CN111848763A - Application of rice protein OsSWC6 in regulation and control of rice plant type - Google Patents
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Abstract
The invention relates to application of rice protein OsSWC6 in regulation and control of rice plant types. The invention also relates to a method for regulating the plant type of rice, which comprises the step of deleting the function of the OsSWC6 protein. The OsSWC6 protein functional deletion can reduce the plant height of rice and reduce tillering of rice.
Description
Technical Field
The invention relates to the field of genetic engineering, in particular to a rice plant height and tillering related protein OsSWC6, a coding gene thereof and application thereof.
Background
Rice (Oryza sativa L.) is a staple food that provides food for half of the world's population, and approximately more than 50% of the human main source of nutrition is rice[1]. 95% of the world's rice is produced and consumed in asia, where the dietary spectrumThe upper part of the body takes up 40-80% of the calories[2]. Since 1960, the rapid growth of the population and the drastic reduction of the cultivation area have made it increasingly difficult to meet the food demand, resulting in a global food crisis and thus also opening the green revolution of crops.
In modern agriculture, plant height is an important trait determining grain yield [3]. The green revolution of the rice has positive influence on the yield potential of the rice, and the breeding of dwarf varieties is taken as a representative[4]. The rice semi-dwarf gene sd-1 plays an important role in modern rice breeding, and semi-dwarf plants can effectively prevent lodging and increase the utilization rate of nitrogen fertilizer[5,6]。
Tillering is also an important agronomic character affecting rice yield, and tillering number is a premise for determining spike number and is an important basis for forming yield. Proper amount of effective tillering is more beneficial to high yield of rice. Therefore, the gene research for controlling the plant height and tillering of the rice is beneficial to the improvement of rice varieties.
Disclosure of Invention
The invention provides a gene related to rice tillering and plant height, which is named as OsSwc6, is derived from rice (Oryzasativvar), encodes OsSWC6 protein, and has an amino acid sequence of SEQ ID No: 2, the nucleotide coding sequence is SEQ ID No: 1. the functional deletion of the protein expressed by the gene can reduce the plant height of rice and the tillering of the rice.
In one aspect, the invention provides application of rice protein in regulating rice plant type, wherein the protein is OsSWC6 protein, and the amino acid sequence of the protein is shown as SEQ ID No: 2, respectively.
In one embodiment, wherein the variety of rice is, for example, Nipponbare or 9311, preferably Nipponbare.
In one embodiment, the nucleotide coding sequence of the OsSWC6 protein is as set forth in SEQ ID No: 1 is shown.
In one embodiment, wherein the rice plant type is plant height and/or tillering.
In one embodiment, wherein the modulating the plant type of rice is reducing the plant height of rice and/or reducing the number of tillers of rice.
In another aspect, the present invention provides a method of modulating plant type in rice, comprising the step of functionally deleting an OsSWC6 protein, wherein the amino acid sequence of the OsSWC6 protein is SEQ ID No: 2.
In one embodiment, wherein the variety of rice is, for example, Nipponbare or 9311, preferably Nipponbare.
In one embodiment, wherein the rice plant type is plant height and/or tillering.
In one embodiment, wherein the modulating the plant type of rice is reducing the plant height of rice and/or reducing the number of tillers of rice.
In one embodiment, the step in which the function of the OsSWC6 protein is deleted is achieved by gene knockout, gene knockdown, frameshift mutation, or the like.
In one embodiment, wherein the knockout and/or frameshift mutation uses a CRISPR/Cas9 vector. In one embodiment, the method further comprises selecting NGG within exons 1 to 3 within the genomic nucleotide sequence of the OsSwc6 gene. Because of the NGG selected at the front position of the genome, the CRISPR/Cas9 gene editing technology can be used for carrying out frame shift mutation on the target gene at the front position, so that the function of the target protein is lost.
In one embodiment, wherein the CRISPR/Cas9 vector comprises a target sequence for gene knock-out, the nucleotide sequence of the target sequence being set forth in SEQ ID NO: 5 or SEQ ID NO: and 6.
In another aspect, the invention provides a CRISPR/Cas9 vector comprising a target sequence as described in any preceding claim.
In another aspect, the invention provides a mutant gene of OsSwc6, which has the nucleotide sequence:
(a) SEQ ID No: 1, inserting a nucleotide sequence of T between the 165 th and 166 th positions (the obtained sequence is shown as SEQ ID No. 15); or
(b) SEQ ID No: 1 between positions 316 and 317 (the resulting sequence is shown as SEQ ID No: 16).
