With the closely linked molecular labeling SIsv1083 of millet fertile gene
Technical field
The invention belongs to biology field, relate to a kind of molecular labeling, particularly relate to a kind of and millet fertility baseBecause of closely linked molecular labeling. The invention still further relates to primer, this molecular labeling and the primer of this molecular labeling of amplification in milletPurposes in fertile gene location or millet genetic breeding.
Background technology
China is the country of origin of millet (SetariaitalicaL.Beauv.), is the concentrated plantation of millet in the worldState, millet occupies an important position in the national economy of China and social production, and dry farming ecological agriculture construction is had to important meaningJustice. Therefore, the breeding process of acceleration millet is particularly important. Because millet is region importance crop, therefore current relevant paddyResearch means and the method for son are relatively backward, and how to do Millet Breeding well be a sternness to the research means of application of advanced scienceProblem. Along with molecular biological development, the appearance of molecular marking technique, for genetic research and the breeding of millet have been opened up newlyThinking and means. Develop the molecular labeling of the important character gene with China's characteristic and carry out assisted selection research,To play facilitation to improving China's Millet Breeding level.
Millet is the cereal crops of economizing on water most, and water consumption is only the 1/2-2/3 of corn, is China west droughty area and poorLean mountain area solves the selection of the unique reality of food problem. Constantly reduce at cultivated land resource, water resource worsening shortages, balanced diet heatUnder the situation of intensification, animal husbandry development, carrying forward vigorously millet industry can increase grain output, promote animal husbandry to send out graduallyExhibition, can promote again water-saving agriculture, drive related industry development, achieves many things at one stroke, and social benefit is remarkable.
Millet is typical self pollination crop, and whether close with the Relationship between breeding of millet the fertility of millet is, directly impactTo the breeding work of millet.
Summary of the invention
The object of this invention is to provide a kind of and the closely linked molecular labeling of millet fertile gene.
Another object of the present invention is to provide one and can be used for pcr amplification and the closely linked molecule mark of millet fertile geneThe primer pair of note, and the molecular labeling being obtained by this primer pair amplification.
It is auxiliary in millet fertile gene location, detection and millet that a further object of the present invention is to provide above-mentioned molecular labelingPurposes in breeding and the detection method of above-mentioned molecular labeling.
Object of the present invention also comprises provides a kind of carrier that comprises above-mentioned molecular labeling, and the restructuring that contains this carrierCell; A kind of localization method that comprises the millet fertile gene that uses above-mentioned molecular labeling is provided, and uses described molecular labelingMillet auxiliary breeding means.
To achieve these goals, the present invention has adopted following technical scheme:
The invention discloses a kind of and the closely linked molecular labeling of millet fertile gene, described molecular labeling contains SeqSequence shown in IDNo.1; Preferred described molecular labeling has sequence shown in SeqIDNo.1. Described in it is pointed out that, educateProperty gene refers to the gene that millet selfing can be solid, and the full tassel seed of millet sample plant that contains this gene all can be educated, and can enterRow self-pollination.
The invention also discloses the primer pair of a kind of amplification and the closely linked molecular labeling of millet fertile gene, described in drawThe right primer 1 of thing contains sequence shown in SeqIDNo.2, and primer 2 contains sequence shown in SeqIDNo.3; Described in preferred, drawThing 1 has sequence shown in SeqIDNo.2, and primer 2 has sequence shown in SeqIDNo.3;
SeqIDNo.2:5’-GATCAGCTTTGTACCCAGCT-3’;
SeqIDNo.3:5’-GGACCGTGCTGGAGCATGTT-3’
The invention also discloses a kind of and the closely linked molecular labeling of millet fertile gene, described molecular labeling is by upperThe primer pair of stating obtains through pcr amplification taking the millet genomic DNA of fertility as template.
Preferably contain sequence shown in SeqIDNo.1 by the above-mentioned primer pair molecular labeling obtaining that increases.
