CN108048598A - For detecting the SNP marker of rice sterile gene pms3 - Google Patents
For detecting the SNP marker of rice sterile gene pms3 Download PDFInfo
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- CN108048598A CN108048598A CN201810073675.7A CN201810073675A CN108048598A CN 108048598 A CN108048598 A CN 108048598A CN 201810073675 A CN201810073675 A CN 201810073675A CN 108048598 A CN108048598 A CN 108048598A
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- 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
- C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
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- 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
- C12Q2600/13—Plant traits
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- 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
Abstract
The present invention provides the SNP marker of one group of rice sterile gene pms3, the molecular labeling K_120522, wherein, the polymorphism of K_120522 is C or G.Using the molecular labeling, pms3 genes can be fast, accurately detected, greatly improve efficiency of selection of the gene in rice breeding.Digestion, electrophoresis and sequencing etc. is not required in detection process, easy to operate, can realize commercialized high-throughput quick detection, thoroughly prevented PCR product Aerosol Pollution and EB to the harm of the pollution, formaldehyde of environment to human body.
Description
Technical field:
The present invention relates to field of molecular marker, specifically, being related to the SNP marker of a rice sterile gene.
Background technology:
Rice is important cereal crops, and it is the important channel for improving rice yield to promote hybrid rice.In double-line hybrid
In rice breeding, sterile line is mainly temperature sensitivity and light sensitive two types.Temp-sensing sterile line has in actual production
Consequence, Nongken 58S be light thcrmo-scnsitivc genie male stcrility rice varieties, under long day high temperature infertility, under short day low temperature
It is fertile, it is the important germ plasm resource in two line method rice breeding.The selection and breeding of traditional two-line sterile line are observed in heading flowering period
The pollen fertility of rice and selection field sterile plant are, it is necessary to undergo pollen microscopic examination, bagging selfing, the sterile plant selected cut root and stem of certain plants regeneration
The time-consuming and laborious processes such as fertility turn selection are carried out with ecological environment is changed.With the development of biotechnology, breeder is available
Molecular labeling identifies the gene of the sterile character of control, accurately distinguishes homozygous infertility, heterozygosis infertility and fertile plant, significantly carries
High selection efficiency and the breeding process for accelerating two-line hybrid rice.
The molecular labeling type mainly utilized in previous literature report is AFLP, RFLP, SSR and InDel label screening base
Cause, relatively low there are polymorphism in breeding, the smaller shortcoming of difference.The EB or Polyscrylamide used in detection process is easily to ring
Border pollutes, generates harm to human body.Traditional detection means are based on flower pesticide microscopy and the observation identification of setting percentage isophenous, consumption
Time-consuming length, and easily being limited by environmental condition, for qualification result there are error, efficiency of selection is relatively low.
What Zhang Qifa consulted that Shou Jiu team points out control Nongken 58S infertility is a long non-coding RNA, LOC_
The transcript 1 of 12g36030 is pms3 (CN102952795A).Their research shows a length as 1236bp, and with long light
According to the lower relevant RNA molecule of special male sterility (LDMAR).Under long-day conditions, enough LDMAR transcription amounts are to maintain just
Necessary to normal pollen development, but since a single base mutation causes LDMAR secondary structural changes, LDMAR is resulted in spy
Transcription amount reduces under the different long-day, and the flower pesticide for being in development is caused to shift to an earlier date programmed cell death, shows male sterility (Ding
et al.2012).Zhuan Chuxiong professors seminar it is further noted that p/tms12-1 (i.e. pms3) is a non-coding RNA base
Cause, compared with normal rice varieties, temperature sensitive male sterile rice is in the tiny RNA sequential memory in a single base mutation, this single alkali
Base mutation is to generate temperature sensitive sterility in long-grained nonglutinous rice and generate common cause (the Zhou et of photosensitive sterility in japonica rice
al.2012)。
CN105463072A discloses a kind of rice Photo-sensitive male sterile geng pms3 detections and classifying method, using fluorescent PCR
Parting is carried out to pms3 genes.But this method design of primers is relatively complicated, and result verification is also not directly perceived enough, affects Genotyping
Efficiency.
Therefore this field there is an urgent need for it is a kind of being capable of the fast and convenient detection method to pms3 partings.
The content of the invention:
In view of this, the present invention is proposed.
Two background documents of CN102952795A, CN105463072A are herein incorporated by reference.
