CN108456734A - A kind of and the relevant SNP marker of litopenaeus vannamei high alkalinity resistance, detection primer and its application - Google Patents
A kind of and the relevant SNP marker of litopenaeus vannamei high alkalinity resistance, detection primer and its application Download PDFInfo
- Publication number
- CN108456734A CN108456734A CN201810174718.0A CN201810174718A CN108456734A CN 108456734 A CN108456734 A CN 108456734A CN 201810174718 A CN201810174718 A CN 201810174718A CN 108456734 A CN108456734 A CN 108456734A
- Authority
- CN
- China
- Prior art keywords
- litopenaeus vannamei
- high alkalinity
- snp marker
- polr2a
- breeding
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Granted
Links
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- 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
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- 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
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/124—Animal traits, i.e. production traits, including athletic performance or the like
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- 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
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Analytical Chemistry (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Organic Chemistry (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Microbiology (AREA)
- Immunology (AREA)
- Molecular Biology (AREA)
- Biotechnology (AREA)
- Biophysics (AREA)
- Physics & Mathematics (AREA)
- Biochemistry (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Genetics & Genomics (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Abstract
The invention discloses a kind of and the relevant SNP marker of litopenaeus vannamei high alkalinity resistance, detection primer and its applications.SNP marker disclosed by the invention is located at the 237th base positions of SEQ ID POLR2A sequences, and the base of variant sites is A or C, and when the genotype of variant sites is AC, survival rate of the prawn under high alkalinity environment is considerably lower.The invention also discloses for detect the variant sites primer combine and its Breeding Application method.In the work of litopenaeus vannamei high alkalinity breeding for stress tolerance, standby parental population is screened using method disclosed by the invention, is excluded early individual to the litopenaeus vannamei that high alkalinity environmental pressure is sensitive, it will help the high-alkali breeding for stress tolerance of prawn.
Description
Technical field
The invention belongs to aquatic wholesale market and field of molecular breeding, and in particular to a kind of anti-with litopenaeus vannamei high alkalinity
The relevant SNP marker of property, detection primer and its application.
Background technology
Litopenaeus vannamei (Litopenaeus vannamei, be commonly called as Penaeus Vannmei) originates in Central and South America Pacific Ocean edge
Bank marine site, litopenaeus vannamei in 1988 introduce China from the U.S., and 1998 start large-scale cultivation, have nowadays been that China is most important
Prawn culturing kind.Cut-off is to 2016, and it is more than 1,600,000 tons that China, which cultivates annual output, and annual value of production is more than 60,000,000,000 yuan, seedling year
Demand is more than 500,000,000,000 tails, and stock breeding is of great significance to litopenaeus vannamei aquaculture.
Since there is litopenaeus vannamei stronger environmental suitability and higher economic value, this kind of prawn to be generalized to
A variety of waters are cultivated, including the salt-soda soils such as Shanxi, northern Shensi, Shandong sea, freshwater.According to reports, high alkalinity ring
Border can reduce immunocompetence (the Chang-Che Li and Jiann-Chu Chen.The immune response of of prawn
white shrimp Litopenaeus vannamei and its susceptibility to Vibrio
alginolyticus under low and high pH stress.Fish&Shellfish Immunology,2008,25,
701-709.).Therefore, scientific and technological branch can be provided for the aquaculture of litopenaeus vannamei by carrying out the degeneration-resistant character breeding work of high alkalinity
Support.
Traditional selection places one's entire reliance upon phenotype, and there are the period is long, efficiency is low, the unfavorable factors such as unstable.Molecule
Breeding, i.e. molecular marker assisted selection breeding refer to the technology for carrying out selection to breeding material using DNA molecular marker, molecule
Breeding method carries out standby Juvenile stage according to effective molecular labeling, breeds out the advantageous offspring of economic characters.SNP is
The abbreviation of Single Nucleotide Polymorphism, refers to the variation of mononucleotide in the genome, and SNP site is generally
Two equipotential polymorphisms, the frequency of occurrences is about 1/300 base in human genome.SNP marker and RAPD (first generation molecules
Label), SSR marker (second generation molecular labeling) compare, have inheritance stability, quantity is more, distribution is wide, information content is high, detect hand
The advantages that section is various is current most widely used, newest molecular labeling.