In one embodiment of the invention, described molecular labeling (contains nucleotide sequence shown in SeqIDNo.1DNA fragmentation) be the DNA fragmentation of nucleotide sequence shown in SeqIDNo.1 in millet genome, the SeqID that comprisedNucleotide sequence beyond 5 ' end and/or the 3 ' end of No.1 is also the sequence in millet genome, preferred, is millet genome5 ' the end of middle SeqIDNo.1 and/or the upstream and downstream sequence of 3 ' end. It will be understood by those skilled in the art that if amplification orThis molecular labeling in the millet genomic DNA of detection fertility, must detect or increase to and contain shown in SeqIDNo.1Sequence. The length of the 5 ' end of SeqIDNo.1 and/or the upstream and downstream sequence of 3 ' end is suitable length, is not particularly limited exampleAs, the length that meets molecular labeling is less than 10,000bp, is less than 5,000bp, is less than 2,000bp, is less than 1,500bp, is less than 1,200bp, be less than 1,000bp or be less than 800bp.
In one embodiment of the invention, described molecular labeling (contains nucleotide sequence shown in SeqIDNo.1DNA fragmentation) be operably connected artificial sequence and/or control order of the 5 ' end of the SeqIDNo.1 that comprises and/or 3 ' endRow, for example promoter, enhancer, terminator, restriction enzyme site, primer sequence etc. Wherein, term " operationally " is in the present inventionIn be defined as a kind of following conformation, in this conformation, for example promoter of control sequence is suitably placed in one of SeqIDNo.1On individual position, so that this control sequence instructs the generation of the polypeptide of SeqIDNo.1 coding.
The invention also discloses a kind of recombinant vector, it contains molecular labeling of the present invention. Described recombinant vector can beBe inserted with expression vector or the cloning vector of molecular labeling of the present invention. Obtain after above-mentioned recombinant vector art technology peopleMember is appreciated that according to different needs, and recombinant vector is transformed in suitable cell, obtains the weight that contains this recombinant vectorGroup cell. Therefore, the invention also discloses a kind of recombinant cell that contains described recombinant vector.
The invention also discloses the preparation method of molecular labeling of the present invention, comprise the steps: to use the millet of fertilityGenomic DNA as template, carry out pcr amplification with above-mentioned primer pair, the 661bp amplified production obtaining contains described moleculeMark; Preferably, also comprise the step of pcr amplification product being carried out to purifying.
To those skilled in the art, be appreciated that also can DNA chemical synthesis method obtain molecule of the present inventionMark.
The detection method that the invention also discloses described molecular labeling, comprises step: according to the nucleosides of above-mentioned molecular labelingAcid sequence design primer, increases as template to be detected millet genomic DNA, and judges in amplified production whether have thisMolecular labeling. Preferably, described primer is the above-mentioned primer pair that contains respectively SeqIDNo.2 and SeqIDNo.3.
For example, can be taking the genomic DNA that is detected millet as template, with above-mentioned primer (SeqIDNo.2 and SeqIDNo.3) carry out pcr amplification, obtain amplified production. The amplified production obtaining can be checked order or gel electrophoresis.
The invention also discloses the purposes of described molecular labeling in millet fertile gene location or in detecting.
The invention also discloses the method for a kind of millet fertile gene location, described method comprises use molecule of the present inventionThe step of mark.
The invention also discloses the purposes of described molecular labeling in millet assistant breeding.
The invention also discloses a kind of millet auxiliary breeding means, described method comprise detect molecular labeling of the present invention orUse the step of the primer pair of amplifier molecule mark in the present invention.
Molecular labeling of the present invention can be used in molecular mark from now on, and those skilled in the art can manageSeparate, such as by detect whether exist molecular labeling of the present invention screen millet whether contain control fertility gene (for example,Can reference, the purposes of DNA molecular marker in wheat breeding for disease resistance, Long Dong institute journal (natural science edition), in April, 2006The 16th the 1st phase of volume, P65-69). Described detection can be the method that PCR detects, and particularly, can use above-mentioned of the present inventionThe primer pair of amplifier molecule mark. Described detection can also be undertaken by sequence measurement. This millet auxiliary breeding means has letterJust, quick, high-throughout advantage.
