Differentiate molecule marking method and the primer of low phytic acid mutator gene IPK1-a in the soybean kernel
Technical field
The invention belongs to the agricultural biotechnology engineering technical field, be used to contain the evaluation and the seed selection of the low phytic acid soybean varieties of IPK1-a mutator gene, relate in particular to a kind of molecule marking method and primer of differentiating soybean low phytic acid mutator gene IPK1-a.
Background technology
Phytic acid accounts for the 50%-80% of total phosphorus in plant; Phytic acid accounts for more than 75% of the full phosphorus amount of seed usually in the Soybean and Other Crops seed.Common and the K of phytic acid in the seed
+, Ca
2+, Mg
2+, Zn
2+Deng metal ion-chelant, build up to spherule is deposited in the cotyledon of dicotyledons seed with protein binding, therefore, phytate is the storage of metallic cation and phosphoric.Although phytic acid has many important physical functions in farm crop such as soybean; But because the activity of Sumizyme PHY is extremely low in the digestive tube of human and non-ruminant animal; Almost nil; Therefore phytic acid can not be by its digestibility and utilization, and this has significantly reduced phytic acid institute bonded phosphorus, metallic element and proteic biological effectiveness; It is reported; There is the nearly half the trace element deficiency that the population existence form is different, degree is different in the whole world; Pregnant woman and preschool children in developing country 90% suffers from anemia or the relative disease that sideropenia causes especially, and phytic acid is one of essential substance that causes trace element deficiency.Phytate in the seed can not be by the non-ruminant animal utilization, and the follower defecate is in environment, and the phytate in the animal excrement is difficult to utilized by plant again, causes the waste and the pollution of phosphoric; In order to satisfy the demand of the plain nutrition of animal phosphorus, often adopt the method for adding inorganic phosphorus or Sumizyme PHY in the fodder industry.Add inorganic phosphorus in the feed and not only increased the cost of feed, and can not solve the phosphorus pollution problem that the animal drainage causes, also caused the excessive utilization of phosphorus prime element; Add the drainage that Sumizyme PHY can reduce the phosphorus in the ight soil, but in the feed granulating process inactivation easily.Therefore reducing the content of phytic acid in the crop seed, is economy, effective means the most, and it can effectively improve metallic element, albumen and the phosphorus biological effectiveness in humans and animals nutrition; Reduce the eutrophication of the water surrounding of bringing thus; Reduce the fodder prodn cost; Practice thrift phosphate rock resource.
Genetic research in the past shows that the low phytic acid of low phytic acid mutant generally is to be controlled by single recessive gene.Different mutator genes is equipotential not only, and the reduction degree of phytic acid content also is not quite similar.Further research shows, changes the function and the activity of the various proteolytic enzyme of control phytic acid metabolic pathway of synthesizing, can significantly change the content of phytate phosphorus and non-phytate phosphorus in the seed, like MIPS, IPK1, MIK and the MRP etc. in Different Crop, to clone.1,3,4,5, the anabolic final step reaction of 6 inositols-2 phosphokinase (IPK1) albumen catalysis phytic acid, inositol five phosphoric acid are through the reaction of the synthetic phytinic acid of phosphorylation.Grow the reduction of IPK1 kinase activity in the plant or the change of function and will interrupt the synthetic of phytic acid, the content of phytate phosphorus and non-phytate phosphorus in the change plant seed.The equipotential sudden change of IPK1 all has report in corn and Arabidopis thaliana, its sudden change has directly caused the decline significantly of phytic acid content in these plant seeds.At document (Fengjie Yuan etc.; Theor Appl Genet (2007) 115:945 – 957) disclosed soybean low phytic acid mutant material Gm-lpa-ZC-2 in; Through further Fine Mapping and metabolism group research show; It is that equipotential sudden change institute by IPK1 causes (Yuan Fengjie etc., Zhejiang agricultural journal, 2011 (having employed article) that phytic acid content in this two mutants reduces; Frank T etc., J Agric Food Chem, 2009), its cDNA complete sequence is shown in SEQIDNO:1.Along with development of molecular biology; Molecule marker based on nucleotide diversity has produced important effect in crop genetic improvement; Therefore; If can obtain and the closely linked molecule marker of goal gene, can not only effectively identify the low phytic acid crop germ plasm resource that contains goal gene, also can quicken the seed selection of low phytic acid variety of crops simultaneously.