The technical problem to be solved by the present invention is to develop the molecular labeling of one group of sterile gene pms3, pms3 bases can be used for
The efficient identification of cause and assisted selection.In order to solve the above technical problem, the present invention provides the SNP that pms3 is isolated
(single nucleotide polymorphism) molecular labeling.
Firstly, since pms3 genes have been cloned, according to pertinent literature pms3 genes be as caused by single base mutation not
The difference of fertility.Pms3 gene orders will have been delivered and compared with Nipponbare reference gene group (MSU7.0), determined the SNP in water
22054886 of No. 12 chromosome of rice.Both sides 50bp flanking sequences are extracted centered on candidate SNP locus, and carries out primer and sets
Meter is marked with three primers, two specific primers for the design of critical sites base difference, a universal primer.Utilize 8
Rice donor kind of the part containing pms3 genes and 27 parts of non-donor rice varieties carry out KASP reaction test verifications, mark K_
120522 expanding effects are good, and can accurately distinguish the haplotype of pms3 genes in test material.Label information is as shown in table 1.
Table 1:Label information
Therefore, the first aspect of the present invention, provides a kind of SNP marker of rice sterile gene pms3, described point
Son mark is that polymorphic site base is C or G, and detection site is located at the 22054886 of No. 12 chromosome of rice
Position.
The mark includes two specific primers and a universal primer, wherein, specific primer is respectively
AAAAATTTTACTCTTGATGGATGGTAG(Primer Seq Allele X)、AAAAATTTTACTCTTGATGGATGGTAC
(Primer Seq Allele Y), universal primer TATAGGAGTGGGAGGCATGG.
Preferably, two ends of specific primer 5 ' connect different fluorescent linker sequences respectively.It is furthermore preferred that fluorescent linker
Sequence is FAM or HEX.
Another aspect of the present invention, provides a kind of method for detecting rice sterile gene pms3, and detection method includes as follows
Step:
S1, extraction rice sample gene group DNA;
S2, using oryza sativa genomic dna as template, using the primer sets of K_120522, K_120522 molecular labelings are carried out
Detection;
If the SNP site base of S3, K_120522 are C, the rice sample of discriminating test is free of pms3 genes;If detection
Site base is G, and the rice sample of discriminating test contains homozygous pms3 genes;If detection site is detected simultaneously by C, G, judge
Rice to be measured contains the pms3 genes of heterozygosis.
Preferably, in S1, genomic DNA is extracted from rice leaf, using simplified CTAB methods.
Preferably, in S2, SNP site is detected using KASP technologies.Wherein, two end of specific primer 5 ' difference
Connect different fluorescent linker sequences.The fluorescent linker sequence can be FAM the or HEX joint sequences of LGC companies.
Preferably, KASP reaction systems are as shown in table 2 in S2.KASP Master Mix reagents and mating with it
The LGC SNPline Genotypings platforms used are purchased from LGC companies of Britain.
Table 2:The reaction system of KASP detections
Preferably, KASP reaction steps are as described below in S2:20~50ng DNA samples are added in micro reaction plate, are dried
KASP reaction mixtures are added in after dry, reaction system is shown in Table 2.PCR amplification is completed in water-bath thermal cycler, Touchdown
PCR reaction conditions are:94 DEG C of pre-degenerations 15 minutes;First step amplified reaction, 94 DEG C are denatured 20 seconds, and 65 DEG C~57 DEG C are annealed and prolonged
It stretches 60 seconds, 10 Xun Huans, the temperature of each cycle annealing and extension reduces by 0.8 DEG C;Second step amplified reaction, 94 DEG C of denaturation 20
Second, 57 DEG C are annealed and extended 60 seconds, 26 Xun Huans.Fluorescence data reading is carried out to KASP reaction products after the completion of reaction.
Therefore, in S3, if sample P CR products, which only detect primer PrimerX, corresponds to fluorescence signal, detection site is
Base C, the rice sample of discriminating test are free of pms3 genes;If only detecting primer PrimerY corresponds to fluorescence signal, detect
Site is bases G, and the rice sample of discriminating test contains homozygous pms3 genes;It is examined if two kinds of fluorescence signals are detected simultaneously by
Location point is C:G judges the pms3 genes that rice to be measured contains heterozygosis.
Another aspect of the present invention provides a kind of application of above-mentioned molecular labeling in rice breeding, utilizes K_
The detection method of 120522 molecular labelings is detected K_120522 molecular labelings, and selection carries the rice sample of pms3 genes
Product carry out follow-up breeding.