Invention content
It with the relevant SNP marker of litopenaeus vannamei high alkalinity resistance, detection primer and its is answered the present invention is intended to provide a kind of
With the molecular labeling can be applied to the molecular marker assisted selection breeding of the degeneration-resistant character of litopenaeus vannamei, be high alkalinity resistance phase
The SNP variant sites of pass provide useful information, are conducive to improve the culture trait under litopenaeus vannamei high alkalinity environment.
Sequence dna fragment (SEQID-POLR2A, nucleotide sequence such as SEQ ID of litopenaeus vannamei POLR2A genes
Shown in NO.1) in, there are variant sites, which deposits the 237th base positions with prawn under high alkalinity pressure environment
Motility rate is significantly correlated；When the genotype of variant sites is AC, survival rate of the prawn under high alkalinity environment is considerably lower.SEQID-
The base sequence of POLR2A is：5’-AGCACCTCAAGCAGCACATCACCAAGGTCATCATCAAGGGCCTGCCATCCGTCAA
TCGAGCTGTCATCAATCAGAATGACACGAGTGGGGTTTCCCAGTACGAGCTGCTTGTGGAAGGGGACAACTTGCAGG
AAGTCATTGCAACCTATGGTGTTGATGGCACACGTTGCACCTCAAACAACACGTATGAAGTCTTCACCTCATTAGGG
ATTGAGGCAGCAAGAGCAACAATCATC(A/C)AAGAGATCACAGTGACTATGGAGACTCACGGCCTGAGTGTGGACC
ACAGGCATGTAATGCTACTGGCTGAC-3’。
Therefore, the first purpose of the invention is to provide a kind of with the relevant SNP marker of litopenaeus vannamei high alkalinity resistance,
The SNP marker is located at sequence shown in SEQ ID NO.1 from 5 ' ends at the 237th bit base, and base is A or C.
Second object of the present invention is to provide a kind of and relevant SNP marker of litopenaeus vannamei high alkalinity resistance detection
Primer, including following primer：
POLR2A-F：5 '-AGCACCTCAAGCAGCACAT-3 ' (as shown in SEQ ID NO.2)；
POLR2A-R：5 '-GTCAGCCAGTAGCATTACATGCC-3 ' (as shown in SEQ ID NO.3).
Third object of the present invention is to provide described with the relevant SNP marker of litopenaeus vannamei high alkalinity resistance all
The application received in the prawn molecular marker assisted selection breeding of shore.
Fourth object of the present invention is to provide a kind of selection of litopenaeus vannamei high alkalinity anti-adversity, including with
Lower step：
A, litopenaeus vannamei genomic DNA to be measured is extracted；
B, litopenaeus vannamei genomic DNA to be measured is carried out using the detection primer POLR2A-F and POLR2A-R
PCR amplification；
C, amplified production is sequenced, determines the genotype of the SNP marker, selects AA genotype individuals as after
Standby parent carries out litopenaeus vannamei high alkalinity anti-adversity breeding.
SNP marker disclosed by the invention is located at the 237th base positions of SEQID-POLR2A sequences, the alkali of variant sites
Base is A or C, and when the genotype of variant sites is AC, survival rate of the prawn under high alkalinity environment is considerably lower.The present invention also public affairs
Primer combination and its Breeding Application method for detecting the variant sites are opened.In litopenaeus vannamei high alkalinity breeding for stress tolerance work
In work, standby parental population is screened using method disclosed by the invention, is excluded early quick to high alkalinity environmental pressure
The litopenaeus vannamei individual of sense, it will help the high-alkali breeding for stress tolerance of prawn.
Specific implementation mode
The present invention is described in further details below by embodiment, these embodiments are only used for illustrating the present invention, and
It does not limit the scope of the invention.
Embodiment：
With pH 9.6 ± 0.2 for stressed condition, to the offspring in 642 " honest " and " middle section 1 " colony hybridization source into
Row high alkalinity tolerance test all is received using litopenaeus vannamei dead in 2h as high pH sensitivities group by what is still survived after for 24 hours
Shore prawn is as high pH tolerances group.