In the present invention, particularly, described millet can or open assorted for a paddy No. 1, millet A2 sterile line, No. 3, a confused flour beetleThe F2 generation that No. 3 selfings of paddy produce. Wherein, open paddy No. 1, confused flour beetle No. 3 or the performance in the part F2 generation that No. 3 selfings of confused flour beetle produceIt is identical that type and male parent are opened paddy No. 1; In the part F2 generation that millet A2 sterile line, No. 3 selfing of confused flour beetle produce, is sterile with maternal millet A2The phenotype of system is identical.
Owing to adopting above technical scheme, the beneficial effect that the present invention possesses is:
The invention provides and the closely linked molecular labeling of millet fertile gene, this molecular labeling is by genomic DNA orderRow connect with millet fertile gene, are conducive to the foundation of millet molecular mark system; Described molecular labeling withThe hereditary close linkage distance of millet fertile gene is 3.5cM. Molecular labeling of the present invention and molecular labeling amplimer are passableEasy, quick, be applied to Millet Breeding practice and resource and cultivar identification high flux.
Brief description of the drawings
Fig. 1: the part knot of molecular labeling primer (SeqIDNo.2 and SeqIDNo.3) to 480 the individual plant amplifications of F2 generationReally. Wherein: swimming lane 1-12 is the pcr amplification product of the millet individual plant that in F2 generation, 12 strain phenotypes are identical with male parent with genotype;Swimming lane 13-24 is 12 strain phenotypes and the pcr amplification product of genotype with maternal identical millet individual plant in F2 generation. Swimming lane M isMarker, it is 100bpDNALadder; Its molecular weight comprises: 1500bp, 1000bp, 900bp, 800bp, 700bp,600bp, 500bp, 400bp, 300bp, 200bp and 100bp.
Detailed description of the invention
The invention discloses a kind of primer pair and with the closely linked molecular labeling SIsv1083 of millet fertile gene. ProfitUse primer pair of the present invention, carry out PCR taking millet genomic DNA as template, can obtain and millet fertile gene close linkageMolecular labeling, this molecular labeling is called after molecular labeling SIsv1083 in the present invention. It is pointed out that art technologyPersonnel are appreciated that except obtaining molecular labeling of the present invention by above-mentioned pcr amplification, can also obtain by chemical synthesisMolecular labeling of the present invention.
Primer pair of the present invention contains respectively sequence shown in ordered list SeqIDNo.2 and SeqIDNo.3,
SeqIDNo.2:5’-GATCAGCTTTGTACCCAGCT-3’;
SeqIDNo.3:5’-GGACCGTGCTGGAGCATGTT-3’
Those skilled in the art know, in sequence shown in above-mentioned SeqIDNo.2 and SeqIDNo.3, can its 5 'End or 3 ' end increase respectively 1~10 base, the base type increasing can according on millet genomic DNA with SeqIDNo.2 and SeqIDNo.3 match region base type and determine the primer obtaining thus according to basepairing ruleTo with basic identical (the DNA sequence dna phase between upstream and downstream primer of the amplified production of SeqIDNo.2 and SeqIDNo.3With). Therefore, the above-mentioned 5 ' end at SeqIDNo.2 and SeqIDNo.3 or 3 ' end increase respectively 1~10 base and can expandIncrease the primer pair that obtains basic identical DNA fragmentation, include in primer pair of the present invention. At the concrete embodiment of the present inventionIn, primer pair of the present invention is preferably sequence shown in SeqIDNo.2 and SeqIDNo.3.
