# Patent

## Title
Protein IPA1 related to plant architecture, its coding genes and uses

## Abstract

The present invention discloses a protein IPA1 related to plant architecture, its coding genes and uses, wherein the protein is 1) or 2) as follows: 1) the protein consisting of the amino acid sequence showed by sequence 1 in the sequence list; 2) the protein derived from the protein of 1) by substitution and/or deletion and/or addition of one or several amino acid residues in the amino acid sequence defined in 1) and relating to plant architecture. IPA1 gene can be used for molecular marker-assisted breeding, cultivating new rice varieties and improving rice yield.

## Background
SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Nov. 6, 2013, is named 205333-0012-00-US-489273_SL.txt and is 32,224 bytes in size.
FIELD OF THE INVENTION
The invention relates to a field of plant gene engineering technology, specifically relates to a protein IPA1 associated with plant architecture, coding genes and uses thereof.
BACKGROUND OF THE INVENTION
The plant architecture of rice includes traits such as tiller number, tillers angle, panicle type and plant height. A good plant architecture is a key factor to improve the yield of rice. A majority of cultivars for an application in production currently are dwarf varieties containing a semi-dwarf gene SD1. The dwarf varieties have many advantages compared with the traditional long-stalk varieties, thus the first “green revolution” was set off and the yield of rice was largely increased. However, a further increase of the yield was limited by the inherent shortcomings of the dwarf varieties, including more unproductive tillers, smaller panicles and higher leaf area index, serious leaf shading phenomenon and decreased canopy photosynthesis and so on. In order to overcome the disadvantage of the limited yield potential of current most cultivars and further meet the people's demand for foodstuff, the breeders of the International Rice Research Institute proposed the concept of new plant type of rice and the main features of the new plant type were fewer tillers, no unproductive tillers, bigger panicles, more grains per panicle, thick and sturdy stems and lodging resistance.
The tiller number of rice is an important agronomic trait in the rice production. The number of productive tillers per unit area decides the number of panicles, which in turn is one of three critical factors to decide the rice yield per unit area. Thus, the reasonable controlling of the occurrence of rice tillering and minimizing the unproductive tillers are of great importance to production.
The grain number per panicle is another important factor in determining the yield of rice. The typical characteristic of most high-yield varieties used currently in production is the significant increase of grain number per panicle. The increase of grain number per panicle is mainly attributed to more primary rachis branch and secondary rachis branch on the panicles and denser grains grown. It is very important to increase the grain number per panicle in breeding high-yield varieties. The 1000-seed weight is the third critical factor to the yield of rice, which is the direct reflection of good or bad dry matter accumulation and grouting in rice grains and is closely associated with the size of the grains.
The lodging resistance ability is always an aspect to which rice breeders have been attaching great importance. It plays a very important role in stabilizing yield and is a limiting factor to further increase the yield, though it does not directly improve the yield of rice. The dwarf varieties enhance the lodging resistance ability through reducing the plant height and thus ensure the stable production of rice and make it possible to increase the yield, compared with the traditional long-stalk varieties. Further enhancing the lodging resistance ability of the plants therefore is critical to further increasing the yield of rice. In the regard, it is always a goal of the breeders to enhance the traits of stem and to breed a variety whose stems are more thick and sturdy and whose lodging resistance ability is stronger.
The basic characteristics of the new plant type proposed by the International Rice Research Institute are few tillers, thick stems and big panicles. The simulation studies suggested that the yield of the variety with new plant type increased by 25% compared with current varieties in the dry season in the tropical regions. It is important to demonstrate the genetic basis and molecular mechanism of tillering, stems and panicles development for obtaining a higher yield variety. Currently, there is no report on genes which may systematically change the plant type of rice overall to produce new plant type characteristics, though many genes associated with the yield were cloned.
SUMMARY OF THE INVENTION
The object of the invention is to provide a protein associated with plant architecture and coding gene thereof.
The name of the protein associated with plant architecture of invention is IPA1, which originates from rice (Oryza saliva L.), as protein shown in the following 1) or 2):
1) a protein consists of amino acid sequence as sequence 1 in the sequence list; and
2) a protein related to plant architecture which derived from amino acid sequence as sequence 1 in the sequence list via substitution and/or missing and/or addition of one or more amino acid residues.
To facilitate the purification of IPA1 in 1), the amino-terminal or carboxyl-terminal of the protein consisting of amino acid sequence as sequence 1 in the sequence list may be added with tags as listed in Table 1.