During the experiment, it is observed 1 time every half an hour, dead individuals is placed in 95% alcohol preserves in time.High pH
Sensitivity group and high pH tolerances group prawn genome DNA extracting method according to Tiangeng marine animal tissue gene group extracts kit into
Row (TIANGEN, Tiangeng biochemical technology Co., Ltd).
Utilize detection primer POLR2A-F disclosed by the invention (5 '-AGCACCTCAAGCAGCACAT-3 ', such as SEQ ID
Shown in NO.2) and POLR2A-R (5 '-GTCAGCCAGTAGCATTACATGCC-3 ', as shown in SEQ ID NO.3), it is quick to high pH
Sense group and high pH tolerances group prawn genomic DNA carry out PCR detections, and response procedures are：95 DEG C of pre-degenerations 4 minutes, (95 DEG C of denaturation
Anneal within 30 seconds, 52-57 DEG C 20 seconds, 72 DEG C and extend 1 minute) × 35 cycles, last 72 DEG C extend 10 minutes.To PCR results into
Row sequencing, individual genotype results are as shown in table 1：
1 different disposal group idiotype of table counts
Note：Sensitivity represents high pH sensitivities group in table, and tolerance represents high pH tolerances group
Statistics high alkalinity is carried out to the result in table 1 and is resistant to association analysis, the results are shown in Table 2：
The genotype frequency of 2 SNP site of table and association analysis with high pH tolerances
As shown in Table 2, the AC genotype overwhelming majority appears in high pH sensitivities group, illustrates reducing for AC genotype
Tolerance of the prawn in high pH environment increases the death rate of individual.Therefore, during high alkalinity resistance breeding, this
The genotype of the base position of disclosure of the invention can be used as the label to high pH environment sensitives, carry out resistant to high pH standby parental line selection
When, the individual containing AC genotype should be excluded.
Sequence table
<110>Chinese Academy of Science Nanhai Ocean Research Institute
<120>A kind of and the relevant SNP marker of litopenaeus vannamei high alkalinity resistance, detection primer and its application
<160> 3
<170> SIPOSequenceListing 1.0
<210> 1
<211> 308
<212> DNA
<213>Litopenaeus vannamei (Litopenaeus vannamei)
<400> 1
agcacctcaa gcagcacatc accaaggtca tcatcaaggg cctgccatcc gtcaatcgag 60
ctgtcatcaa tcagaatgac acgagtgggg tttcccagta cgagctgctt gtggaagggg 120
acaacttgca ggaagtcatt gcaacctatg gtgttgatgg cacacgttgc acctcaaaca 180
acacgtatga agtcttcacc tcattaggga ttgaggcagc aagagcaaca atcatcmaag 240
agatcacagt gactatggag actcacggcc tgagtgtgga ccacaggcat gtaatgctac 300
tggctgac 308
<210> 2
<211> 19
<212> DNA
<213>Litopenaeus vannamei (Litopenaeus vannamei)
<400> 2
agcacctcaa gcagcacat 19
<210> 3
<211> 23
<212> DNA
<213>Litopenaeus vannamei (Litopenaeus vannamei)
<400> 3
gtcagccagt agcattacat gcc 23
Claims (4)
1. a kind of and relevant SNP marker of litopenaeus vannamei high alkalinity resistance, which is characterized in that the SNP marker is located at SEQ
For sequence shown in ID NO.1 from 5 ' ends at the 237th bit base, base is A or C.
2. a kind of and relevant SNP marker of litopenaeus vannamei high alkalinity resistance detection primer, which is characterized in that draw including following
Object：
POLR2A-F：5’-AGCACCTCAAGCAGCACAT-3’；
POLR2A-R：5’-GTCAGCCAGTAGCATTACATGCC-3’.
3. the described in claim 1 and relevant SNP marker of litopenaeus vannamei high alkalinity resistance is in litopenaeus vannamei molecular labeling
Application in assisted selection.