Another aspect of the present invention provides a kind of kit for detecting pms3 gene SNP molecular labelings, the kit
Include the primer sets of K_120522 molecular labelings.
Preferably, the end of specific primer 5 ' of each molecular labeling connects different fluorescence sequences respectively.The fluorescence sequence
Row can be FAM and HEX fluorescence sequences.
The kit is used for rice breeding.
Beneficial effects of the present invention are:
The present invention provides a kind of Specific primer pairs for identifying rice sterile gene, solve asking in background technology
Topic can quickly and the high-throughput sterile gene pms3 for identifying rice can be completed pair using primer combination before transplanting
Manpower and the input cost of land resource is greatly decreased in the accurate selection of breeding material, improves work efficiency.And establish height
Effect, environmental-friendly coherent detection system, to applications of the sterile gene pms3 in Hybrid breeding in commercial system is promoted to be of great significance.
The present invention provides the primer and methods of genotyping of detection rice sterile gene pms3, mark K_120522 references
Gene internal sequence is developed, and is isolated with target gene, in breeding will not occur separating as not close linked marker and
Cause testing result inaccurate, and heterozygote and homozygote can be distinguished as codominant marker, most critical is specificity
Mark, can be widely used in molecule assist-breeding.Primer using the present invention carries out KASP parting detections, is wrapped in each PCR reactions
Two specific primers and a universal primer of the amplifying specific base of the present invention are included, pass through two kinds of different fluorescence of PCR product
Signal is detected, and is realized that the genotype of the SNP site to each detection sample judges, can be solved existing Morphological Identification
Method detection cycle is long, environment influences the problems such as big, experience accordance with tolerance is strong and detection method is complicated for operation, avoids existing existing
Health threat of the toxic carcinogen to laboratory technician and the pollution to environment in molecular markers for identification experimental method, have it is easy,
Reliably, quickly, high throughput, high specificity, high sensitivity, environmental-friendly remarkable advantage.
Description of the drawings:
It in order to illustrate more clearly about the embodiment of the present invention or technical scheme of the prior art, below will be to embodiment or existing
There is attached drawing needed in technology description to be briefly described, it should be apparent that, the accompanying drawings in the following description is only this
Some embodiments of invention, for those of ordinary skill in the art, without creative efforts, can be with
Other attached drawings are obtained according to these attached drawings.
Fig. 1 natural populations genotyping result.
Specific embodiment
Here exemplary embodiment will be illustrated in detail, example is illustrated in the accompanying drawings.Following description is related to
During attached drawing, unless otherwise indicated, the same numbers in different attached drawings represent the same or similar element.Following exemplary embodiment
Described in embodiment do not represent and the consistent all embodiments of the present invention.On the contrary, they be only with it is such as appended
The example of the consistent apparatus and method of some aspects being described in detail in claims, of the invention.
It is only merely for the purpose of description specific embodiment in terminology used in the present invention, is not intended to limit the invention.
It is also intended in " one kind " of singulative of the invention and used in the attached claims, " described " and "the" including majority
Form, unless context clearly shows that other meanings.It is also understood that term "and/or" used herein refers to and wraps
Containing one or more associated list items purposes, any or all may be combined.
It will be appreciated that though various information, but this may be described using term first, second, third, etc. in the present invention
A little information should not necessarily be limited by these terms.These terms are only used for same type of information being distinguished from each other out.For example, it is not departing from
In the case of the scope of the invention, the first information can also be referred to as the second information, and similarly, the second information can also be referred to as
One information.Depending on linguistic context, word as used in this " if " can be construed to " ... when " or " when ...
When " or " in response to determining ".
The present invention will be described in detail by way of examples below.
1 common rice varieties of embodiment detect
With mark K_120522 to totally 8 parts of genes such as rice varieties GD-1S, 7001S containing pms3 genes, Peiai 64S
Donor material and other 27 rice varieties without restoring gene carry out the reaction verification of KASP primary dcreening operations, as a result such as table 3.Containing pms3
The rice varieties of gene are all detected as G type bases in labeled test site, and 27 parts of non-donor rice varieties are examined in test site
Measure base C, it was demonstrated that molecular labeling K_120522 provided by the present invention and its primer sets testing result are accurate, and specificity is good.