TABLE 1 







Sequence of Tags









Tags
Residues
Sequences





Poly-Arg
 5-6 (typically 5)
RRRRR



(SEQ ID NO: 8)
(SEQ ID NO: 8)


 


Poly-His
2-10 (typically 6)
HHHHHH



(SEQ ID NO: 10)
(SEQ ID NO: 11)


 


FLAG
 8
DYKDDDDK




(SEQ ID NO: 12)


 


Strep-tag II
 8
WSHPQFEK




(SEQ ID NO: 13)


 


c-myc
10
EQKLISEEDL




(SEQ ID NO: 14)









IPA1 as described above in 2) may be artificially synthesized; alternatively obtained by expressing its coding gene in organisms. The coding gene of IPA1 as described above in 2) may be achieved through deleting or adding codons for one or more amino acid residues in DNA sequence from 124 to 1377 bp of 5′-end of sequence 2 in the sequence list, and/or through one or more missense mutation of base pair, and/or through adding the tags as listed in Table 1 to 5′-end and/or 3′-end thereof.
The coding gene for the protein associated with plant architecture as described above (denominated as IPA1 gene) is also within the scope of the invention.
The coding gene for the protein associated with plant architecture as described above specifically is one of genes described as following 1)-5):
1) its coding sequence as listed from 124 to 1377 bp of 5′-end of sequence 2 in the sequence list;
2) its nucleotide sequence is sequence 2 in the sequence list;
3) its nucleotide sequence of genetic DNA as listed from 1 to 7229 bp of 5′-end of sequence 3 in the sequence list;
4) a gene which is hybridized with the gene in 1), 2) or 3) under the stringent conditions and codes the said protein; and
5) a gene which has above 90% homology with the gene in 1), 2) or 3) and codes the said protein.
The sequence 2 in the sequence list consists of 1624 bases; its open reading frame (ORF) is from 124 to 1377 base of 5′-end and it codes IPA1 protein having amino acid sequence of sequence 1 in the sequence list.
The stringent conditions as described above may use 0.1×SSPE (or 0.1×SSC) and 0.1% SDS solution, hybridize at 65° C. and wash the membrane in DNA or RNA hybridization assay.
The primers for the amplification of full length IPA1 gene or any portion thereof are also within the scope of the invention.
Expression cassettes, recombinant vectors, transgenic cell lines and recombinant bacteria containing the coding gene for the protein associated with plant type as described above are also within the scope of the invention.
The recombinant expression vector containing IPA1 gene may be constructed using the existing plant expression vectors. The said plant expression vectors include binary Agrobacterium vector and vectors for plant bombarding and the like, such as pCAMBIA3301, pCAMBIA1300, pB11121, pBin19, pCAMBIA2301, pCAMBIA1301-UbiN or other derived plant expression vectors.
Any enhanced promoter, constitutive promoter, tissue-specific promoter or inducible promoter, such as cauliflower mosaic virus (CAMV) 35S promoter and ubiquitin gene promoter (pUbi) and the like, alone or combined with other plant promoters, may be added to the transcription start nucleotide when using IPA1 gene to construct the recombinant expression vector. Additionally, an enhancer may also be used, including a translation enhancer or a transcription enhancer when using the gene of the invention to construct the plant expression vector, these enhancer regions are ATG start code or start code in adjacent region, but they have to be the same as the reading frame of the coding sequence to ensure the correct translation of the whole sequence. The origins of the said translation control signals and start codes are extensive; they may be either natural or synthetic. The translation start region can be derived from transcription start region or structural genes.
To facilitate the identifying and screening of transgenic plant cell or plant, the plant expression vectors used can be modified, such as adding enzymes producing color changing in the expression of plant or genes for luminous compounds (GUS gene, GFP gene and luciferase gene and so on), antibiotic resistance gene (gentamycin resistance, kanamycin resistance and so on) or chemical reagents resistance gene (such as gene for anti-rust agent) and the like.
The said recombinant expression vectors may be specifically a recombinant expression vector that is produced through inserting the coding gene for the protein associated with plant type as described above into the multi-clonal site of the plant expression vector pCAMBIA1300.
Another object of the invention is to provide a method for breeding transgenic plants.
The method for breeding the transgenic plant of the invention comprises introducing the coding gene IPA1 for the protein associated with the plant type as described above or genomic DNA into a plant to produce transgenic plants; the said transgenic plants are of fewer tillers, thick and sturdy stems, more panicles and rachis branches and more grain number per panicle compared with the said target plant.
The said coding gene IPA1 for the protein associated with plant type as described above was introduced into the target plant via the recombinant expression vectors as described above.
The plant expression vectors carrying the coding gene IPA1 for the protein associated with plant type of the invention can be transformed into the plant cells or tissues through conventional biological methods such as Ti plasmid, Ri plasmid, plant virus vectors, direct DNA transformation, microinjection, electrically transduction, Agrobacterium-mediated method and so on. The transformed plant hosts (the target plants) are dicotyledon or monocotyledon, preferably rice, more preferably Nipponbare.
Another object of the invention is to provide a method for breeding transgenic plants. The method comprises introducing an interference vector into a target plant to obtain a transgenic plant; the said transgenic plants are of much more tillers, thinner stems, less primary rachis branches and fewer grain numbers per panicle compared with the said target plant; the said interference vector is a recombinant vector achieved through inserting sequentially the nucleotide sequence listed as sequence 4 in the sequence list and the nucleotide sequence listed as sequence 5 in the sequence list into site between BamHI and KpnI and site between SpeI and SacI sites in the vector pTCK303. The target plants are dicotyledon or monocotyledon, preferably rice, more preferably Ri22.
The sequence 4 is a fragment from 1014 bp to 1623 bp of the sequence 2 and the sequence 5 is a reverse complementary sequence to the sequence 4. It was confirmed that there was no other homological sequence with the sequence 4 and 5 in the genome of rice through a whole genome alignment analysis.
A pleiotropic gene IPA1 which can control the tiller number and the development of the stems and panicles was isolated using a map-based cloning method, and the function of the gene was confirmed through a functional complementation experiment.
It was proved by the experiment: the tiller number of the rice was reduced, the stems became thick and sturdy, the number of the panicles and rachis branches were increased and grain number per panicle was improved after the gene of the invention was overexpressed in the rice; the plant height was decreased, the tillers was increased, the stems became thinner and the number of the panicles and rachis branches were reduced after the gene of the invention was loss of function or the activity of the gene was reduced, which suggested that the gene can control the plant architecture of the rice. Thus, the IPA1 gene provides a powerful tool to breed a new plant type rice variety using molecular marker assisted breeding and using genetic engineering method, whereby to further improve the yield of the rice, and this gene has important theoretical significance and great potential for application.



