CN105543356A - SNP (single nucleotide polymorphism) locus relevant to litter size on sow chromosome 9 - Google Patents
SNP (single nucleotide polymorphism) locus relevant to litter size on sow chromosome 9 Download PDFInfo
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- 239000002773 nucleotide Substances 0.000 title claims abstract 3
- 125000003729 nucleotide group Chemical group 0.000 title claims abstract 3
- 210000000349 chromosome Anatomy 0.000 title abstract 3
- 238000009396 hybridization Methods 0.000 claims description 7
- 239000003147 molecular marker Substances 0.000 claims description 3
- 108090000623 proteins and genes Proteins 0.000 abstract description 7
- 239000003550 marker Substances 0.000 abstract description 4
- 230000002068 genetic effect Effects 0.000 abstract description 3
- 230000003321 amplification Effects 0.000 abstract description 2
- 238000012214 genetic breeding Methods 0.000 abstract description 2
- 238000003199 nucleic acid amplification method Methods 0.000 abstract description 2
- 240000002853 Nelumbo nucifera Species 0.000 abstract 5
- 235000006508 Nelumbo nucifera Nutrition 0.000 abstract 5
- 235000006510 Nelumbo pentapetala Nutrition 0.000 abstract 5
- 101150111062 C gene Proteins 0.000 abstract 3
- 108700028369 Alleles Proteins 0.000 abstract 2
- 101150050863 T gene Proteins 0.000 abstract 2
- 238000012163 sequencing technique Methods 0.000 abstract 1
- 241000282898 Sus scrofa Species 0.000 description 38
- 241000282887 Suidae Species 0.000 description 9
- 239000003153 chemical reaction reagent Substances 0.000 description 7
- 238000006243 chemical reaction Methods 0.000 description 6
- 238000009395 breeding Methods 0.000 description 3
- 230000001488 breeding effect Effects 0.000 description 3
- 239000011259 mixed solution Substances 0.000 description 3
- 230000001850 reproductive effect Effects 0.000 description 3
- 101100433727 Caenorhabditis elegans got-1.2 gene Proteins 0.000 description 2
- 241001237732 Microtia Species 0.000 description 2
- 238000012408 PCR amplification Methods 0.000 description 2
- 230000004087 circulation Effects 0.000 description 2
- 238000010219 correlation analysis Methods 0.000 description 2
- 238000013461 design Methods 0.000 description 2
- 230000000694 effects Effects 0.000 description 2
- 238000000605 extraction Methods 0.000 description 2
- PMHURSZHKKJGBM-UHFFFAOYSA-N isoxaben Chemical compound O1N=C(C(C)(CC)CC)C=C1NC(=O)C1=C(OC)C=CC=C1OC PMHURSZHKKJGBM-UHFFFAOYSA-N 0.000 description 2
- 238000005259 measurement Methods 0.000 description 2
- 244000309715 mini pig Species 0.000 description 2
- 239000000047 product Substances 0.000 description 2
- 108010007577 Exodeoxyribonuclease I Proteins 0.000 description 1
- 241001465754 Metazoa Species 0.000 description 1
- 230000000996 additive effect Effects 0.000 description 1
- 238000013459 approach Methods 0.000 description 1
- 230000009286 beneficial effect Effects 0.000 description 1
- 239000008280 blood Substances 0.000 description 1
- 210000004369 blood Anatomy 0.000 description 1
- 239000007795 chemical reaction product Substances 0.000 description 1
- 239000003795 chemical substances by application Substances 0.000 description 1
- 230000007812 deficiency Effects 0.000 description 1
- 238000001514 detection method Methods 0.000 description 1
- 238000002474 experimental method Methods 0.000 description 1
- 238000003205 genotyping method Methods 0.000 description 1
- 230000009027 insemination Effects 0.000 description 1
- 230000008774 maternal effect Effects 0.000 description 1
- VNWKTOKETHGBQD-UHFFFAOYSA-N methane Natural products C VNWKTOKETHGBQD-UHFFFAOYSA-N 0.000 description 1
- -1 methane amide Chemical class 0.000 description 1
- 238000000034 method Methods 0.000 description 1
- 230000000869 mutational effect Effects 0.000 description 1
- 238000000746 purification Methods 0.000 description 1
- 239000012264 purified product Substances 0.000 description 1
