ATT TCA A-3 '；Extend
The nucleotide sequence of primer is as follows: Chr6-2-SNPU:5 '-ACT GAC TGA CTG ACT CTG
ACA AGA ACG TGT CCA CCG AGC C-3 ', described pig is white Duroc × Erhualian hybridization
Resource population F2 godmother pig, described SNP site is the Chr6 of genome version NCBI Sscrofal10.2:
64826013, the allele in this site is T and C, has tri-kinds of genotype of C/C, T/C and T/T, with
The litter size of pig of C/C genotype is higher than the pig with T/C and T/T genotype, and wherein allele C is for improving
The useful allele of litter size of pig.
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Citations (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2007133075A2 (en) * | 2006-05-12 | 2007-11-22 | Institute For Pig Genetics B.V. | Igf2 marker assisted selection for porcine reproductive traits |
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| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2007133075A2 (en) * | 2006-05-12 | 2007-11-22 | Institute For Pig Genetics B.V. | Igf2 marker assisted selection for porcine reproductive traits |
Non-Patent Citations (3)
| Title |
|---|
| Quantitative trait loci for litter size and prenatal loss in a White Duroc Chinese Erhualian resource population;K. Li et al.;《Animal Genetics》;20090420;第40卷;全文 * |
| ss736944115;NCBI;《NCBI dbSNP数据库》;20130316;第一页 * |
| 猪产仔性状的分子标记研究与QTLs定位;雷雪芹等;《洛阳农业高等专科学校学报》;20011227;263-266 * |
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