DESCRIPTION OF THE FIGURES
FIG. 1 shows a phenotype of rice materials, including Shaoniejing (SNJ) with fewer tillers and conventional indica rice variety TN1.
FIG. 2 is map-based cloning of the IPA1 gene. FIGS. 2a and 2b are drawings showing QTL analysis and location using BC2F2. FIG. 2c is a fine location map; a number under a tag represents a recombinant individual; FIG. 2d is a predicted gene within a range of 78 kb, and an arrow represents a predicted gene; FIG. 2e is a schematic diagram of the structure of the IPA1 gene of invention, a white blank box represents 5′ and 3′ untranslated region, a black box represents an exon, a middle horizontal line represents an intron and a red star represents miRNA156 target site. The change of the bases above the box represents a base mutation in the Shaoniejing materials. The number in the brackets represents the position of the base mutation.
FIG. 3 is sequence diagram of cDNA_(SEQ ID NO: 2) and protein (SEQ ID NO: 1) of the IPA1 gene, the blue nucleotides represent 5′ and 3′ noncoding region, the protein sequence underlined represents SBP structure domain, a red star represents miRNA156 target site and a red letter represents a nucleotide mutation in the Shaoniejing material and an amino acid change resulted from the mutation.
FIG. 4 is gIPA1 vector map and the statistical analysis of phenotype and agronomic traits of the transgenic rice in the functional complementation experiment. FIG. 4a is giPA1 vector map; FIG. 4b is the phenotype of the gIPA1 transgenic rice; FIG. 4c is the expression level of IPA1 determined by RT-PCR; FIG. 4d is the statistical comparisons of the agronomic traits associated with gIPA1 transgenic materials via T test, a single-star represents significant and a double-star represents very significant; Nipponbare is wild type control and gIPA1 is the transgenic plant in FIGS. 4b, 4c and 4d. 
FIG. 5 is the comparison of the phenotype and agronomic traits of the transgenic rice obtained with RNA interference, FIG. 5a is the phenotype of the transgenic rice obtained with RNA interference; FIG. 5b is the expression level of IPA1 in the transgenic plant determined by RT-PCR; FIG. 5c is the comparisons of the agronomic traits associated with the transgenic rice obtained with RNA interference via T test and a double-star represents very significant; Ri 22 is non-transgenic control and IPA1-RNAi is the transgenic plant in FIGS. 5a, 5b and 5c. 