For SEQ ID No: 15, SEQ ID No: 1, in SEQ ID No: 1 at nucleotide positions-177-179 may be transcribed as a stop codon. For SEQ ID No: 16, SEQ ID No: 1, the zinc finger domain after the mutation site is destroyed as a result of undergoing the frameshift mutation described above.
After transcription of the wrong RNA, the cell self-clearing mode is started, and the RNA with the transcription error is cleared, so that the OsSWC6 protein is not expressed and/or the OsSWC6 protein with the transcription error is cleared.
In one embodiment, the gene is mutated as described above for use in reducing the plant height of rice and/or reducing tillering of rice.
In one embodiment, wherein the variety of rice is, for example, Nipponbare or 9311, preferably Nipponbare.
Drawings
FIG. 1 shows a map of pHUN411-OsSwc6 vector.
FIG. 2 shows OsSwc6 genotype in Osswc6 mutants.
FIGS. 3A and 3B show the phenotype observation (FIG. 3A) and plant height and tillering (FIG. 3B) statistics of Osswc6 mutant plants.
Detailed Description
In order that the objects, technical solutions and advantages of the present invention will become more apparent, the present invention will be further described in detail with reference to the accompanying drawings in conjunction with the following specific embodiments.
The research technology of the invention comprises the following steps:
(1) cloning and functional identification of OsSwc6 gene:
1) according to the technical principle of CRISPR/Cas9 gene editing and the OsSwc6 gene cDNA sequence, the DNA sequence is analyzed through a database and a tool website (http: // skl.scau.edu.cn /), obtaining a specific gRNA target sequence of the OsSwc6 gene, cloning the target sequence into a CRISPR/Cas9 gene editing vector pHUC411 (purchased from agricultural institute of Anhui province), and obtaining the pHUC411-OsSwc6 gene editing vector (figure 1).
2) Genotyping of OsSwc 6:
And carrying out phenotype observation on the obtained transgenic progeny T1 generation plants in the whole growth period, carrying out specific primer amplification sequencing on genome regions near gRNA target sequences of all T1 generation plants, and identifying the target sequences and the mutation conditions near the target sequences. Through the analysis of genotype-to-phenotype, the OsSwc6 mutant line plants are obtained.
In conclusion, the OsSwc6 gene in the rice genome is knocked out by using the CRISPR/Cas9 gene editing technology, and the phenotype of plant height reduction and tiller reduction is obtained through genotype identification, so that a foundation is laid for improving the rice plant morphology and increasing the rice yield potential.
Examples
The experimental procedures mentioned in the following examples are conventional procedures known in the art unless otherwise specified.
Example 1: cloning of OsSwc6 Gene
Reverse transcription
Trizol method for extracting RNA from Nipponbare rice (purchased from Nongjic, Anhui);
approximately 8ug of the above RNA was taken in a 1.5ml EP tube and treated with DNase I37 ℃ for 30min as follows to remove DNA:
add 170ul of EDPC water to the above EP tube and add an equal volume of phenol-chloroform, shake well and mix. Centrifuging at 12000rpm at 4 deg.C for 10 min;
transfer the supernatant (about 200ul) to a new 1.5ml EP tube, add 1/10 volumes of 3M NaAC and 2.5 volumes of pre-cooled absolute ethanol and 1.5ul of glycogen, mix by inversion, -stand at-20 ℃ for more than 30 min;
Centrifuging at 12000rpm at 4 deg.C for 15min, discarding the supernatant, washing with 70% ethanol pre-cooled on ice for 2 times, and removing residual ethanol;
air-dry by inversion, add 25ul DEPC water, 2ul olig (dT)18, shake, dissolve, mix well, and centrifuge briefly. Incubating at 65 ℃ for 5min, rapidly cooling on ice to obtain a mixed solution of RNA and oligdT, and adding the components according to the following table by using a reverse transcription kit of Novonoprazan company;
after incubation at 55 ℃ for 1h in a water bath, heat treatment was carried out at 80 ℃ for 5 min.
The cells were dissolved in 160ul EDPC water and stored at-20 ℃.
cDNA of Nipponbare rice was obtained.
PCR
A gene homologous to Arabidopsis thaliana Swc6 (LOC _ Os03g25260.1, the nucleotide sequence of which is shown in SEQ ID NO: 1 and the amino acid sequence of which is shown in SEQ ID NO: 2) was found from a database (http:// rice. plant biology. msu. edu /), named OsSwc6, and corresponding primers (forward primer: ATGGAGGGGGAGGAGGAGGAGAACG (shown in SEQ ID NO: 3) and reverse primer: TCAGGCCACGAATTTCAGGCAGCGG (shown in SEQ ID NO: 4)) were designed to amplify the cDNA of the Nipponbare rice obtained in this example to obtain the cDNA of OsSwc6 gene.
