Molecular marker SIsv0067 closely linked with millet Heading date gene
Technical field
The invention belongs to biology field, relate to a kind of molecular marker, particularly relate to a kind of and the closely linked molecular marker of millet Heading date gene. The invention still further relates to the amplification primer of this molecular marker, this molecular marker and the primer purposes in millet Heading date gene location or millet genetic breeding.
Background technology
China is the country of origin of millet (SetariaitalicaL.Beauv.), is that the concentration of millet in the world plants state, and millet occupies an important position in the national economy and social production of China, and dry farming ecological agriculture construction is significant. Therefore, the breeding process accelerating millet is particularly important. Owing to millet is region importance crop, therefore current relatively backward about research means and the method for millet, how the research means of application of advanced science does Millet Breeding well is a severe problem. Along with molecular biological development, the appearance of molecular marking technique, genetic research and breeding for millet open new thinking and means. Exploitation has the molecular marker of the important character gene of China's characteristic and carries out assisted selection research, will play facilitation to improving China's Millet Breeding level.
The plantation area that decide kind heading stage and the cropping system adapted to, be the important goal character of crop breeding. Heading stage belongs to quantitative trait, its hereditary basis is complex, it is generally acknowledged that heading stage is by major gene resistance and minor gene co-controlling, the research of its hereditary basis is respectively provided with significance (Huang Cheng to instructing breeding practice, breed improvement and popularization, Jiang Shukun, Liu Menghong etc. the QTL of rice ear sprouting period dissects. North China agronomy report, 2009). Studying at present relatively more on heading stage is Oryza sativa L., but the research for millet heading stage is substantially free of bibliographical information.
Summary of the invention
It is an object of the invention to provide a kind of and the closely linked molecular marker of millet Heading date gene.
It is a further object of the present invention to provide a kind of primer pair that can be used for pcr amplification and the closely linked molecular marker of millet Heading date gene and the molecular marker obtained by this primer pair amplifies.
Another object of the present invention is to provide the detection method of above-mentioned molecular marker purposes in millet Heading date gene location, detection and millet assistant breeding and above-mentioned molecular marker.
The purpose of the present invention also includes providing a kind of carrier including above-mentioned molecular marker and the reconstitution cell containing this carrier; The localization method of a kind of millet Heading date gene including using above-mentioned molecular marker is provided, and uses the millet auxiliary breeding means of described molecular marker.
To achieve these goals, present invention employs techniques below scheme:
The invention discloses a kind of and the closely linked molecular marker of millet Heading date gene, described molecular marker contains sequence shown in SeqIDNo.1; Preferred described molecular marker has sequence shown in SeqIDNo.1.
The invention also discloses the primer pair of a kind of amplification and the closely linked molecular marker of millet Heading date gene, the primer 1 of described primer pair is containing sequence shown in SeqIDNo.2, and primer 2 contains sequence shown in SeqIDNo.3; Preferred described primer 1 has sequence shown in SeqIDNo.2, and primer 2 has sequence shown in SeqIDNo.3;
SeqIDNo.2:5 '-AGCCAGCTGGAGAAGAGAAT-3 ';
SeqIDNo.3:5 '-CCCAAGTCCAACTGAAGGC-3 '.
The invention also discloses a kind of and the closely linked molecular marker of millet Heading date gene, described molecular marker is to be obtained through pcr amplification for template with the millet genomic DNA that heading stage is late period by above-mentioned primer pair.
The preferred molecular marker obtained by above-mentioned primer pair amplifies contains sequence shown in SeqIDNo.1.
In one embodiment of the invention, described molecular marker (DNA fragmentation containing nucleotide sequence shown in SeqIDNo.1) is the DNA fragmentation of nucleotide sequence shown in SeqIDNo.1 in millet genome, nucleotide sequence beyond the 5 ' ends of the SeqIDNo.1 namely comprised and/or 3 ' ends is also the sequence in millet genome, preferably, for 5 ' end and/or 3 ' the upstream and downstream sequences held of SeqIDNo.1 in millet genome. As long as it will be understood by those skilled in the art that amplification or detection are this molecular marker in the millet genomic DNA in late period heading stage, necessarily can detect or expanding and obtain containing the sequence shown in SeqIDNo.1. 5 ' the ends of SeqIDNo.1 and/or the length of 3 ' the upstream and downstream sequences held are suitable length, it is not particularly limited, such as, meet the length of molecular marker less than 10,000bp, less than 5,000bp, less than 2,000bp, less than 1,500bp, less than 1,200bp, less than 1,000bp or less than 800bp.