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- 238000012216 screening Methods 0.000 description 1
- 241000894007 species Species 0.000 description 1
- 230000008080 stochastic effect Effects 0.000 description 1
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Abstract
The invention relates to an SNP (single nucleotide polymorphism) locus relevant to character of litter size, in particular to an SNP locus relevant to the litter size on a sow chromosome 9 and primers thereof, and belongs to the technical field of biology. The SNP locus is Chr9: 59516174 of genome version NCBI Build Sscrofa 10.2. The alleles of the lotus are T and C, and the lotus has the three gene types of C/C, T/C and T/T. The primers and extended primers for amplification of the lotus are Chr3-2-PCRU: 5'-TAG TGG CCT CTT CCT GTC AC-3', Chr3-2-PCRL: 5'-CAA AAT AAG GAG CTG GTTCCT-3', Chr3-2-SNPU: 5'-AGG GGC AGC ACA GGC CCC CAT TCA G-3'.The litter size of the sow with the T/C gene type is bigger than that of the sow with the C/C gene type, T is a desirable allele for increasing the little size of a sow, and the litter size of a heterozygous sow with the T/C gene type is highest. The SNP locus relevant to the litter size on a sow chromosome 9 and the primers thereof have the advantages that the SNP lotus or genes relevant to characters can be quickly screened in batches through the whole genome re-sequencing method, the lotus Chr9: 59516174 of the genome version NCBI Build Sscrofa10.2 can serve as a genetic marker for sow genetic breeding and litter size increasing of sows.
Description
Technical field:
The present invention relates to the SNP site relevant to pig number born character, to be specifically related on pig No. 9 karyomit(e)s a SNP site relevant to nest litter size and primer thereof, to belong to biological technical field.
Background technology:
The characters of number born of pig is the chief component of pig reproductive trait, improves litter size of pig significant to the overall economic benefit improving pig industry.The Taihu pigs of China is well-known with high yield, and nest litter size is than nest litter size many 4-5 head (" Chinese pig breeds will " Zhang Zhongge edits, Science and Technology of Shanghai press, 1986) of other Chinese native pig breed of great majority and external pig kind.Polymorphic site relevant to high litter size in Taihu pigs, can as genetic marker for improving the litter size of sow.
The heavy sequence measurement of full-length genome has been widely used in the correlative study of each species, and it can filter out the gene relevant to proterties, function or mutational site fast all sidedly, compensate for QTL and to locate and candidate gene approach is wasted time and energy, the deficiency such as single.
There is not yet the open source literature report that in the present invention, SNP site is relevant to Litter Size in Pigs at home and abroad.
Summary of the invention:
To the object of this invention is to provide on pig No. 9 karyomit(e)s a SNP site relevant to nest litter size and primer thereof.
The present invention have selected Erhualian (one of Taihu pigs), hides pig, BaMa miniature pig, Laiwu Pigs, and the southern regions of the Yunnan Province microtia pig 5 Chinese native pig breeds and wild boar have carried out full-length genome and to resurvey sequence.The sequence number of individuals of resurveying of 6 pig kinds is respectively 11,11,9,10,10 and 10.Order sequenced data of resurveying is compared with reference to genome (NCBIBuildSscrofa10.2), utilizes SAMTools software to carry out the extraction in SNPs site.Contriver compares Erhualian and other 5 pig kinds, No. 9 karyomit(e)s finds a SNP site (Chr9:8179045 of genome version NCBIBuildSscrofa10.2) is relevant to the litter size of pig.The allelotrope in this site is T and C, has C/C, T/C and T/T tri-kinds of genotype.