EMBODIMENTS OF THE INVENTION
The following embodiments are presented to further illustrate the invention, but the invention is not limited to the examples.
The methods in the following examples are all conventional methods, unless otherwise indicated.
The rice in the following examples was obtained through a cultivation method as follows: (1) field cultivation of the rice materials: The rice seeds were soaked in the water for 2 days, and then were transferred into a culture room at 37° C. to accelerate the germination of the seeds for 3 days, the seeds showing white were then seeded into a seedbed to raise rice seedlings and the rice seedlings were transplanted into a paddy field when the seedlings had 4 leaves.
Example 1
The Discovery of the Gene
The seeds of Shaoniejing with fewer tillers, sturdier stems and big panicles and conventional indica rice variety TN1 of rice (Oryza sativa L.) were grown according to the field cultivation method as described above and the morphology of the mature plant was shown in FIG. 1. The DNA was extracted from the leaf.
Extraction of Rice Genomic DNA:
The genomic DNA was extracted using the adapted CTAB method (Mou Z, He Y, Dai Y, et al. Deficiency in fatty acid synthase leads to premature cell death and dramatic alterations in plant morphology. The Plant Cell. 2000, 12, 405-418.) from the leaf of rice. 100 mg leaves of the rice was collected and frozen in liquid nitrogen and milled into powder in a small mortar with 5 cm diameter, transferred into a 1.5 ml centrifuge tube to extract DNA and the achieved DNA was dissolved into 100μ MQ H2O.
The map-based cloning was performed according to the steps as follows:
1. Primary Mapping of the IPA1 Gene
To isolate the IPA41 gene, a mapping population was firstly constructed using Shaoniejing and TN1. And then the QTL analysis and mapping was performed using BC2F2 individual of the segregating population. The result of the mapping showed that IPA1 was primarily mapped between two markers RM149 and RM1345 at chromosome 8 and the genetic distance was 2.1 cM and 1.8 cM respectively (FIGS. 2a and 2b).
2. Fine Mapping of the IPA1 Gene
To further narrow the definite region of the target gene, 5500 individual plants whose phenotype type was close to TN1 were selected from BC2F2 segregating population to perform the fine mapping. At the same time, a difference site was searched within mapping region through genome sequence between Indica rice and Japonica rice using 93-11 and Nipponbare published to exploit new STS and SSR makers. An individual plant whose gene was exchanged with that of the target gene was screened firstly using markers RM149 and RM1345 and then these exchanged individual plants were screened using a new molecule marker to find that the molecule markers M3 and M6 were closely linked to the target gene when the fine mapping was performed. There were 5 and 3 recombinants identified respectively. Finally, IPA1 locus was finely mapped in a section of approximately 78 kb between markers M4 and M5 (FIGS. 2c and 2d).
3. Identification and Sequence Analysis of Candidate Genes
A candidate gene prediction was performed on the 78 kb section and a sequence alignment was conducted between TN1 and Shaoniejing materials. The result showed that one point mutation from C to A occurred in the third exon of gene OsSPL14 (LOC_0s08g39890) in the Shaoniejing materials. However, there is no mutation in the same region of Nipponbare and Zhonghua11 and the like. We found that the mutation position was located at the target site of miRNA156 and thus it may affect regulation of miRNA156 on OsSPL14 (FIG. 2e) through an in-depth analysis. Based on the information as above, the gene was determined as a candidate gene. There is a corresponding full-length cDNA sequence AK107191 of the candidate gene in KOME database. An analysis of the protein sequence showed that the candidate gene contained a conserved SBP (SQUAMOSA promoter binding protein) domain (FIG. 3).
Example 2
Acquisition and Testing of the Transgenic Plants
1. Acquisition of the Transgenic Plants
(1) Construction of a Recombinant Expression Vector
(a) Cloning of the Genes
A DNA fragment comprising the IPA1 gene (The sequencing showed that the nucleotide sequence of the preparatory fragment was listed as sequence 3 in the sequence list) was amplified from the genomic DNA of Nipponbare (The public can obtain the material from Institute of Genetics and Developmental Biology, Chinese Academy of Science and the material was reported in a non-patent literature Lin H, Wang R, Qian Q, et al. DWARF27, an iron-containing protein required for the biosynthesis of strigolactones, regulated rice tillers bud outgrowth. Plant Cell 2009, 21, 1512-1525.). The preparatory fragment was digested with Kpn I and Xba I to obtain a final genomic DNA fragment comprising the full-length IPA1 (The nucleotide sequence was listed as 1-7229 bp from 5′-end of sequence 3 in the sequence list).
In the genomic DNA listed as 1 bp to 7229 bp of sequence 3, 1118 bp to 1566 bp is the first exon, 1567 bp to 3996 bp was the first intron, 3997 bp to 4130 bp was the second exon, 4131 bp to 4232 bp was the second intron and 4233 bp to 4903 bp was the third exon.
The nucleotide sequence of cDNA corresponding to the genomic DNA listed as 1 bp to 7229 bp of sequence 3 is shown as sequence 2 in the sequence list. The sequence 2 consists of 1624 bp; its open reading frame (ORF) is from 124 to 1377 base of 5′-end and it codes IPA1 protein having amino acid sequence of sequence 1 in the sequence list.