In one embodiment of the invention, 5 ' the ends of the SeqIDNo.1 that described molecular marker (DNA fragmentation containing nucleotide sequence shown in SeqIDNo.1) comprises and/or 3 ' are held and have been operably connected artificial sequence and/or have controlled sequence, for instance promoter, enhancer, terminator, restriction enzyme site, primer sequence etc. Wherein, term " operationally " is defined as a kind of following conformation in the present invention, in this conformation, controls sequence such as promoter and is appropriately placed on a position of SeqIDNo.1, so that the generation of the polypeptide of the sequence-directed SeqIDNo.1 coding of this control.
The invention also discloses a kind of carrier, it contains the molecular marker of the present invention. Described carrier can be expression vector or the cloning vehicle of the molecular marker being inserted with the present invention. After obtaining above-mentioned carrier, it will be understood by those skilled in the art that according to different needs, by vector to suitable cell, obtain the reconstitution cell containing this carrier. Therefore, the invention also discloses a kind of reconstitution cell containing described recombinant vector.
The preparation method that the invention also discloses the molecular marker of the present invention, comprise the steps: that the genomic DNA of the millet using be late period as template at heading stage, carrying out pcr amplification with above-mentioned primer pair, namely the 557bp amplified production obtained contains described molecular marker; Preferably, the step being purified by pcr amplification product is also included.
To those skilled in the art, it is possible to understand that, it is also possible to the method for DNA chemosynthesis obtains the molecular marker of the present invention.
The invention also discloses the detection method of described molecular marker, including step: design primer according to the nucleotide sequence of above-mentioned molecular marker, expand for template with detected millet genomic DNA, and judge whether amplified production exists this molecular marker. Preferably, described primer is the above-mentioned primer pair containing SeqIDNo.2 and SeqIDNo.3 respectively.
For example, it is possible to the genomic DNA of detected millet for template, carry out pcr amplification with above-mentioned primer (SeqIDNo.2 and SeqIDNo.3), obtain amplified production. Can be undertaken checking order or gel electrophoresis by the amplified production obtained.
The invention also discloses described molecular marker purposes in millet Heading date gene location or detection.
The method that the invention also discloses a kind of millet Heading date gene location, described method includes the step using the molecular marker of the present invention.
The invention also discloses described molecular marker purposes in millet assistant breeding.
The invention also discloses a kind of millet auxiliary breeding means, described method includes the molecular marker of the detection present invention or the step of molecular marker primer pair.
The molecular marker of the present invention can be used in molecular mark from now on, it will be appreciated by those skilled in the art that, as by detect whether the molecular marker that there is the present invention to screen millet whether contain control heading stage be late period Heading date gene (such as, it is referred to, DNA molecular marker purposes in wheat breeding for disease resistance, Long Dong institute journal (natural science edition), volume the 1st phase April the 16th in 2006, P65-69). Described detection can be the method for PCR detection, specifically, it is possible to use the primer pair of the molecular marker of the above-mentioned present invention. Described detection can also be undertaken by sequence measurement. This millet auxiliary breeding means has simplicity, advantage quick, high-throughout.
In the present invention, specifically, described millet can be the F2 generation that a paddy No. 1, millet A2 sterile line, a confused flour beetle 3 or No. 3 selfings of a confused flour beetle produce. Wherein, open paddy No. 1, confused flour beetle 3 or part F2 that No. 3 selfings of confused flour beetle produce for being heading stage in late period; The part F2 that millet A2 sterile line, No. 3 selfings of a confused flour beetle produce is for being early stage heading stage.
Owing to adopting above technical scheme, make what the present invention possessed to have the beneficial effects that:
The invention provides molecular marker closely linked with millet Heading date gene, genomic dna sequence and millet Heading date gene are connected by this molecular marker, are conducive to the foundation of millet molecular mark system; The hereditary close linkage distance of described molecular marker and millet Heading date gene is 3cM. The molecular marker of the present invention and molecular marker amplimer can be applied to Millet Breeding practice and resource and cultivar identification easy, quickly, high flux.