Table 3:Mark K_120522 test cdna typing datas
2 natural population of embodiment is detected
Natural population's verification is carried out to SNP marker K_120522 using 95 parts of materials.95 parts of materials include 34 parts it is common
Hybrid paddy rice and 60 parts of core rice breeds.Mark is in natural population's genotyping result as shown in Figure 1,95 parts of material partings are bright
Really, except detecting homozygous pms3 in the wide Hunan 24S of core rice breed, 34 parts of common paddy rice cross breeding kinds and remaining 59
Part material is all detected without pms3, is met the present situation that the application of pms3 genes is still short of in actual breeding, is demonstrated exploitation of the present invention
SNP marker detection method feasibility and accuracy, identification and assisted selection available for pms3 genes.
It should be pointed out that for those of ordinary skill in the art, without departing from the principle of the present invention, may be used also
With to the present invention, some improvement and modification can also be carried out, these improvement and modification are also fallen into the protection domain of the claims in the present invention.
Claims (10)
1. the SNP marker of one group of rice sterile gene pms3, the molecular labeling is K_120522, wherein K_120522's
Polymorphism is C or G.
2. molecular labeling according to claim 1, it is characterised in that:The polymorphic site of K_120522 is located at No. 12 dye
At 22054886 bit bases of colour solid.
3. application of the SNP marker of claim 1 or 2 in rice breeding.
4. a kind of primer sets for detection molecules mark K_120522,
Specific primer sequence is:
Primer Seq Allele X, SEQ ID NO.1:TCCTCTGAACCCTACTCGACA
Primer Seq Allele Y, SEQ ID NO.2:CTCTGAACCCTACTCGACG
Universal primer sequence is:
SEQ ID NO.3:TGTATGTTGATGTTGATGAGCT.
5. primer sets according to claim 4, it is characterised in that:Specific primer connects different fluorescent linker sequences respectively
Row.
6. primer sets according to claim 5, it is characterised in that:Fluorescent linker sequence is FAM or HEX.
7. application of any primer sets of claim 4-6 in rice breeding.
8. a kind of method for detecting rice sterile gene pms3, detection method include the following steps:
S1, extraction rice sample gene group DNA;
S2, using rice sample gene group DNA as template, using the primer sets of K_120522, K_120522 molecular labelings are directed to
SNP site be detected;
If S3, K_120522 detection site base are C, the rice sample of discriminating test is free of pms3 genes;If detection site
Base is G, and the rice sample of discriminating test contains homozygous pms3 genes;If detection site is detected simultaneously by C and G, judge to treat
Survey the pms3 genes that rice contains heterozygosis.
9. according to the method described in claim 8, it is characterized in that:In S2, SNP site is detected using KASP technologies,
Wherein, two ends of specific primer 5 ' connect different fluorescent linker sequences respectively.
10. a kind of kit, the kit includes the primer of sequence such as SEQ ID NO.1-3.
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Cited By (6)
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CN109355421A (en) * | 2018-12-03 | 2019-02-19 | 浙江省农业科学院 | Detect KASP labeled primer and its application of rice PTGMS genes tms9-1 and pms3 |
CN109628628A (en) * | 2018-12-11 | 2019-04-16 | 华智水稻生物技术有限公司 | The development and application of the SNP marker of rice blast resistant gene Pi2 |
CN112442547A (en) * | 2020-12-11 | 2021-03-05 | 华智生物技术有限公司 | Development and application of SNP molecular marker of rice blast resistance gene Pita |
CN112522432A (en) * | 2020-12-17 | 2021-03-19 | 华智生物技术有限公司 | Molecular marker for assisted breeding of rice blast resistance gene Bsr-d1 and application thereof |
CN112609018A (en) * | 2020-12-11 | 2021-04-06 | 华智生物技术有限公司 | SNP molecular marker of rice grain type related gene GLW2 and application thereof |
CN114427006A (en) * | 2022-02-24 | 2022-05-03 | 湖北省农业科学院粮食作物研究所 | Primer and method for molecular marker of photo-thermo-sensitive male sterile gene pms3 of rice |
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CN109355421A (en) * | 2018-12-03 | 2019-02-19 | 浙江省农业科学院 | Detect KASP labeled primer and its application of rice PTGMS genes tms9-1 and pms3 |
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CN112609018A (en) * | 2020-12-11 | 2021-04-06 | 华智生物技术有限公司 | SNP molecular marker of rice grain type related gene GLW2 and application thereof |
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CN114427006A (en) * | 2022-02-24 | 2022-05-03 | 湖北省农业科学院粮食作物研究所 | Primer and method for molecular marker of photo-thermo-sensitive male sterile gene pms3 of rice |
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