The reaction system of PCR is as follows:
the reaction sequence for PCR was as follows: pre-denaturation at 98 deg.C for 5min, denaturation at 98 deg.C for 15s, annealing at 58 deg.C for 30s, extension at 72 deg.C for 2min, reaction for 35 cycles, post-extension at 72 deg.C for 8min, and holding at 4 deg.C.
After the end of the PCR, the amplified DNA fragment was recovered and purified using DNA recovery kit from merga, then the purified DNA fragment was ligated into vector pGEM-T (Promega), E.coli DH5a competent cells were transformed, positive clones were selected and plasmid sequencing was performed, and OsSwc6 cDNA fragment with a length of 528bp having the sequence shown in SEQ ID NO: 1.
Example 2: construction of the rice pHUC411-OsSwc6 gene editing vector:
according to the technical principle of CRISPR/Cas9 gene editing, NGG is selected in the first and third exons of the nucleotide sequence of the OsSwc6 gene genome through database and tool website analysis, a target sequence 1 GAGGTCGTAGATCTTAACGA (shown as SEQ ID NO: 5, which is in the first exon of the OsSwc6 gene genome) of the specific gRNA of the OsSwc6 gene and a target sequence 2 ATCTTTCATGGACGTGTTACAGG (shown as SEQ ID NO: 6, which is in the third exon of the OsSwc6 gene genome) of the specific gRNA of the OsSwc6 gene are obtained, and the target sequences are cloned into a CRISPR/Cas9 gene editing vector pHUC411 to obtain the pHUC411-OsSwc6 gene editing vector (FIG. 1).
The target joint primers of the gRNA target sequences 1 and 2 are respectively as follows:
Target sequence for gRNA 1:
f: 5-GGCATCGTTAAGATCTACGACCTC-3 (shown as SEQ ID NO: 7),
r: 5-AAACGAGGTCGTAGATCTTAACGA-3 (shown as SEQ ID NO: 8)
Target sequence for gRNA 2:
f: 5-GGCAATCTTTCATGGACGTGTTACAGG-3 (shown as SEQ ID NO: 9)
R: 5-AAACCCTGTAACACGTCCATGAAAGAT-3 (shown in SEQ ID NO: 10).
Example 3: breeding an Osswc6 mutant system and identifying:
entrusted to agricultural institute of Anhui province, a mature rice embryo callus dip-dyeing transformation method mediated by agrobacterium EHA105 (purchased from agricultural institute of Anhui province) is adopted to transfer a gene editing vector pHUC411-OsSwc6 into a mature rice embryo, and the specific transformation method is as follows: (1) induction of rice mature embryo callus: mature Nipponbare seeds (purchased from Nongkouchi, Anhui) are hulled, surface-sterilized with 70-75% alcohol for 1-2min, soaked in 30% NaClO solution for 15min, and repeated 2 times, and then washed with sterilized water for 4-5 times. Then the seeds are placed on an induction culture medium for culture, and the callus is cultured and induced for transformation at the temperature of 26-28 ℃ in a dark place. (2) Co-culturing rice callus and agrobacterium: the EHA105 strain identified in example 3 as containing the gene editing vector pHUC411-OsSwc6 was activated, enriched, resuspended, and adjusted to an OD600 of 0.5 to 0.6. The callus was collected in a 50ml sterile centrifuge tube and the resuspended agrobacterium suspension was poured into it to contaminate the callus. After soaking for 15-30min, the suspension is poured off, and the impregnated callus is placed on sterile filter paper to suck off the excess agrobacterium liquid. Then placing the callus in a culture dish paved with sterile filter paper, and culturing for 2-3 days at 26 ℃ in a dark place. (3) Screening of resistant calli: after the co-cultivation is completed, the callus is transferred to a selection medium containing 50-100mg/ml of G418 antibiotic and resistance selection is carried out at 26-28 ℃. (4) Differentiation of resistant calli: and placing the callus with good growth state in the screening culture medium in a differentiation culture medium, and performing differentiation culture under the conditions of 16-hour light/8-hour dark and the environment temperature of 26-28 ℃ until the callus is differentiated and grows into small seedlings. (5) Rooting of differentiated plantlets: and when the differentiated plantlets are about 2-5cm in month, transferring the plantlets into a rooting culture medium for rooting culture. Transplanting the seedlings with the grown root systems to a greenhouse or a transgenic garden for growth.