Accompanying drawing explanation
Fig. 1: molecular marker primer (SeqIDNo.2 and the SeqIDNo.3) partial results to 480 the individual plant amplifications of F2 generation. Wherein:
Swimming lane 1-12 is that in F2 generation, 12 strain millets are the pcr amplification product of the individual plant in late period heading stage; Swimming lane 13-24 is that in F2 generation, 12 strains are the pcr amplification product of the individual plant of early stage heading stage. Swimming lane M is marker, and it is 100bpDNALadder; Its molecular weight includes:, 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 molecular marker SIsv0067 closely linked with millet Heading date gene. Utilize the primer pair of the present invention, carry out PCR with millet genomic DNA for template, it is possible to obtaining molecular marker closely linked with millet Heading date gene, this molecular marker is called after molecular marker SIsv0067 in the present invention. It is pointed out that except the molecular marker that it will be understood by those skilled in the art that except being obtained the present invention by above-mentioned pcr amplification, it is also possible to obtained the molecular marker of the present invention by chemosynthesis.
The primer pair of the present invention respectively containing sequence shown in ordered list SeqIDNo.2 and SeqIDNo.3,
SeqIDNo.2:5 ' AGCCAGCTGGAGAAGAGAAT-3 ';
SeqIDNo.3:5 '-CCCAAGTCCAACTGAAGGC-3 '.
Those skilled in the art know, in sequence shown in above-mentioned SeqIDNo.2 and SeqIDNo.3,1��10 base can be increased respectively at its 5 ' end or 3 ' ends, the base type increased can be determined according to the base type in the region that matches with SeqIDNo.2 and SeqIDNo.3 on millet genomic DNA foundation basepairing rule, the primer pair thus obtained essentially identical with the amplified production of SeqIDNo.2 and SeqIDNo.3 (DNA sequence between upstream and downstream primer is identical). Therefore, the above-mentioned 5 ' ends at SeqIDNo.2 and SeqIDNo.3 or 3 ' ends increase by 1��10 base respectively and can expand the primer pair obtaining essentially identical DNA fragmentation, are included in the primer pair of the present invention. In specific embodiment of the present invention, the primer pair of the present invention is preferably sequence shown in SeqIDNo.2 and SeqIDNo.3.
General Millet Seed needs about 70 days from sprouting to earing, and in the present invention, refers to more late than general millet about 10 days of heading described late period at heading stage, and early stage at heading stage refers to more Zao than general millet about 10 days of heading.
The present invention is by the homozygote hybridization in male parent late period at heading stage and maternal early stage at heading stage, it is thus achieved that F1 generation (confused flour beetle 3), then produces F2 for colony with F1 generation selfing, totally 480 individual plants.
Preferred employing SV molecular markers development method, first carries out denovo order-checking (60XcontigN50:22K, scaffoldN50:320K to male parent; Totalsize:400Mb), female parent is resurveyed sequence (10X); Then according to Parent sequencing data, utilize the sequence difference between the SOAP comparison Parent of Hua Da independent development, respectively in 5 ' ends of male parent diversity sequence and 3 ' about 50bp positions, end outside, randomly select the primer of the Design of length diversity sequence amplification of about 20bp, devise 1105 pairs of primers according to different diversity sequences. Expand for template with the DNA of Parent and F1, from 1105 pairs of primers, filter out 616 pairs of primers with polymorphism and effectiveness. Adopt the 616 pairs of primers developed, 480 individualities of F2 colony are carried out PCR detection, and carries out data statistic analysis, carry out genetic map drafting with MapMaker3.0 software, obtain molecular marker closely linked with Heading date gene of the present invention and amplimer thereof. Adopt the male parent sequence that the primer pair amplifies filtered out obtains, i.e. molecular marker SIsv0067 in the present invention. F2 individuality is carried out character analysis, and according to gene character data and phenotype trait data, millet Heading date gene is positioned on genetic map.
Below by specific embodiment and in conjunction with accompanying drawing, the present invention is described in further detail. The present invention is only further detailed by following example, 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, and bristle is red, and grain husk shell is red, can educate, and leaf colour cast is green, pollen yellow-white, and heading stage is late period. Male parent is No. 1 seed of paddy.
Maternal: not anti-Sethoxydin, plant type is short, boot leaf short-wide, and bristle is green, and grain husk shell is green, partial sterility, and leaf colour cast is yellow, and pollen is brown, and heading stage is early stage. Female parent is millet A2 male-sterile seed.