TABLE 2 







Sequence of the primers








Name of



the primers
Sequence of the primers (5′-3′)





gIPA11F
AGGTACCGCAATGTAGAGCCACGTAGGCAAG



(SEQ ID NO: 15)


 


gIPA11R
AGGGCCCGCTTACCAGCTATTGGTTACACATATT



(SEQ ID NO: 16)









A Kpn I enzyme cutting site was added into 5′-end of the primer gIPA11F and an Apa I enzyme cutting site was added into 5′-end of primer gIPA11R.
(b) Construction of the Expression Vector
The final genomic DNA fragment comprising the full-length IPA1 gene obtained in step (a) was inserted into a site between Kpn I and Xba I sites of vector pCAMBIA1300 (commercially available from Cambia company) to achieve a recombinant expression vector gIPA1 (FIG. 4a) and it was confirmed that the construction was correct.
(2) Acquisition of the Transgenic Plants
The gIPA1 plasmid was transformed into Agrobacterium tumefaciens line EHA05 (The public can obtain the material from Institute of Genetics and Developmental Biology, Chinese Academy of Science and the material was reported in a non-patent literature Lin H, Wang R, Qian Q, et al. DWARF27, an iron-containing protein required for the biosynthesis of strigolactones, regulated rice tillers bud outgrowth. Plant Cell 2009, 21, 1512-1525) through electroporation to screen recombinant Agrobacterium tumefaciens strains containing the recombinant plasmid gIPA1.
The callus of Nipponbare was infected with the recombinant Agrobacterium tumefaciens strains containing the recombinant plasmid gIPA1, cultured at 25° C. in the darkness for 3 days and resistant callus and transgenic plants were screened on a selective medium containing 50 mg/L hygromycin. The hygromycin resistant plants were acclimated in the shade and transplanted into a paddy field to obtain a transgenic plant T0-generation. The seeds of T0-generation plant were recovered and cultured according to the field cultivation method as described above and T1 transgenic plants with transformed gIPA1 were obtained through the conventional molecular detection.
Nipponbare was transformed with empty vector pCAMBIA1300 to obtain empty vector control plants according to the method of obtaining the T1 transgenic plants with transformed gIPA1.
2. Plant Type Characterization of the Transgenic Plants
(1) Detecting the Expression Level of the IPA1 Gene Through RT-PCR
The total RNA of the plants was extracted from the transgenic plants and the control Nipponbare plants by using TRIZOL (commercially available from Invitrogen Company) and a reverse transcription was performed by using reverse transcription kit (commercially available from Promega Company) to obtain cDNA. The expression of the IPA1 gene was detected through PCR by using primers IPA1RT1F and IPA1RT1R (The sequence of amplified fragment was from 681 bp to 1362 bp region of 5′-end of sequence 2). The Ubiquitin gene was amplified as internal standard by using primers UbiRTF and UbiRTR and the sequence of the primers was listed in Table 3. The results showed that the expression level of IPA1 was increased in transgenic plants (FIG. 4c).