4. a kind of selection of litopenaeus vannamei high alkalinity anti-adversity, which is characterized in that include the following steps：
A, litopenaeus vannamei genomic DNA to be measured is extracted；
B, using the detection primer POLR2A-F and POLR2A-R described in claim 2 to litopenaeus vannamei genomic DNA to be measured
Carry out PCR amplification；
C, amplified production is sequenced, determines the genotype of SNP marker described in claim 1, select AA genotype individuals
Litopenaeus vannamei high alkalinity anti-adversity breeding is carried out as standby parent.
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN201810174718.0A CN108456734B (en) | 2018-03-02 | 2018-03-02 | SNP marker related to high alkalinity resistance of litopenaeus vannamei, detection primer and application of SNP marker |
Applications Claiming Priority (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN201810174718.0A CN108456734B (en) | 2018-03-02 | 2018-03-02 | SNP marker related to high alkalinity resistance of litopenaeus vannamei, detection primer and application of SNP marker |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CN108456734A true CN108456734A (en) | 2018-08-28 |
| CN108456734B CN108456734B (en) | 2020-09-29 |
Family
ID=63216677
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CN201810174718.0A Active CN108456734B (en) | 2018-03-02 | 2018-03-02 | SNP marker related to high alkalinity resistance of litopenaeus vannamei, detection primer and application of SNP marker |
Country Status (1)
| Country | Link |
|---|---|
| CN (1) | CN108456734B (en) |
Cited By (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN111041012A (en) * | 2019-12-13 | 2020-04-21 | 中国科学院南海海洋研究所 | Litopenaeus vannamei endoplasmic reticulum Ca-ATP enzyme LvSERCA gene and encoding protein and application thereof |
| CN111850133A (en) * | 2020-05-28 | 2020-10-30 | 广东省农业科学院动物科学研究所 | Low-temperature-resistant associated SNP molecular marker of litopenaeus vannamei, detection primer and application of detection primer |
| WO2024027254A1 (en) * | 2023-03-13 | 2024-02-08 | 中国科学院南海海洋研究所 | Molecular marker combination for enterocytozoon hepatopenaei resistance trait of litopenaeus vannamei, kasp detection primers, and use |
Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN106048016A (en) * | 2016-06-06 | 2016-10-26 | 中国科学院海洋研究所 | Multi-combination molecular markers related to resistance of litopenaeus vannamei and application |
| CN106834439A (en) * | 2016-12-26 | 2017-06-13 | 中国科学院海洋研究所 | A kind of related molecular labeling of Growth of Litopenaeus vannamei and its application |
-
2018
- 2018-03-02 CN CN201810174718.0A patent/CN108456734B/en active Active
Patent Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN106048016A (en) * | 2016-06-06 | 2016-10-26 | 中国科学院海洋研究所 | Multi-combination molecular markers related to resistance of litopenaeus vannamei and application |
| CN106834439A (en) * | 2016-12-26 | 2017-06-13 | 中国科学院海洋研究所 | A kind of related molecular labeling of Growth of Litopenaeus vannamei and its application |
Cited By (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN111041012A (en) * | 2019-12-13 | 2020-04-21 | 中国科学院南海海洋研究所 | Litopenaeus vannamei endoplasmic reticulum Ca-ATP enzyme LvSERCA gene and encoding protein and application thereof |
| CN111041012B (en) * | 2019-12-13 | 2022-04-26 | 中国科学院南海海洋研究所 | Litopenaeus vannamei endoplasmic reticulum Ca-ATP enzyme LvSERCA gene and encoding protein and application thereof |
| CN111850133A (en) * | 2020-05-28 | 2020-10-30 | 广东省农业科学院动物科学研究所 | Low-temperature-resistant associated SNP molecular marker of litopenaeus vannamei, detection primer and application of detection primer |
| CN111850133B (en) * | 2020-05-28 | 2021-10-19 | 广东省农业科学院动物科学研究所 | Low-temperature-resistant associated SNP molecular marker of litopenaeus vannamei, detection primer and application of detection primer |
| WO2024027254A1 (en) * | 2023-03-13 | 2024-02-08 | 中国科学院南海海洋研究所 | Molecular marker combination for enterocytozoon hepatopenaei resistance trait of litopenaeus vannamei, kasp detection primers, and use |
Also Published As
| Publication number | Publication date |
|---|---|