Summary of the invention
In order whether to contain the IPK1-a gene in the identification of Soybean material effectively quickly; One object of the present invention provides a kind of molecule marking method of differentiating low phytic acid mutator gene IPK1-a in the soybean kernel; This method is through the comparison to marker site; Can have or not the IPK1-a gene in the identification of Soybean plant, and then predict the content of phytic acid in the soybean kernel, accelerate the selection progress of low phytic acid soybean.Another object of the present invention is to differentiate the molecule marking method of low phytic acid mutator gene IPK1-a in the soybean kernel.
In order to realize first above-mentioned purpose, the technical scheme below the present invention has adopted:
Differentiate the molecule marking method of low phytic acid mutator gene IPK1-a in the soybean kernel, this method comprises the steps:
(1) the young tender seed in growing after soybean varieties was bloomed 20 days obtains total RNA;
(2) total RNA reverse transcription obtains total cDNA;
(3) with primer total cDNA is carried out pcr amplification, the forward primer sequence of pcr amplification is: CTTGGAGGACTGGGAGGT, and the reverse primer sequence is: ATACCCCTTTGCATTCAGCT;
(4) the PCR product separates on 1.2% agarose electrophoresis glue, if the PCR product has the electrophoretic band of 303bp, then for not containing the soybean varieties of IPK1-a gene; If the electrophoretic band of 192bp is arranged, then for containing IPK1-a gene pure body soybean; If two electrophoretic bands are arranged, then be the soybean varieties that contains IPK1-a genetic heterozygosis body.
As preferably, E.Z.N.A. is adopted in the extraction of above-mentioned total RNA
TMPlant RNA extracts test kit.The concrete grammar that above-mentioned total RNA extracts is: total RNA sample 10 μ l of extraction, 10 * buffer (contains Mg
2+) 2 μ l, DNase1 enzyme 2.5 μ l, DEPC water 5.5 μ l, total reaction system 20 μ l; At first 37 ℃ of insulations 30 minutes of reaction conditions, next 65 ℃ of enzyme-deactivatings are 10 minutes, add the EDTA termination reaction of 2 μ l at last; The RNA sample of removing DNA utilizes spectrophotometric determination concentration, and all samples concentration adjustment is consistent the most at last, is 200ng/ μ l.
As preferably, ReverTra Ace qPCR RT Kit FSQ101 test kit is adopted in the reverse transcription of above-mentioned RNA.The concrete grammar of the reverse transcription of above-mentioned RNA is: the RNA sample was put in cooled on ice immediately after under 65 ℃ of conditions 5 minutes; 20 μ l reaction systems are: 5 * RT Buffer, 4 μ l, enzyme mixed solution 1 μ l, random primer 1 μ l, RNA sample 10 μ l, DEPC water 4 μ l; Reaction conditions is: carry out 15 minutes reverse transcription reaction under 37 ℃ of conditions, under 98 ℃ of conditions, carry out 5 minutes enzyme deactivation reaction.
As preferably, the concrete grammar that above-mentioned total cDNA carries out pcr amplification is: reaction system is 20 μ l, and wherein 10 * buffer (contains Mg
2+) 2 μ l, dNTP mixed solution 0.4 μ l, forward and reverse primer is respectively 0.6 μ l, cDNA sample 1.5 μ l, Taqplus enzyme 0.2 μ l, ddH
2O14.7 μ l; The PCR program is: 94 ℃ of sex change 5 minutes, get into 35 circulations, and each circulation comprises 94 ℃ of sex change 1 minute, 50 ℃ of annealing 1 minute, 72 ℃ were extended 1 minute, and loop ends was extended 4 ℃ of preservations 10 minutes for 72 ℃.