Specific primers are used for carrying out PCR amplification sequencing on the target sequences 1 and 2 of gRNA of a Nipponbare transformed plant and a wild Nipponbare plant by using the following specific primers, and the target sequences and the mutation conditions of the adjacent regions are identified. The amplification reaction procedure was as follows: pre-denaturation at 98 ℃ for 5min, denaturation at 98 ℃ for 15s, annealing at 58 ℃ for 15s, extension at 72 ℃ for 30s, reaction for 35 cycles, and post-extension at 72 ℃ for 8 min. The PCR product is separated by 2 percent agarose gel electrophoresis and stained by ethidium bromide, and the cut target band is sent to the general gene of Senhua Dagen for sequencing. The specific primer sequences for PCR were as follows:
for target sequence 1:
1) osswc 6-S1F: 5-GCCTTCTTGGTTATCCATGGATA-3 (shown as SEQ ID NO: 11)
Osswc 6-S1R: 5-CTGCAAGATAAACTGATTCAGCT-3 (shown as SEQ ID NO: 12)
For target sequence 2:
2) osswc 6-S2F: 5-GAGAGTTTAAGTTTCCCCAGAAA-3 (shown as SEQ ID NO: 13)
Osswc 6-S2R: 5-TATCGTTGTGAATGACCTGGCA-3 (shown as SEQ ID NO: 14)
Through sequencing result analysis, two Osswc6 homozygous mutants can be obtained and can be stably inherited. Target sequences 1 and 2 of gRNA correspond to Osswc6 mutant genotypes I and II, respectively, as shown in fig. 2:
Osswc6 mutant genotype I has a T base inserted between 165 and 166 of OsSwc6, and results in the nucleotide sequence shown in SEQ ID No: 1 can code a stop codon (the nucleotide sequence of the Osswc6 mutant genotype I is shown as SEQ ID NO: 15 correspondingly);
the Osswc6 mutant genotype II is characterized in that a T base is inserted between 316 th and 317 th positions of Osswc6, and the zinc finger domain behind the mutation site is damaged (the nucleotide sequence of the Osswc6 mutant genotype II is shown as SEQ ID NO: 16 correspondingly).
After transcription of the wrong RNA, the cell self-clearing mode is started, and the RNA with the transcription error is cleared, so that the OsSWC6 protein is not expressed and/or the OsSWC6 protein with the transcription error is cleared.
The above sequencing results were repeated 3 times, all giving the same results.
Example 4: phenotype identification of rice Osswc6 mutant system plant
The rice Osswc6 mutant I and II plants and wild type rice Nipponbare plants are planted in a field, and the phenotypic difference between the rice Osswc6 mutant system plant and the wild type rice Nipponbare (WT for short) plant in the whole growth period is observed. Observed results (rice heading period) as shown in fig. 3A and 3B, when compared with WT plants, both the Osswc6 mutant I and II line plants exhibited dwarfing and reduced tillering phenotypes, with the Osswc6 mutant I line plant dwarfing by about 46% and reduced tillering by about 54% compared with the wild-type rice japonica plant, and the Osswc6 mutant II line plant dwarfing by about 50% and reduced tillering by about 54% compared with the wild-type rice japonica plant. Thus proving that the OsSwc6 gene participates in controlling the plant height and tillering of rice.
The above-mentioned embodiments are intended to illustrate the objects, technical solutions and advantages of the present invention in further detail, and it should be understood that the above-mentioned embodiments are only exemplary embodiments of the present invention and are not intended to limit the present invention, and any modifications, equivalents, improvements and the like made within the spirit and principle of the present invention should be included in the protection scope of the present invention.
Reference documents:
1.White P T.Rice:The essential harvest[J].Natl.Geogr.,1994,185:48-79.
2.Paramita Bhattacharjee,Rekha S Singhal,Pushpa R Kulkarni.Basmatirice:a review[J].International journal of food science&technology,2002,37(1):1-12.
3.Tomoaki Sakamoto,Makoto Matsuoka.Identifying and exploiting grainyield genes in rice[J].Current opinion in plant biology,2008,11(2):209-214.
4.Thomas R Hargrove,VictoriaL Cabanilla.The impact of semidwarfvarieties on Asian rice-breeding programs[J].BioScience,1979,29(12):731-735.