After screening this site, contriver is at white Duroc × Erhualian hybridization resource population F
2in godmother pig individuality, it is verified and correlation analysis, found that this site and litter size of pig have significant correlation.
Beneficial effect of the present invention is: the heavy sequence measurement of full-length genome can screen the SNP site relevant to proterties or gene fast, in bulk, and this SNP site of Chr9:8179045 of genome version NCBIBuildSscrofa10.2 can be used for the litter size of the genetic breeding raising sow of pig as genetic marker.
Accompanying drawing illustrates:
Fig. 1 is white Duroc × Erhualian F
2in godmother pig resource population, the genotypic litter size in 3 kinds, Chr9:8179045 site compares that (when two kinds of genotype litter sizes compare in figure, * represents 0.01≤P≤0.05; * represents P < 0.01).
Specific embodiments:
(1) the population distribution feature of SNP site
The present invention selects Erhualian (one of Taihu pigs), hides pig, BaMa miniature pig, Laiwu Pigs, and the southern regions of the Yunnan Province microtia pig 5 Chinese native pig breeds and wild boar have carried out full-length genome and to resurvey sequence.The sequence number of individuals of resurveying of 6 pig kinds is respectively 11,11,9,10,10 and 10.Order sequenced data of resurveying is compared with reference to genome (NCBIBuildSscrofa10.2), utilizes SAMTools software to carry out the extraction in SNPs site.Contriver compares Erhualian and other 5 pig kinds, No. 9 karyomit(e)s finds a SNP site (Chr9:8179045 of genome version NCBIBuildSscrofa10.2) is relevant to the litter size of pig.
(2) qualification of SNP site
At design of primers website design SNAPSHOT primer, comprise a pair pcr amplification primer (Chr9-PCRU:5 '-TATAAAAGACTGTGTTGCTGCTAGA-3 '; Chr9-PCRL:5 '-AATGTCAAACTAGTTTAAGGAGTTGAA-3 ') and extension primer (Chr9-SNPU:5 '-TGACTTTAGTGGGTGGCTGAGAACTTACAT-3 ').This site and totally 24, other 11 sites (12 to) primer is respectively got 1 μ l and is mixed into new multiple PCR primer pond.First carry out 12 heavy PCR reactions, reaction system agents useful for same is: multiple PCR primer pond (6.25 μMs of each) 8 μ l, dNTP (10mMeach) 8 μ l, 10 × PCRBufferII116 μ l, MgCl
2(25mMStock) 234 μ l, FastStartTaq (5U/ μ l) 24 μ l and ddH
2o460 μ l, the 10 μ l systems that are mixed into by above reagent mixed liquor 8.5 μ l and 1.5 μ lDNA (50ng/ μ l) carry out 12 heavy 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: ExoI (10U/ μ l) 60 μ l, SAP (1U/ μ l) 130 μ l, 10 × SAPBuffer35 μ l and ddH
2o125 μ l, add in the PCR primer of each sample 3.5 μ l above-mentioned purifying mixed solution centrifugal after react by following program: 37 DEG C of 40min, 96 DEG C of 10min.Then single base extension is carried out, required reagent is: SNAPSHOTMultiplexreadyreactionMix100 μ l, extension primer pond (6.25 μMs of each, 12 extension primers are respectively got 1 μ l and mixed) 8 μ l, 5 × SequencingBuffer200 μ l and ddH
2o300 μ l, is mixed into 10 μ l systems by the purified product of above reagent mixed liquor 6 μ l and 4 μ l 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 carry out the purifying of extension product, required reagent is: SAP (1U/ μ l) 120 μ l, 10 × SAPBuffer70 μ l and ddH
2o140 μ l, add in the extension product of each sample above-mentioned 3.3 μ l purifying mixed solutions centrifugal after react by following program: 37 DEG C of 40min, 75 DEG C of 20min, 4 DEG C save backup.SNAPSHOT reaction product after the above-mentioned purifying of 5-4 μ l got by each sample and high-purity methane amide (Hi-DiFormamide) of 5-6 μ l be mixed into 10 μ l systems centrifugal after be splined on ABI3730XL sequenator and carry out gene type, use GeneMarker software analysis genotyping result.