| CN108456734B (en) | 2020-09-29 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| CN105936937B (en) | A kind of relevant SNP marker of dissolved oxygen tolerance low to litopenaeus vannamei and its screening and application | |
| CN101696452B (en) | Method for identifying molecules of recessive white feather genes of chicken | |
| CN105603098B (en) | For the microsatellite marker primer and identification method of Penaeus monodon microsatellite Parentage determination and application | |
| CN104357553B (en) | A kind of Pelteobagrus fulvidraco microsatellite Parentage determination method | |
| CN109055571B (en) | Specific primer of yellow fin spine porgy microsatellite marker and application | |
| CN105200160B (en) | A kind of relevant SNP marker of dissolved oxygen tolerance low to litopenaeus vannamei and its screening and application | |
| CN105506162B (en) | SNP (single nucleotide polymorphism) marker related to rapid growth of crassostrea gigas as well as identification method and application thereof | |
| CN106834439B (en) | Molecular marker related to growth of litopenaeus vannamei and application thereof | |
| CN108456734A (en) | A kind of and the relevant SNP marker of litopenaeus vannamei high alkalinity resistance, detection primer and its application | |
| CN106381331A (en) | SNP markers related to grass carp growth speed and application thereof | |
| CN108998547A (en) | A kind of microsatellite marking method for C. guichenoti paternity test | |
| CN108179200B (en) | Microsatellite marker linked with procambarus clarkii high fertility character and application thereof | |
| CN109055580B (en) | Molecular marker related to growth in C-type scavenger receptor of litopenaeus vannamei and application | |
| CN111394445B (en) | Indel marker for sex identification of channa maculata and application thereof | |
| CN111304337A (en) | SRAP molecular marker, kit and method for identifying first filial generation of pelteobagrus fulvidraco, pelteobagrus vachelli and hybride and application | |
| CN108192894A (en) | A kind of degeneration-resistant character associated gene SNP marker of litopenaeus vannamei high alkalinity, detection primer and its application | |
| CN103484459B (en) | Primer group, marking method and application of EST-SSR (Expressed Sequence Tag-Simple Sequence Repeats) molecular marker of macrobrachium nipponense | |
| CN116426653A (en) | DNA (deoxyribonucleic acid) marker for identifying genetic sex of palaemon carinicauda and application thereof | |
| CN109536624B (en) | Fluorescent molecular marker and detection method for discriminating true and false male fish of cynoglossus semilaevis | |
| CN101892318A (en) | Method and kit for detecting correlated mutation allele of total farrow number of sow as well as application | |
| CN110452992A (en) | A kind of labeling method of litopenaeus vannamei EST microsatellite locus primer | |
| CN113604587B (en) | Molecular marker T5198 for rapidly identifying low-temperature tolerant variety of penaeus japonicus and application thereof | |
| CN110295238A (en) | A kind of relevant OSR1 gene SNP molecular labeling of pteria martensii growth traits and its application | |
| CN103966316A (en) | Microsatellite family identifying method for diploid misgurnus anguillicaudatus and application of method | |
| CN105603097A (en) | Microsatellite marker primers used for pinctada fucata martensii microsatellite family identification, identification method and application |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| PB01 | Publication | ||
| PB01 | Publication | ||
| SE01 | Entry into force of request for substantive examination | ||
| SE01 | Entry into force of request for substantive examination | ||
| CB02 | Change of applicant information |
Address after: No.1119 Haibin Road, Nansha District, Guangzhou City, Guangdong Province Applicant after: SOUTH CHINA SEA INSTITUTE OF OCEANOLOGY, CHINESE ACADEMY OF SCIENCES Address before: 510301 No. 164 West Xingang Road, Guangdong, Guangzhou Applicant before: SOUTH CHINA SEA INSTITUTE OF OCEANOLOGY, CHINESE ACADEMY OF SCIENCES |
|
| CB02 | Change of applicant information | ||
| GR01 | Patent grant | ||
| GR01 | Patent grant |