In order to realize second above-mentioned purpose, the technical scheme below the present invention has adopted:
The molecule marking method of low phytic acid mutator gene IPK1-a is used primer in the discriminating soybean kernel, and its forward primer sequence is: CTTGGAGGACTGGGAGGT, the reverse primer sequence is: ATACCCCTTTGCATTCAGCT.
The present invention utilize molecular biological method obtain one with the directly related PCR mark of soybean low phytic acid mutator gene IPK1-a; The advantage of this mark is following: 1, to effective utilization of low phytic acid soybean, at first must be based upon on the basis of clear and definite gene source.Because the low phytic acid mutant gene of having found at present is more; And difference in appearance is very little between the two mutants; Be difficult to effectively distinguish through the phenotype observation; The PCR mark that utilizes the present invention to obtain can screen the low phytic acid resource of soybean, accurately identifies low phytic acid mutant and whether contains the IPK1-a gene.2, the PCR mark that the present invention obtained is according to the inner base mutation that produces of IPK1 gene, does not therefore have the exchange of heredity, does not also need the further checking of phenotype.3, the observation of low phytic acid mutation proterties just can be carried out after must waiting for seed results, and utilizes the molecule marker directly related with IPK1-a and detect, and can judge its low phytic acid genotype in seedling stage, and hanging down the phytic acid soybean varieties for effective seed selection provides foundation.4, carry out the molecular marker assisted selection breeding with the inventive method, improved the efficiency of selection of soybean varieties.
Description of drawings
Fig. 1 is IPK1 Gene Partial cDNA Sequence comparison figure in suddenly change germplasm Gm-lpa-ZC-2 and Zhejiang spring No. 3, the Willams soybean varieties.The cDNA sequence deletion 110bp of equipotential sudden change IPK1-a gene in the Gm-lpa-ZC-2 germplasm wherein.
Fig. 2 is the cDNA sequence amplification result of PCR molecule marker to IPK1 gene in Zhejiang spring No. 3 and the Gm-lpa-ZC-2 germplasm.
Fig. 3 is a molecule marker to the selection effect of No. 4 F2 of the bright beans in Gm-lpa-ZC-2 * Zhejiang for individual plant, and the 1-5 swimming lane is the low phytic acid individual plant of IPK1 homozygous mutant type; The 7-11 swimming lane is not for containing the non-low phytic acid individual plant of IPK1 mutator gene.
Embodiment
Heredity is analyzed, molecule is located and the metabolism group analysis revealed, and soybean low phytic acid mutant Gm-lpa-ZC-2 low phytic acid is by IPK1 equipotential mutator gene IPK1-a control (Fengjie Yuan etc., Theor Appl Genet, 2007; Frank T etc., J Agric Food Chem, 2009).Design primer according to soybean whole genome sequence information, and the PCR product is directly checked order, obtain the IPK1-a whole genome sequence of about 2600bp among the low phytic acid mutant soybean low phytic acid mutant material Gm-lpa-ZC-2.As shown in Figure 1; The difference of IPK1 gene full DNA sequence between Clustal X software analysis mutant material and Zhejiang spring No. 3 and the Willams; A G/A sudden change has taken place in the shearing sequence of the 5th exon and intron in the dna sequence dna of finding mutant material IPK1 sequence; This sudden change makes in the eukaryote ubiquitous shearing conserved sequence GT/AC sequence change into AT/AC, and causing the RNA of this gene in transcription to shear enzyme can't discern, and finally causes shearing unusual.Clustal X software is mutant plant and Zhejiang spring No. 3 cDNA sequence relatively, result's discovery, the cDNA sequence deletion of mutant plant the complete sequence of 110bp of the 5th exon.The present invention has designed to increase and has comprised the cDNA aligning primer of the 5th Exon deletion sequence.Its forward primer sequence of this series is: CTTGGAGGACTGGGAGGT, the reverse primer sequence is: ATACCCCTTTGCATTCAGCT.