(note: the reaction reagent mixed solution consumption of above 4 steps is amount of reagent needed for 100 samples, from single base extension, needs lucifuge to carry out.)
(3) white Duroc × Erhualian reproductive performance hybridization resource population builds
Follow-up confirmatory experiment used resource group's individual sample and trait data thereof are provided by Animal Biotechnology National Key Laboratory of Agricultural University Of Jiangxi cultivation base.
In December, 1998, on Agricultural University Of Jiangxi's scientific research pig farm, the Erhualian sow of 3 Erhualian conservation field purchases from Jiangsu Province is carried out the intersection breeding of blood relationship between field.January calendar year 2001, according to parent's Farrowing Traits, have selected maternal for generations as sources group of 17 Erhualian sows from the pure breeding offspring of 3 boars and 11 sows.2 high-qualitys white Duroc boars that SygenPIC company is so kind as to give are as the male parent for generations of Resource family.By the F that these 2 white Durocs and 17 Erhualian hybridization produce
1breed for individuality, avoid full, and every boar usually with same head insemination of sows, to obtain the F of large sample
2family half sibs.In January, 2003, March and June, project team is respectively by the 1st crowd and the 2nd crowd of F
2sow is sent to Jiangxi Province's Yichun City herding seed multiplication farm (59), state-run Red Star kind pig farm, Jiangxi Province (52) and quaternionic breeding pig farm, Shangyou County, Jiangxi (118) for the mensuration of sow reproductive trait.
(4) SNP site is at hybridization resource population F
2the gene type of godmother swinery body
According to the method described in above-mentioned steps (2), with 192 white Durocs × Erhualian hybridization resource population F
2the individual DNA of godmother pig is the genotype of this SNP site of template detection.192 F
2for there being 179 successful somatotypes of individuality in resource population individuality, the number of individuals of 3 kinds of genotype C/C, T/C and T/T is 5,72 and 102 respectively.
(5) SNP site is to the regulating effect of characters of number born
At F
2for in resource population individuality, the average litter size with C/C genotype individuals is 10.4509, and standard deviation is 1.489; Average litter size with T/C genotype individuals is 11.6084, and standard deviation is 0.9154; Average litter size with T/T genotype individuals is 10.7238, and standard deviation is 0.887.
The present invention adopts general linear model (GLM) to analyze the impact of SNP site on pig total yield coefficient, number born alive.Whole statistical study adopts SAS software to carry out.Model is as follows:
Y
ijklm＝u+A
i+G
j+B
k+P
l+e
ijklm
Wherein Y
ijklmfor pig total yield coefficient or number born alive, u is colony's average, A
ibe i-th individual additive effect, G
jfor the genotypic fixed effect of a jth SNP site, B
kfor a batch effect (k=1,2,3,4), P
lfor stochastic effect (l=1,2,3).
Analytical results finds that this SNP site of Chr9:8179045 has significant correlation with litter size.With the genotypic F of T/C
2the litter size of godmother pig is than with the genotypic sow of C/C on average many 1.1575 (P=0.04), as can be seen from Figure 1, minimum with the genotypic number born of sow of C/C.T is the useful allelotrope of raising litter size of pig and T/C heterozygosis litter size of pig is the highest.
Find out from SNP site and litter size correlation analysis, this SNP site of Chr9:8179045 can be applied to as molecule marker the litter size that molecular marker assisted selection (MAS) improves sow.