TABLE 3 







The sequence of the primers








Name of



the primers
Sequence of the primers (5′-3′)





IPA1RT1F
CGGTCGACTAGCTGCATCTGTTGG



(SEQ ID NO: 17)


 


IPA1RT1R
CATCGTGTTGCTGGTTTGGTCGAAG



(SEQ ID NO: 18)


 


UbiRTF
CCCTCCACCTCGTCCTCAG



(SEQ ID NO: 19)


 


UbiRTR
AGATAACAACGGAAGCATAAAAGTC



(SEQ ID NO: 20)









(2) Plant Type Characterization of the Transgenic Plants
A statistical analysis of plant type was performed on the T1 transgenic plants with transformed gIPA1, Nipponbare control plants and empty vector control plants, and 10 individual plants were taken from each material. The results were shown in FIGS. 4b and 4d (The phenotype of the empty vector control plants was the same as Nipponbare control plants in FIGS. 4b and 4d, not shown in Figure), which the number of the tillers was reduced (from 11.9 to 6.7 in average), the number of primary rachis branch was significantly increased (from 10.8 to 15.5 in average), the number of secondary rachis branch was also significantly increased (from 21.9 to 25.6 in average), the stems became thicker (the diameter of the third branches was increased from 0.35 cm to 0.47 cm in average) and the grain number per panicle was significantly increased (from 117.1 to 135.7 in average) when the T1 transgenic plants transformed with gIPA1 were compared with plants transformed with the empty vector and Nipponbare.
Example 3
Acquisition and Testing of the Transgenic Plants
1. Acquisition of the Transgenic Plants
(1) Obtaining the Interference Fragment
PCR amplification was performed by using primer pair RNA1F/RNAi1R and primer pair RNAi2F/RNAi2R in Table 4 and using KOME full-length cDNA clone (No. AK107191) as template (commercially available from Genome Resource Center, National Institute of Agrobiological Science, Japan), and sequencing was performed on the resulting product. The nucleotide sequence of the gene fragment obtained through the amplification by using these two pairs of primers were shown in sequence 4 and sequence 5 in sequence list respectively.







TABLE 4 







The sequence of the primers








Name of



the primers
Sequence of the primers (5′-3′)





RNAi1F
AGGATCCCCAGCCATGGGATACTACTACC



(SEQ ID NO: 21)


 


RNAi1R
AGGTACCCAGCATTAACACTGATACTTAAA



(SEQ ID NO: 22)


 


RNAi2F
AACTAGTCAGCATTAACACTGATACTTAAA



(SEQ ID NO: 23)


 


RNAi2R
AGAGCTCCCAGCCATGGGATACTACTACC



(SEQ ID NO: 24)