5.Peter R Jennings.Plant Type as a Rice Breeding Objective 1[J].CropScience, 1964,4(1):13-15.
6.JJ Walcott,DR Laing.Some physiological aspects of growth and yieldin wheat crops:a comparison of a semidwarf and a standard height cultivar[J].Australian Journal of Experimental Agriculture,1976,16(81):578-587.
Claims (14)
1. the application of rice protein in regulating rice plant type is OsSWC6 protein, and the amino acid sequence of the protein is shown as SEQID No: 2, wherein the rice variety is, for example, nipponlily or 9311, preferably nipponlily.
2. The use of claim 1, wherein the nucleotide coding sequence of the OsSWC6 protein is as set forth in SEQ ID No: 1 is shown.
3. The use according to claim 1 or 2, wherein the rice plant type is plant height and/or tillering.
4. The use according to any one of claims 1 to 3, wherein the regulation of the plant type of rice is reduction of the plant height of rice and/or reduction of the number of tillers of rice.
5. A method for regulating rice plant type, comprising the step of deleting the function of OsSWC6 protein, wherein the amino acid sequence of the OsSWC6 protein is SEQ ID No: 2, wherein the variety of the rice is, for example, nipponlily or 9311, preferably nipponlily.
6. The method of claim 5, wherein the rice plant type is plant height and/or tillering.
7. The method of claim 5 or 6, wherein the modulating the plant type of rice is reducing the plant height of rice and/or reducing the number of tillers of rice.
8. The method of any one of claims 5-7, wherein the step of functionally deleting OsSWC6 protein is accomplished by a method of gene knockout, gene knockdown, or frameshift mutation.
9. The method of claim 8, wherein the knockout and/or frameshift mutation uses a CRISPR/Cas9 vector.
10. The method of claim 9, further comprising selecting NGG within exons 1-3 within the genomic nucleotide sequence of the OsSwc6 gene.
11. The method of claim 9 or 10, wherein the CRISPR/Cas9 vector comprises a target sequence for gene knock-out, the nucleotide sequence of the target sequence being as set forth in SEQ ID NO: 5 or SEQ ID NO: and 6.
12. Comprises the amino acid sequence shown as SEQ ID NO: 5 or SEQ ID NO: 6 and a CRISPR/Cas9 vector for the target sequence shown in figure 6.
A mutant gene of OsSwc6, having the nucleotide sequence:
(a) SEQ ID No: 1 between positions 165 and 166 of the nucleotide sequence of a T; or
(b) SEQ ID No: 1 between positions 316 and 317 of which a nucleotide sequence of T is inserted.
14. The mutant gene according to claim 13, which is used for reducing the plant height and/or tillering of rice, wherein the variety of rice is, for example, nipponica or 9311, preferably nipponica.
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Citations (2)
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JP2015171326A (en) * | 2014-03-11 | 2015-10-01 | 国立大学法人愛媛大学 | Gene that provides plants with disease resistance, drought resistance, salinity tolerance, increased photosynthesis efficiency and increased number of tillers |
CN108103092A (en) * | 2018-01-05 | 2018-06-01 | 中国农业科学院作物科学研究所 | System and its application for downgrading rice are obtained using CRISPR-Cas systems modification OsHPH genes |
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JP2015171326A (en) * | 2014-03-11 | 2015-10-01 | 国立大学法人愛媛大学 | Gene that provides plants with disease resistance, drought resistance, salinity tolerance, increased photosynthesis efficiency and increased number of tillers |
CN108103092A (en) * | 2018-01-05 | 2018-06-01 | 中国农业科学院作物科学研究所 | System and its application for downgrading rice are obtained using CRISPR-Cas systems modification OsHPH genes |
Non-Patent Citations (4)
Title |
---|
ANA LA´ZARO,ET AL.: "Mutations in the Arabidopsis SWC6 gene, encoding a component of the SWR1 chromatin remodelling complex, accelerate flowering time and alter leaf and flower development", 《JOURNAL OF EXPERIMENTAL BOTANY》 * |
REFSEQ.: "Accession No:XM_015773567.2,PREDICTED: Oryza sativa Japonica Group SWR1 complex subunit 6 (LOC4332920), mRNA", 《GENBANK DATABASE》 * |
崔志波: "水稻染色质重塑复合体SWR1的功能研究", 《中国博士学位论文全文数据库 农业科技辑》 * |
许永汉等: "拟南芥SWR1复合体亚单位编码基因ARP6和SWC6的水稻同源基因功能研究", 《浙江农业学报》 * |
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