Claims (2)
1. on pig No. 9 karyomit(e)s a SNP site relevant to litter size at white Duroc × Erhualian hybridization resource population F
2application in godmother's litter size of pig molecular marker assisted selection, it is characterized in that: the allelotrope of described SNP site is T and C, there are C/C, T/C and T/T tri-kinds of genotype, minimum with the genotypic number born of sow of C/C, T is the useful allelotrope of raising litter size of pig and T/C heterozygosis litter size of pig is the highest.
2. a test right requires that the primer of SNP site described in 1 is at white Duroc × Erhualian hybridization resource population F
2application in godmother's litter size of pig molecular marker assisted selection, is characterized in that: the nucleotide sequence of described primer is as follows:
Chr9-PCRU：5’-TATAAAAGACTGTGTTGCTGCTAGA-3’；
Chr9-PCRL：5’-AATGTCAAACTAGTTTAAGGAGTTGAA-3’；
Chr9-SNPU:5 '-TGACTTTAGTGGGTGGCTGAGAACTTACAT-3 ', described SNP site is minimum with the genotypic number born of sow of C/C, and T is the useful allelotrope of raising litter size of pig and T/C heterozygosis litter size of pig is the highest.
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| CN201610003002.5A CN105543356B (en) | 2016-01-04 | 2016-01-04 | SNP site relevant to nest litter size on No. 9 chromosomes of pig |
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| CN105543356B CN105543356B (en) | 2019-05-31 |
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Cited By (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN105969890A (en) * | 2016-07-07 | 2016-09-28 | 贵州大学 | SNP (Single Nucleotide Polymorphism) molecular marker related to litter size of fragrant pig and application of SNP molecular marker |
| CN113736890A (en) * | 2021-07-30 | 2021-12-03 | 华南农业大学 | SNP molecular marker related to Jian' er number and survival rate and application thereof |
| CN114085914A (en) * | 2021-10-27 | 2022-02-25 | 华南农业大学 | SNP molecular marker located on pig chromosome 9 and related to Jian 'er number and Jian' er rate and application |
Citations (2)
| 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 |
| CN103757003A (en) * | 2013-12-26 | 2014-04-30 | 中国科学院昆明动物研究所 | Litter size related SNP (Single Nucleotide Polymorphism) locus of swine 13# chromosome and primers thereof |
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2016
- 2016-01-04 CN CN201610003002.5A patent/CN105543356B/en not_active Expired - Fee Related
Patent Citations (2)
| 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 |
| CN103757003A (en) * | 2013-12-26 | 2014-04-30 | 中国科学院昆明动物研究所 | Litter size related SNP (Single Nucleotide Polymorphism) locus of swine 13# chromosome and primers thereof |
Non-Patent Citations (3)
| Title |
|---|
| 《GENETICS SELECTION EVOLUTION》 * |
| 《中国优秀硕士学位论文全文数据库（电子期刊）》 * |
| 《广东农业科学》 * |
Cited By (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN105969890A (en) * | 2016-07-07 | 2016-09-28 | 贵州大学 | SNP (Single Nucleotide Polymorphism) molecular marker related to litter size of fragrant pig and application of SNP molecular marker |
| CN113736890A (en) * | 2021-07-30 | 2021-12-03 | 华南农业大学 | SNP molecular marker related to Jian' er number and survival rate and application thereof |
| CN113736890B (en) * | 2021-07-30 | 2023-07-14 | 华南农业大学 | SNP molecular marker related to healthy number and living number rate and application thereof |
| CN114085914A (en) * | 2021-10-27 | 2022-02-25 | 华南农业大学 | SNP molecular marker located on pig chromosome 9 and related to Jian 'er number and Jian' er rate and application |
| CN114085914B (en) * | 2021-10-27 | 2023-07-14 | 华南农业大学 | SNP molecular marker located on chromosome 9 of pig and related to litter size and application thereof |
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