CN106636346A - SNP molecular marker related to daily gain of Duroc and application thereof - Google Patents
SNP molecular marker related to daily gain of Duroc and application thereof Download PDFInfo
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- CN106636346A CN106636346A CN201610974002.XA CN201610974002A CN106636346A CN 106636346 A CN106636346 A CN 106636346A CN 201610974002 A CN201610974002 A CN 201610974002A CN 106636346 A CN106636346 A CN 106636346A
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- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
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Abstract
The invention discloses a SNP molecular marker related to daily gain of Duroc and an application thereof. Through genome-wide association study (GWAS), an SNP site (ASGA0056780) related to the daily gain of Duroc is identified at the No. 13 chromosome of a pig; the GG type individual at the site has faster daily gain. The invention also provides a method for detecting the SNP molecular marker at the same time; the Taq probe can judge the site rapidly. The method can exactly and rapidly classify the ASGA0056780 with low cost, and provide technical support to the establishment of the breeding method of the Duro type daily gain molecular marker.
Description
Technical field
The invention belongs to technical field of molecular biology, be related to affect plus be the SNP site of Duroc daily gain character and
Its application in kind of swine improvement.
Background technology
Duroc originates in the ground such as the New Jersey and New York of eastern United States, the Duroc of main parent New York and
The damp western red cross breeding of New Jersey, original claims Duroc pool west, and Duroc is referred to as afterwards, and it is Duroc to be divided into U.S. system and add；Produce
Duroc in China Taiwan is passed through and cultivated certainly into style, thus weighting platform gulf Duroc or platform system Duroc.
Because duroc adaptability is good, without stress sensitive phenomenon, easy feeding and management success is fast with weightening, feedstuff report
Reward high (feedstuff-meat ratio is 2.8～3.2: 1), the advantages of carcass quality is good, lean meat percentage is high, is extensively suitable for industrial pig and peasant household
Raise.
The daily gain of pig is an important economic characters.Daily gain and pig marketing time positive correlation, higher daily gain
Speed is delivered faster in representative for sale.In conventional herd breeding for daily gain selection-breeding mainly the birth stage, 24 ages in days, 30kg,
60kg, 100kg stage weighs, and then picks out the high individuality of daily gain.But this work is wasted time and energy, therefore develop a kind of fast
Speed, simply, efficient molecule selection has aborning very big necessity, will accelerate plus be the heredity of Duroc daily gain
Progress.
The content of the invention
Present invention is primarily targeted at a kind of SNP marker related to Duroc daily gain character is provided, the SNP marks
The sequence of note is located at No. 13 chromosomes of pig, ASGA0056780, and the base on the site is G or A.
Application of the described SNP site in Duroc selection and use.
Application of the described SNP site in identification Duroc daily gain.
Another object of the present invention is to provide for detecting the aforesaid SNP marker related to Duroc daily gain character
Sequence, including：
Primer sequence
Forward primer AATAAGACACTGTTCTGAGGATGTAACAC
Reverse primer TCATGGATCTGTGCGCTAAAGA
Probe ATGGAGAAAGGGCATAC.
Advantage of the present invention is as follows：
Present invention finds the SNP site of an impact Duroc daily gain, the SNP marker that the present invention is provided is by Du Luo
Gram age, the impact of sex, can be used for the daily gain early stage breeding selection of Duroc, promote breeding process.
Description of the drawings
Fig. 1 is 83 Duroc table property distribution figures；Note：X-axis represents Distribution of phenotypic value, and Y-axis represents Density Distribution,
ADGEBV：Daily gain estimated breeding value；Density:Frequency distribution.
Fig. 2 is Duroc daily gain whole-genome association to add；
X-axis is chromosome title, and Y-axis is-logP values, Chromosome：Chromosome title
Fig. 3 is the respective value of ASGA0056780 genotype and phenotype；
X-axis represents genotype, and Y-axis represents daily gain offset, Genotype：Genotype, Phenotype：Phenotype
Specific embodiment
In order to probe into plus be the Genetic Mechanisms of Duroc daily gain, and develop it is a kind of fast and efficiently with daily gain selection-breeding
Related molecular breeding technology, the present invention utilizes 83 Duroc colonies, by methods such as full-length genome association (GWAS) analyses,
It was found that and authenticated a SNP site for affecting plus be Duroc daily gain, on this basis, the present invention also builds a kind of fast
Fast, efficient molecule sentences type technology.By have extensively studied the corresponding phenotype of different genotype, it is determined that relevant with daily gain
Genotype, by the selection to genotype, can accelerate the genetic progress for being Duroc daily gain.
1st, it is Duroc experimental population that laboratory animal 83 adds, from Duroc country core seed farm.
83 plus be Duroc daily gain phenotypic number as shown in figure 1, as can be seen from Figure 1 phenotypic number meets normal distribution.