F2 informative population: male parent and hybridization of female parent obtain F1 generation (F1 heading stage be late period), and F1 selfing obtains F2. Wherein F1 is No. 3 seeds of a confused flour beetle. There are F2 for individual plant 480 strain,
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 " molecular marker SIsv0372s closely linked with millet anti-herbicide gene ", publication number CN101974521A, date of publication on February 16th, 2011.
Embodiment 2: Parent and F1 generation, F2 are for the extraction of genes of individuals group DNA
Extract the genomic DNA of the Parent in embodiment 1, F1 generation and 480 F2 generation individualities respectively by CTAB method, concrete grammar is as follows:
(1) weigh the fresh blade of 1.0g, shred and put into mortar, with adding 3mL1.5 �� CTAB after liquid nitrogen grinding, grind to form in the centrifuge tube that homogenate proceeds to 15mL, in mortar, then add 1mL1.5 �� CTAB flushing proceed to again in centrifuge tube. In 65 DEG C of water-bath 30min after mixing, period slowly shakes up frequently.
Wherein 1.5 �� CTAB formula following (1L):
Add deionized water and be settled to 1L, before using, add the mercaptoethanol of final concentration of 0.2% (2ml).
(2) it is cooled to room temperature, adds equal-volume chloroform/isoamyl alcohol (24: 1), mix gently, become bottle green to subnatant.
(3) the centrifugal 10min of 4200rpm, moves on to upper water new 15mL centrifuge tube mutually, adds the dehydrated alcohol of 2 times of volume pre-coolings, mix static 5min. Place 30min in-20 DEG C and precipitate DNA.
(4) the centrifugal 10min of 4200rpm, discards supernatant, adds 1mL75% washing with alcohol and precipitates 1 time, is inverted centrifuge tube dry DNA, adds 200 �� LTE dissolving DNAs.
(5) genomic DNA is detected with the agarose gel of 0.8%.
(6) the genomic DNA individual Parent obtained and F1 generation, F2 generation is stored in-20 DEG C standby.
Embodiment 3: the preparation of molecular marker
(SeqIDNo.2 and SeqIDNo.3), for template, is carried out pcr amplification with molecular marker amplimer by the male parent, F1 generation or the genomic DNA in F2 generation that extract in embodiment 2.
PCR reaction system is as follows:
PCR response procedures is as follows:
94 DEG C of denaturations 5 minutes; 94 DEG C of degeneration 30 seconds, anneal 30 seconds for 60 DEG C, and 72 DEG C extend 40 seconds, run 35 circulations; Last 72 DEG C extend 3 minutes. Pcr amplification product can 4 DEG C of preservations.
Molecular marker is obtained, it is preferable that after amplification, amplified production is purified operation through above-mentioned amplification procedure. Checking order after purification, result is such as shown in SeqIDNo.1.
To those skilled in the art, it is possible to understand that, it is also possible to obtain this molecular marker by the method for DNA chemosynthesis.
Embodiment 4:SV molecular markers development
Male parent: denovo checks order, 60XcontigN50:22K, scaffoldN50:320K; Totalsize:400Mb; Maternal: resurvey sequence 10X.
According to Parent sequencing data, utilize SOAP software (the such as SOAP2.20 of Hua Da independent development, can download from http://soap.genomics.org.cn/, other sequence alignment program can also be used) sequence difference that compares between Parent, it is then based on the sequence of difference, expands the primer of diversity sequence by primerpremier software design; Based on different diversity sequences, devise 1105 pairs of primers altogether. Table 1 below has illustrated part primer sequence (SeqIDNo.2-SeqIDNo.41) therein
Table 11105 is to the part primer in random primer
Respectively with the genomic DNA of the Parent extracted and F1 generation for template, carry out pcr amplification with 1105 pairs of primers of design.
PCR reaction system (25 �� L):
PCR response procedures: 94 DEG C of denaturation 5min; Subsequently into 35 circulations: 94 DEG C of degeneration 30s, 60 DEG C of annealing 30s, 72 DEG C extend 40s; After loop ends, 72 DEG C extend 3min; 4 DEG C of preservations.
PCR primer electrophoresis detection: agarose gel 120v electrophoresis 25min, the EB dyeing 10min of 1.2%, according to glue record.
The effectiveness of primer and polymorphism: refer to whether there is amplified production at this effectiveness, polymorphism refers to that between Parent, the clip size of amplified production is variant.