The present invention adopts above-mentioned cDNA aligning primer that a kind of molecule marking method of differentiating low phytic acid mutator gene IPK1-a in the soybean kernel is provided, and this method comprises the steps.
(1) extraction of geneome RNA
Total RNA comes from the young tender seed in growing after blooming 20 days.E.Z.N.A. is used in the extraction of total DNA
TMPlant RNA extraction test kit (Omega Bio-tek, Inc.USA), shown in the working method by specification; The RNA that extracts handles with DNase1, and concrete grammar is: total RNA sample 10 μ l of extraction, 10 * buffer (contains Mg
2+) 2 μ l, DNase1 enzyme 2.5 μ l, DEPC water 5.5 μ l, total reaction system 20 μ l; At first 37 ℃ of insulations 30 minutes of reaction conditions, next 65 ℃ of enzyme-deactivatings are 10 minutes, add the EDTA termination reaction of 2 μ l at last.The RNA sample of removing DNA utilizes spectrophotometric determination concentration, and all samples concentration adjustment is consistent the most at last, is 200ng/ μ l.
(2) acquisition of total cDNA
ReverTra Ace qPCR RT Kit FSQ101 test kit (TOYOBO CO., LTD JAPAN) is used in the reverse transcription of RNA.Be specially: the RNA sample was put in cooled on ice immediately after under 65 ℃ of conditions 5 minutes.20 μ l reaction systems are: 5 * RT Buffer, 4 μ l, enzyme mixed solution 1 μ l, random primer 1 μ l, RNA sample 10 μ l, DEPC water 4 μ l.Reaction conditions is: carry out 15 minutes reverse transcription reaction under 37 ℃ of conditions, under 98 ℃ of conditions, carry out 5 minutes enzyme deactivation reaction.
(3) with said primer the total cDNA of soybean is carried out pcr amplification
Reaction system is 20 μ l, and wherein 10 * buffer (contains Mg
2+) 2 μ l, dNTP mixed solution 0.4 μ l, forward and reverse primer is respectively 0.6 μ l, cDNA sample 1.5 μ l, Taqplus enzyme 0.2 μ l, ddH
2O14.7 μ l.The PCR program is: 94 ℃ of sex change 5 minutes, get into 35 circulations, and each circulation comprises 94 ℃ of sex change 1 minute, 50 ℃ of annealing 1 minute, 72 ℃ were extended 1 minute, and loop ends was extended 4 ℃ of preservations 10 minutes for 72 ℃.The PCR product separates on 1.2% agarose electrophoresis glue.As shown in Figure 2, PCR product electrophoresis detection shows that the soybean material of IPK1-a gene pure body is the filial generation of Gm-lpa-ZC-2, Zhejiang 97031 and above-mentioned materials thereof, has the electrophoretic band of 192bp; Zhejiang spring No. 3 (authorization in 1998) and the bright beans in Zhejiang No. 4 (authorizing in 2007) are not contained the IPK1-a gene, the electrophoretic band that to have a size be 303bp.
(4) molecule marker is the selection effect of the soybean filial generation of IPK1-a to genotype
As shown in Figure 3, be for No. 4 that the parent is hybridized with IPK1-a gene pure type material Gm-lpa-ZC-2 and the bright beans in soybean varieties Zhejiang that do not contain IPK1-a.Hybrid soybean F1 receives for mixing; F2 utilizes the PCR mark to carry out the genotypic detection of IPK1-a for individual plant seedling stage, and the F2 material is divided into three types: have 192bp electrophoretic band material, 303bp electrophoretic band material and material that the two has concurrently; Gather in the crops the F2:3 seed on the F2 plant, utilize the phytic acid content of each individual plant of HPLC technology for detection, find that all have 192bp electrophoretic band material and are low phytic acid, and 303bp electrophoretic band material is that phytic acid content is normal with the two material that has concurrently.Continue the F2:3 seed that germplasm has 192bp and 303bp electrophoretic band concurrently; In the offspring, continue to select with molecule marker; Verify with chemical analysis; Discovery has 192bp electrophoretic band material and is low phytic acid, and 303bp electrophoretic band material is that phytic acid content is normal with the two material that has concurrently.Because low phytic acid proterties is recessive mutation, the material that therefore has 192bp and 303bp electrophoretic band concurrently is the heterozygous genes type of IPK1-a, but phenotype is normal phytic acid content.The mark of developing be 100% to the efficiency of selection of low phytic acid proterties.