The present invention can educate male parent with the homozygote of maternal partial sterility and hybridize, and obtains F1 generation (No. 3, a confused flour beetle, can educate),Produce F2 for colony with F1 generation selfing again, totally 480 individual plants. The preferred SV molecular markers development method that adopts, first to male parentCarry out denovo order-checking (60XcontigN50:22K, scaffoldN50:320K; Totalsize:400Mb), maternal heavyOrder-checking (10X); Then according to Parent sequencing data, utilize the order between the SOAP comparison Parent of Hua Da independent developmentRow difference, in 5 ' end and 3 ' the about 50bp position, end outside of male parent diversity sequence, chooses at random the length of 20bp left and right and establishes respectivelyThe primer of meter diversity sequence amplification, has designed 1105 pairs of primers according to different diversity sequences. Taking the DNA of Parent and F1 as mouldPlate increases, and filters out 616 pairs of primers with polymorphism and validity from 1105 pairs of primers. Employing develop 616To primer, 480 of F2 colony individualities are carried out to PCR detection, and carry out data statistic analysis, enter with MapMaker3.0 softwareRow genetic map is drawn, and obtains the of the present invention and closely linked molecular labeling of fertile gene, and amplimer. AdoptThe primer pair filtering out increase the male parent sequence obtaining, i.e. molecular labeling SIsv1083 in the present invention. To carrying out property of F2 individualityShape is analyzed, and according to gene character data and phenotypic character data, millet fertile gene is positioned on genetic map.
Also by reference to the accompanying drawings the present invention is described in further detail below by specific embodiment. Following examples are only rightThe present invention is further detailed, and should not be construed as limitation of the present invention.
Embodiment 1: millet F2 is for the structure of segregating population
Male parent: anti-Sethoxydin, plant type is high, and boot leaf is long and narrow, bristle redness, clever shell redness, can educate, and leaf colour cast is green, pollenYellow-white, be late period heading stage. Male parent is No. 1 seed of paddy.
Maternal: not anti-Sethoxydin, plant type is short, and boot leaf is short and wide, bristle green, clever shell green, partial sterility, leaf colour castHuang, pollen is brown, and be early stage heading stage. Female parent is millet A2 male-sterile seed. In the present invention, the partial sterility of above-mentioned female parent isRefer in each fringe that about 5% seed can educate, all the other are sterile.
F2 colony builds: male parent obtains F1 generation (phenotype of F1 is identical with the phenotype of male parent) with hybridization of female parent, and F1 certainlyFriendship obtains F2. Wherein F1 is No. 3 seeds of a confused flour beetle. Altogether F2 for individual plant 480 strains.
No. 1 seed of above-mentioned paddy, millet A2 male-sterile seed and No. 3 seeds of confused flour beetle can referring to Chinese patent application " withThe closely linked molecular labeling SIsv0372 of millet anti-herbicide gene ", publication number CN101974521A, date of publication 2011 2The moon 16.
Embodiment 2: Parent and F1 generation, F2 are for the extraction of genes of individuals group DNA
Extract respectively Parent, F1 generation and 480 F2 in embodiment 1 for individual genomic DNA by CTAB method,Concrete grammar is as follows:
(1) take the fresh blade of 1.0g, shred and put into mortar, with adding 3mL1.5 × CTAB after liquid nitrogen grinding, grind to formHomogenate proceeds in the centrifuge tube of 15mL, then in mortar, adds 1mL1.5 × CTAB flushing to proceed in centrifuge tube again. After mixingIn 65 DEG C of water-bath 30min, frequently slowly shake up during this time.
Wherein 1.5 × CTAB formula following (1L):
Add deionized water and be settled to 1L, before use, adding final concentration is the mercaptoethanol of 0.2% (2mL).
(2) to be cooled to room temperature, add equal-volume chloroform/isoamyl alcohol (24: 1), mix gently, become dark green to subnatantLook.
(3) the centrifugal 10min of 4200rpm, moves on to new 15mL centrifuge tube mutually by upper water, adds the anhydrous of 2 times of volume precoolingsEthanol, mixes static 5min. Place 30min precipitation DNA in-20 DEG C.