2nd, experimental technique
The extraction of DNA/pig full-length genome 60K SNP sentence type
Every pig gathers a fritter ear sample, and with standard phenol-chloroform method complete genome DNA is extracted, and its concrete steps is such as
Under：
1st, ear sample is shredded, in being put into 1.5mlEP pipes, adds 350ul lysates, 20ul E.C. 3.4.21.64s and 0.9ul
RNaseA, mixes.
2nd, in hot couveuse, 55 DEG C overnight.(just having started to rock once every 30min)
3rd, EP pipes are taken out, equal-volume Tris balance phenol is added, 3min is firmly rocked；12000g, is centrifuged 10 minutes.
4th, gentle aspiration supernatant is into a new 1.5mlEP pipes.
5th, equal-volume phenol/chloroform is added in supernatant, 2 minutes are firmly rocked；12000g, is centrifuged 2 minutes.
6th, draw supernatant into another new 1.5mlEP pipes, add the sodium acetate solution and 2.5 times of volumes of 1/10 volume
Dehydrated alcohol, shakes up.
7th, 12000g, is centrifuged 1 minute, and upper strata ethanol is absorbed as far as possible.
8th, 1ml, 70% ethanol rinse DNA are added, is firmly shaken up, to remove the SDS and phenol of residual；
9th, 12000g, is centrifuged 1 minute, removes ethanol.
10th, EP pipes are upside down in absorbent paper, to blot ethanol.(9,10 can be repeated once)
11st, with the aseptic ddH2O of 65 DEG C of preheatings, 35ul dissolving DNAs, -20 DEG C of preservations.
Unify concentration dilution to 50ng/ μ I Jing after Nanodrop-NDIOOO spectrophotometers detection quality,
On Illumina Beadstation platforms according to company standard flow process carry out pig full-length genome 60K SNP chips (Illumina,
The U.S.) genotype judgement.Quality control is carried out to all sample 60K chip scannings typing datas using plink_1.09 softwares,
Reject the individual rate of detection to be higher than 0.1, minimum gene frequency less than 0.05 less than 95%, family Mendel error rate and breathe out
SNP of the generation-Weinberg equilibrium significance level higher than 10-6, finally gives the effective gene type data of about 40,000 SNP.
Full-length genome association (GWAS) analysis
83 Duluke's sows of the employing of this experiment are plus are Duroc and from a field, therefore there is no colony
Stratification effect, GWAS analyses are carried out with PLINK, and the marking area of genomic level is using conservative Bonferrini bearing calibrations
It is determined that, i.e., genome significant level threshold value is=0.05/40000 (effective SNP quantity).
Experimental result
GWAS analysis results (Fig. 2).As can be seen from Figure 2, in 83 Duroc colonies, exist and add in No. 13 chromosomes of pig
It is the related SNP site of Duroc daily gain：ASGA0056780 (is located at SSC13:At 27347572bp).GG genotype individuals
There is higher daily gain.Refer to Fig. 3.It is Duroc daily gain to show that ASGA0056780 sites can add as molecular marker pair
Selected.
Surely point may be used to lower Sequence Detection for the mutation：
Primer sequence
Forward primer AATAAGACACTGTTCTGAGGATGTAACAC
Reverse primer TCATGGATCTGTGCGCTAAAGA
Probe ATGGAGAAAGGGCATAC.
Primer and probe carry out detecting the experimentation of SNP
Real-time quantitative Taqman pcr gene typing amplification systems：10 μ l reaction systems contain 3.4 μ l water, and 5 μ l 2 ×
Taqman Genotyping Master Mix, 0.2 μ l 10mM forward primers, 0.2 μ l 10mM reverse primers, 0.1 μ l 10mM
Probe 1 (5 '-FAM, 3 '-TAMRA), 0.1 μ l 10mM probes 2 (5 '-VIC, 3 '-TAMRA), 1 μ l DNA.
Real-time quantitative Taqman PCR response procedures：1st, AD-pre read read initial background (background) fluorescence signal.2、
AQ-PCR is expanded：50 DEG C, 2min；95 DEG C, 10min；(95 DEG C, 15sec, 60 DEG C of each primer annealing and elongating temperature, 1min), 40
Individual circulation.3rd, AD-post read read PCR and react and terminate rear fluorescence signal (terminal pronunciation), background signal are removed, after analysis
Automatically sub-clustering obtains sentencing type result.