Sequence table
< 110>Zhejiang Academy of Agricultural Science
< 120>molecule marking method and the primer of low phytic acid mutator gene IPK1-a in the discriminating soybean kernel
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GCCTTCAAGC?CTGTCTCTTC?ATTTCTTCCT?TGATCCATTT?TGATGATTTG?TCTGTAGCAG?60?TTCACTATCT?TCTTATCTAA?TTCATAGTAG?TCTTCCACTT?TACTTAAGCG?CTTTAAATCA?120?AGGTCGATAA?AATACACCTT?ATAATCAAAG?GATTGCTCCG?TTGAGTCCAG?ATATACATTA?180?TCGTACACAG?ATCCAGAATC?CTCCTCATTC?CTTGGTCTAA?AACACAACAT?CAAACTGCAG?240?TCTTTTGCAG?TTGTTGCTAT?CAGGTAGTCC?TTTACAATTC?TCAAACTTTC?ATCCAGTGAA?300?GCTGAATGCA?AAGGGGTATA?TATTTTTGCC?TGTTCTTCAC?TCAATTCTTT?ACATATCATG?360?CACTGTTGAG?GAGTAATGTT?ATAATATAGC?ATGGATGACC?TCCTTCTATG?TCAATATTAT?420?CAAGCTTCTG?CACCTTCAGG?AGCTTATCAA?GGACTCCTGA?TTTTTGCAAA?GCCTCAGTAA?480?CAAGAGTAAA?TAAGTTATTT?GTACATAGAT?CATCATCAGC?TCGAATGATT?GACTTAAGTT?540?CATCTTCAAA?TGCTTTAGCA?ATACCAACAT?CTGTATTTTT?TGCAACACCT?CCCAGTCCTC?600?CAAGTATGAG?AGAGCCATTC?AAAAATACAC?GAAAATTGTT?TTGAGGAGTT?GTAAGGAGAC?660?CTTTAATAGC?TTTCAGAATT?CTTTCCTTGG?ATCCAGAGAA?CAGATCAAGT?GGATTGTACT?720?CACTTAGTTG?CGATATCTTT?ATCTCAACAG?ATAAGCAGAG?GCTAGATCCT?TGACTGCCAT?780?AAGCAAAGAG?AGAATGATCT?GACATGAGAA?GGCCAAAATC?ACAATGTGCA?TCAACCCTGG?840?CAGCTTCAAC?TCGCCACGCA?GGACGTTGAC?CAGAAACATT?CTTCTCAACC?AACTCAAGGA?900?ATTCCCTGGT?CACCAGGACG?TGCATCCCAG?CATCAACAGA?GTTGGAACCA?AGCAAAGGCT?960?TCATAACATG?CTGCACATAT?AGTTGACCAA?CTATTTCCTT?GTCTGAAGAG?GAGATAAGTT?1020?GATGCACATC?TTTCCAGAGA?ACACGTTCAT?GTGGAGTCAA?AGCTATGCTA?TTCCTCACAC?1080?TCACACTCTT?TGACTGCGAT?CCATTCCTTG?GAGCCTTACG?TATGCGGACC?ACTTTCCCAA?1140?TAAAAGAAGG?TGAGGATCCA?GCGTAAGCGA?GCACAAGATT?AACTGCTCCT?TCCCCTCTGT?1200?AAACCCAGTC?1210
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