(4) the centrifugal 10min of 4200rpm, discards supernatant, adds 1mL75% ethanol washing precipitation 1 time, is inverted centrifuge tube dryDry DNA, adds 200 μ LTE dissolving DNAs.
(5) detect genomic DNA with 0.8% Ago-Gel.
(6) by the Parent obtaining and F1 generation, F2 for individual genomic DNA be stored in-20 DEG C for subsequent use.
Embodiment 3: the preparation of molecular labeling
Taking in embodiment 2 extract male parent, F1 generation or the genomic DNA in F2 generation as template, with molecular labeling amplimer(SeqIDNo.2 and SeqIDNo.3) carried out to pcr amplification.
PCR reaction system is as follows:
PCR response procedures is as follows:
94 DEG C of denaturations 5 minutes; 94 DEG C of sex change 30 seconds, 60 DEG C of annealing 30 seconds, 72 DEG C are extended 40 seconds, move 35 circulations;Last 72 DEG C are extended 3 minutes. Pcr amplification product can be 4 DEG C of preservations.
Obtain molecular labeling through above-mentioned amplification procedure, preferably after amplification, amplified production is carried out to purification process. Purifying is laggardRow order-checking, result is as shown in SeqIDNo.1.
To those skilled in the art, be appreciated that also and can obtain this molecule mark by the method for DNA chemical synthesisNote.
Embodiment 4:SV molecular markers development
Male parent: denovo order-checking, 60XcontigN50:22K, scaffoldN50:320K; Totalsize:400Mb; Maternal: the order of resurveying 10X.
According to Parent sequencing data, utilize SOAP software (for example SOAP2.20, the Ke Yicong of Hua Da independent developmentHttp:// soap.genomics.org.cn/ downloads, and also can use other sequence alignment software) relatively between ParentSequence difference, the then sequence based on difference, with the primer of primerpremier Software for Design amplification diversity sequence; Based onDifferent diversity sequences, has designed altogether 1105 pairs of primers. Part primer sequence (Seq has wherein been shown in table 1 belowIDNo.2-SeqIDNo.41)
Table 11105 is to the part primer in random primer
Taking the Parent that extracts and the genomic DNA of F1 generation as template, carry out PCR expansion with 1105 pairs of primers that design respectivelyIncrease.
PCR reaction system (25 μ L):
PCR response procedures: 94 DEG C of denaturation 5min; Then enter 35 circulations: 94 DEG C of sex change 30s, 60 DEG C of annealing 30s,72 DEG C are extended 40s; Circulation finishes latter 72 DEG C and extends 3min; 4 DEG C of preservations.
PCR product electrophoresis detection: 1.2% Ago-Gel 120v electrophoresis 25min, the EB 10min that dyes, according to glue noteRecord.
The validity of primer and polymorphism: refer to whether there is amplified production, polymorphism refers between Parent in this validityThe clip size of amplified production is variant.
Carry out the screening of primer according to following screening criteria: Parent and F1 all have amplified production, and Parent expandsVolume increase thing all only has a distinct banding pattern and big or small variant, and F1 shows as the heterozygosis banding pattern of Parent banding pattern, has fatherTwo bands of basis and maternal banding pattern.
The selection result: according to above-mentioned screening criteria, filter out 616 pairs of primers from 1105 pairs of primers of design.
Embodiment 5: genetic map construction and the assignment of genes gene mapping
(1) genetic map construction
The molecular labeling with 616 couple of exploitation with polymorphism carries out PCR detection to 480 of F2 colony individualities, usedTemplate is 480 individual genomic DNAs of the F2 colony that makes.
PCR product is carried out to agarose gel electrophoresis, obtain the result of 480 individual amplifications of molecular labeling primer pair.