Recognition sites for BamHI and KpnI were added to the 5′ end of forward and reverse primer of RNAil respectively and recognition sites for SpeI and SacI were added to the 5′ end of forward and reverse primer of RNAi2 respectively.
Sequence 4 is a fragment from 1014 bp to 1623 bp of the sequence 2 and sequence 5 is a reverse complementary sequence of the sequence 4. It was confirmed that there was no other homological sequence with sequence 4 and 5 in the genome of rice through a whole genome alignment analysis.
(2) Construction of the Interference Vector
The product amplified by using primer pair RNAi1F/RNAi1R was cut with BamHI and KpnI and BamHI and KpnI sites of vector pTCK303 carrying Ubiquitin promoter (The public can obtain the material from Institute of Genetics and Developmental Biology, Chinese Academy of Science and the material was reported in a non-patent literature Wand Z, Chen C, Xu Y, et al. A practical vector for efficient knockdown of gene expression in rice (Oryza sativa L.). Plant Mol. Biol. Rep. 2004, 22, 409-417) were inserted to obtain vector 1; the product obtained through amplification by using primer pair RNAi2F/RNAi2R was cut with SpeI and SacI, and the resulting fragments were inserted into the vector to achieve SpeI and SacI sites of vector 1 and then a recombinant expression vector was obtained (ie. interference vector IPA1-RNAi). The fragments inserted formed a hairpin structure after expression.
(3) Acquisition of the Transgenic Plants
The interference vector IPA1-RNAi was transformed into Agrobacterium tumefaciens line EHA05 through electrical bombardment method to screen recombinant Agrobacterium tumefaciens strains which contains the interference vector IPA41-RNAi.
The mature seeds of materials Ri22 containing point mutated gene were shelled, sterilized and sowed into a calli induction medium. The callus was grown from the scutellum after three-week culture. The embryonic callus with vigorous growth, light yellow and loose was selected to use as a receptor of transformation.
The callus of Ri22 rice was infected with the recombinant Agrobacterium tumefaciens strains which contains the interference vector IPA1-RNAi and then cultured at 25° C. in the darkness for 3 days and resistant callus and transgenic plants were screened on a selective medium which contains 50 mg/L hygromycin. The hygromycin resistant plants were acclimated in the shade and then transplanted into a paddy field to obtain a transgenic plant T0 generation. The transgenic seeds of T0 generation were recovered and then cultured to obtain T1 generation transgenic plants with transformed gIPA1.
Ri22 was transformed with empty vector pTCK303 to obtain an empty vector control plant according to the method of obtaining the T1 generation transgenic plants transformed with IPA1-RNAi.
2. Detection of the Transgenic Plants
(1) Detecting the Expression Level of the IPA1 Gene Through RT-PCR
The total RNA of the plants was extracted from the transgenic plants and the control Ri22 plants by using TRIZOL (commercially available from Invitrogen Company) and a reverse transcription was performed by using reverse transcription kit (commercially available from Promega Company) to obtain cDNA. The expression of the IPA1 gene was detected through PCR by using primers IPA1RT1F and IPA1RT1R. Ubiquitin gene was amplified as internal standard by using UbiRTF and UbiRTR and the sequence of the primers was listed in Table 3. The result showed that the expression level of the IPA1 was decreased in the transgenic plants (FIG. 5b).
(2) Plant Type Detection of the Transgenic Plants
A statistics of plant type was performed on the T1 generation transgenic plants with transformed IPA1-RNAi, Ri22 control plants and empty vector control plants and 10 individual plants were taken from each material. The results were shown in FIGS. 5a and 5c (The phenotype of the empty vector control was the same as Nipponbare control in FIGS. 5a and 5c, not shown in Figure), which the plant height was reduced (from 115.7 cm to 91.2 cm in average), the number of the tillers was dramatically increased (from 3.7 to 23.3 in average), the number of primary rachis branch was significantly decreased (from 15.2 to 6.2 in average), the number of secondary rachis branch was also significantly decreased (from 57.5 to 9.7 in average), the grain number per panicle was significantly decreased (from 259.6 to 54.6 in average) and the stems became thinner (the diameter of the second branches was decreased from 0.68 cm to 0.29 cm in average) when the T1 transgenic plants with transformed IPA1-RNAi were compared with the empty vector control plants and Ri22 control.

## Claims

1. A method of breeding a transgenic plant comprising introducing an interference vector into a target plant to obtain the transgenic plant having changed phenotypes compared with the target plant,
wherein the interference vector is constructed by sequentially inserting a first nucleic acid comprising the nucleotide sequence of SEQ ID NO: 4 and a second nucleic acid comprising the nucleotide sequence of SEQ ID NO: 5 into a vector thereby allowing the formation of a hairpin structure upon expression; and
wherein the changed phenotypes comprise reduced height, more tillers, thinner stems, fewer primary rachis branches, and fewer grains per panicle.

2. The method of claim 1, wherein the vector is pTCK303, wherein the first nucleic acid is inserted between BamHI and KpnI sites, and wherein the second nucleic acid is inserted between SpeI and SacI sites.

3. The method of claim 1, wherein the plant is a monocotyledon.

4. The method of claim 3, wherein the plant is rice.