<110>1/ Guangxi Ke Xinyuan original seed pigs Co., Ltd,
2/ ZhangZhou Ao Nong modern agriculture development corporation, Ltd.,
3/ Fujian Ao Nong biotechnologies Group Plc,
The proud Xinhua's richness breeding company limited in 4/ Jinggangshan,
The proud Nong Kangrui animal husbandry company limited in 5/ Leshan,
6/ three, Hubei livestock technology company limited,
7/ Dezhou Ao Xin breedings company limited
<120>It is a kind of to plus be the related SNP marker of duroc daily gain and its application
<160>3
210>1
<211>13
<212>DNA
<213>Artificial sequence
<400>1
AATAAGACACTGTTCTGAGGATGTAACAC 13
<210>2
<211>11
<212>DNA
<213>Artificial sequence
<400>2
TCATGGATCTGTGCGCTAAAGA 11
<210>3
<211>16
<212>DNA
<213>Artificial sequence
<400>3
ATGGAGAAAGGGCATAC 16
Claims (4)
1. the SNP marker related to Duroc daily gain character, it is characterised in that：The sequence of the SNP marker is located at pig No. 13
Chromosome, ASGA0056780, the base on the site is G or A.
2. application of the SNP site described in claim 1 in Duroc selection and use.
3. application of the SNP site described in claim 1 in identification Duroc daily gain.
4. the sequence that test right requires the SNP marker related to Duroc daily gain character described in 1 is used for, including：
Forward primer AATAAGACACTGTTCTGAGGATGTAACAC
Reverse primer TCATGGATCTGTGCGCTAAAGA
Probe ATGGAGAAAGGGCATAC.
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| CN201610974002.XA CN106636346A (en) | 2016-11-07 | 2016-11-07 | SNP molecular marker related to daily gain of Duroc and application thereof |
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Cited By (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN108676897A (en) * | 2017-06-08 | 2018-10-19 | 华南农业大学 | It is a kind of influence daily gain in pigs character SNP marker and its application |
| CN109554487A (en) * | 2019-01-19 | 2019-04-02 | 华中农业大学 | A kind of molecular labeling and application with boar semen amount trait associations |
| CN112266968A (en) * | 2020-11-30 | 2021-01-26 | 华南农业大学 | Copy number variation molecular marker influencing weight age in days and daily gain on pig chromosome 13 and application |
| CN114921561A (en) * | 2022-03-22 | 2022-08-19 | 广西扬翔股份有限公司 | Duroc whole genome low-density SNP chip and preparation method and application thereof |
Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN103898107A (en) * | 2014-04-17 | 2014-07-02 | 江西农业大学 | Major SNP (single nucleotide polymorphism) marker influencing growth traits of pigs and application thereof in genetic improvement of productivity of breeding pigs |
| CN105648077A (en) * | 2016-02-29 | 2016-06-08 | 华南农业大学 | Molecular marker affecting daily gain character of pigs and application of molecular marker |
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2016
- 2016-11-07 CN CN201610974002.XA patent/CN106636346A/en active Pending
Patent Citations (2)
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| CN103898107A (en) * | 2014-04-17 | 2014-07-02 | 江西农业大学 | Major SNP (single nucleotide polymorphism) marker influencing growth traits of pigs and application thereof in genetic improvement of productivity of breeding pigs |
| CN105648077A (en) * | 2016-02-29 | 2016-06-08 | 华南农业大学 | Molecular marker affecting daily gain character of pigs and application of molecular marker |
Non-Patent Citations (2)
| Title |
|---|
| Y. LONG等: "Genome Wide Association Study Identifies QTLs for EBV of Backfat Thickness and Average Daily Gain in Duroc Pigs", 《RUSSIAN JOURNAL OF GENETICS》 * |
| 张哲等: "杜洛克猪生长性状全基因组关联分析", 《广东农业科学》 * |
Cited By (7)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN108676897A (en) * | 2017-06-08 | 2018-10-19 | 华南农业大学 | It is a kind of influence daily gain in pigs character SNP marker and its application |
| CN108676897B (en) * | 2017-06-08 | 2020-06-19 | 华南农业大学 | SNP marker influencing daily gain traits of pigs and application thereof |
| CN109554487A (en) * | 2019-01-19 | 2019-04-02 | 华中农业大学 | A kind of molecular labeling and application with boar semen amount trait associations |
| CN112266968A (en) * | 2020-11-30 | 2021-01-26 | 华南农业大学 | Copy number variation molecular marker influencing weight age in days and daily gain on pig chromosome 13 and application |
| CN112266968B (en) * | 2020-11-30 | 2022-06-24 | 华南农业大学 | Copy number variation molecular marker influencing weight age in days and daily gain on pig chromosome 13 and application |
| CN114921561A (en) * | 2022-03-22 | 2022-08-19 | 广西扬翔股份有限公司 | Duroc whole genome low-density SNP chip and preparation method and application thereof |
| CN114921561B (en) * | 2022-03-22 | 2023-03-17 | 广西扬翔股份有限公司 | Duroc whole genome low-density SNP chip and preparation method and application thereof |
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Application publication date: 20170510 |