Whole electrophoresis result are carried out to data statistic analysis, and concrete grammar is as follows: be father by F2 colony individual plant amplified bandThis type be designated as a, what amplified band was maternal type is designated as b, amplified band contains the h that is designated as of male parent type and maternal type simultaneously, bandFuzzy or disappearance be designated as-, be equivalent to shortage of data, finally obtain the base of 480 616 pairs of individual primer amplifications of F2 colonyBecause of type data. Such as, 480 individual data that obtain with pair of primers are a, b, and h ,-, b ... totally 480 data,The data that obtain with second pair of primer are b, a, and h, a ,-... totally 480 data, totally 616 pairs of primers are added up respectively, gainedBe the genotype data of this F2 colony.
With MapMaker3.0 software (ConstructinggeneticmapswithMAPMAKER/EXP3.0, SLincoln, MDaly, ELander-Cambridge, MA:WhiteheadInstitute, 1992) carry out genetic linkage mapSpectrum is drawn, and obtains genetic linkage map. From the genetic linkage map that this obtains, can determine the position of 616 pairs of primers and with millet fertilityThe genetic distance of gene.
(2) assignment of genes gene mapping
According to 480 individual fertility phenotypes, similar to male parent type proterties a, the note similar to maternal type proterties of being designated asFor b. Obtain 480 individual phenotypic datas, by 480 individual phenotypic datas and 480 that obtain before individual genesType data compare, and similar Gao Ze represents this mark and fertility proterties close linkage, and fertile gene is positioned to heredity evenOn lock collection of illustrative plates.
Embodiment 6: with the checking of the closely linked molecular labeling of millet fertile gene
1. on the basis of the genetic linkage maps making at embodiment 5, according to the genetic linkage distance of millet fertile geneFrom, with the hereditary close linkage distance of millet fertile gene be 3.5cM location positioning molecular labeling primer (SeqIDNo.2 and SeqIDNo.3), and find corresponding male parent sequence location, the sequence between upstream and downstream primer is molecular labeling,Its nucleotide sequence is as shown in SeqIDNo.1.
SeqIDNo.2:5’-GATCAGCTTTGTACCCAGCT-3’;
SeqIDNo.3:5’-GGACCGTGCTGGAGCATGTT-3’
2. in addition, in embodiment 5 in the electrophoresis of 480 of F2 generation individual pcr amplification products, for molecule markThe amplification of note primer (SeqIDNo.2 and SeqIDNo.3) is: the amplified production of approximately 360 strain fertile plants all hasThe band of 661bp size, the pcr amplification product of the approximately 120 strains plant identical with maternal phenotype does not all have the band of 661bp(part amplification as shown in Figure 1). And the sequence of the fragment that proves this 661bp through checking order is identical with SeqIDNo.1.
Visible, molecular labeling of the present invention (SeqIDNo.1) is and the closely linked molecular labeling of millet fertile gene.
Embodiment 7: molecular marker clone
The fragment of the 661bp that in embodiment 6, amplification obtains is cloned in pMD18-T carrier, obtains recombinant vector. ShouldRecombinant vector is transformed in e. coli jm109, chooses monoclonal, cultivates and obtains recombinant cell. From recombinant cell, extract plasmid,Described plasmid is recombinant vector, adopts M13 universal primer (sequence information is with reference to TaKaRa goods catalogue) to carry out cloned sequenceOrder-checking, result shows, contains molecular labeling of the present invention (SeqIDNo.1) in recombinant vector. Above-mentioned clone, conversion, cultivation,The steps such as plasmid extraction are with reference to " the molecular cloning experiment guide third edition ", and Huang Peitang etc. translate, and Science Press goes out in September, 2002Version.
Above content is in conjunction with concrete embodiment further description made for the present invention, can not assert thisBright concrete enforcement is confined to these explanations. For general technical staff of the technical field of the invention, not de-Under the prerequisite of the present invention's design, can also make some simple deduction or replace, all should be considered as belonging to protection of the present inventionScope.