The screening of primer is carried out: Parent and F1 all have amplified production according to following screening criteria, and Parent amplified production all only has a distinct banding pattern and size variant, F1 shows as the heterozygosis banding pattern of Parent banding pattern, namely has male parent and two bands of 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 gene mapping
(1) genetic map construction
With 616 couple of exploitation, there is the molecular marker of polymorphism and 480 individualities of F2 colony are carried out PCR detection, 480 individual genomic DNAs of the template used F2 colony for preparing.
PCR primer is carried out agarose gel electrophoresis, obtains the result of the individual amplification of molecular marker primer pair 480.
Whole electrophoresis result are carried out data statistic analysis, concrete grammar is as follows: by F2 colony individual plant amplified band be male parent type be designated as a, amplified band be maternal type be designated as b, what amplified band contained male parent type and maternal type simultaneously is designated as h, band Fuzzy or disappearance be designated as-, be equivalent to shortage of data, finally give the genotype data of 480 individual 616 pair primer amplifications of F2 colony. Such as, 480 the individual data obtained with pair of primers are a, b, h ,-, b ... totally 480 data, data primer obtained with second are b, a, h, a ,-... totally 480 data, totally 616 pairs of primers are added up respectively, and gained is 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 maps drafting, obtain genetic linkage map. The position of 616 pairs of primers and the genetic distance with millet Heading date gene is can determine that from the genetic linkage map that this obtains.
(2) gene mapping
According to 480 individual phenotypes at heading stage, similar to male parent type character is designated as a (heading stage is late period), and similar to maternal type character is designated as b (heading stage is early stage), and character occupy and is designated as h between male parent and female parent. Obtain 480 individual phenotypic datas, 480 individual phenotypic datas are compared with 480 the individual genotype datas obtained before, similar Gao Ze represents this labelling and character close linkage at heading stage, and is positioned on genetic linkage maps by Heading date gene.
Embodiment 6: with the checking of the closely linked molecular marker of millet Heading date gene
1. on the basis of the genetic linkage maps prepared in embodiment 5, according to the genetic linkage distance with millet Heading date gene, the position being 3cM in the hereditary close linkage distance with millet Heading date gene determines molecular marker primer (SeqIDNo.2 and SeqIDNo.3), and find the male parent sequence location of correspondence, sequence between upstream and downstream primer is molecular marker, and its nucleotide sequence is such as shown in SeqIDNo.1.
SeqIDNo.2:5 '-AGCCAGCTGGAGAAGAGAAT-3 ';
SeqIDNo.3:5 '-CCCAAGTCCAACTGAAGGC-3 '.
2. additionally, in embodiment 5 in the electrophoresis of 480 individual pcr amplification products in F2 generation, amplification for molecular marker primer (SeqIDNo.2 and SeqIDNo.3) is: about 360 strains are the band that the amplified production of the plant in late period all has 557bp size heading stage, and about 120 strains are the band (part amplification is as shown in Figure 1) that the pcr amplification product of the plant of early stage does not all have 557bp heading stage. And prove that through order-checking the sequence of the fragment of this 557bp is identical with SeqIDNo.1.
Visible, the molecular marker (SeqIDNo.1) of the present invention is molecular marker closely linked with millet Heading date gene.
Embodiment 7: molecular marker clone
The fragment expanding the 557bp of acquisition in embodiment 6 is cloned in pMD18-T carrier, it is thus achieved that recombinant vector. This recombinant vector is transformed in e. coli jm109, chooses monoclonal, cultivate and obtain reconstitution cell. Plasmid is extracted from reconstitution cell, described plasmid and recombinant vector, adopting M13 universal primer (sequence information is with reference to TaKaRa goods catalogue) that cloned sequence is checked order, result shows, contains the molecular marker (SeqIDNo.1) of the present invention in recombinant vector. The steps such as above-mentioned clone, conversion, cultivation, plasmid extraction are with reference to " the Molecular Cloning: A Laboratory guide third edition ", and yellow training hall etc. is translated, and Science Press's in JIUYUE, 2002 is published.
Above content is in conjunction with specific embodiment further description made for the present invention, it is impossible to assert that specific embodiment of the invention is confined to these explanations. For general technical staff of the technical field of the invention, without departing from the inventive concept of the premise, it is also possible to make some simple deduction or replace, protection scope of the present invention all should be considered as belonging to.