Polymorphic sites and their application in regulating rice leaf tilt angle

Abstract

This invention provides a polymorphic site and its application in regulating rice leaf inclination angle. The invention discloses a single nucleotide polymorphism (SNP) for identifying leaf inclination angle phenotypes, located at the sf0623501417 site in the IAA23 gene of rice, with the corresponding bases being T or G. The sf0623501417 site can be used to predict or analyze rice (population) plant compactness, dense planting and / or lodging resistance, and photosynthetic efficiency; it can also be used for rice germplasm resource identification and targeted breeding of rice. This invention provides a new direction for optimized rice breeding.

Description

Technical Field

[0001] This invention belongs to the field of plant breeding technology; more specifically, this invention relates to a polymorphic site and its application in regulating the leaf tilt angle of rice. Background Technology

[0002] Plant type traits in rice (such as leaf angle, plant height, and number of tillers) have a significant impact on photosynthesis, plant density, and lodging resistance during rice growth. In particular, leaf angle, as a key plant type trait, directly affects the light energy utilization efficiency and the maximization of photosynthesis in rice.

[0003] The leaf tilt angle of rice refers to the angle between the rice leaf and the vertical direction, used to describe the degree of inclination of the rice plant's leaves. Normally, rice leaves should grow vertically, but in actual growth, factors such as sunlight, wind, and nutrients can cause the leaves to tilt to a certain extent. Leaf tilt angle can be measured using common measuring tools such as angle gauges and laser meters. Common methods include: (a) Angle gauge method: using an angle gauge to measure the angle between the rice leaf and the vertical direction. (b) Laser meter method: using a laser instrument to emit a laser beam and measuring the angle between the laser beam and the rice leaf to calculate the leaf tilt angle.

[0004] A suitable leaf tilt angle allows rice to absorb more sunlight, increasing the efficiency of photosynthesis and improving yield; while excessively large or small leaf tilt angles can lead to insufficient light capture or uneven light distribution, affecting photosynthesis and reducing yield. Therefore, rationally controlling the leaf tilt angle of rice is one of the keys to optimizing rice cultivation management. The formation of rice leaf tilt angle is related to several factors, mainly including the following: (a) Light conditions: Sufficient light can promote normal growth of rice leaves and reduce the occurrence of leaf tilt angle. (b) Wind factors: Strong winds can cause rice plants to tilt, leading to an increase in leaf tilt angle. (c) Nutrient supply: Sufficient nitrogen fertilizer supply can promote the increase of rice plant height and reduce the occurrence of leaf tilt angle. (d) High temperature stress: Under high temperature conditions, rice leaves are prone to scorching, leading to an increase in leaf tilt angle.

[0005] The leaf inclination angle of rice is an important indicator reflecting the growth and development status of rice plants and has a significant impact on rice yield. Through reasonable regulation methods and techniques, the size of the leaf inclination angle can be effectively controlled, ensuring the normal growth and development of rice plants. While traditional breeding methods such as hybridization breeding and mutation breeding have made some progress, these methods suffer from problems such as long cycles, low efficiency, and narrow genetic bases.

[0006] In summary, the leaf tilt angle of rice is regulated by multiple genes. Currently, there is a lack of technology in this field that can precisely regulate the leaf tilt angle at the single-base level, which requires further in-depth research and exploration. Summary of the Invention

[0007] The purpose of this invention is to provide a polymorphic site and its application in regulating the leaf tilt angle of rice.

[0008] In a first aspect of the invention, a method is provided for identifying (including predicting) the leaf tilt phenotype of rice, comprising targeting a single nucleotide polymorphism (SNP) or haplotype at the sf0623501417 site of rice (corresponding to position 238 in the sequence shown in SEQ ID NO:1); if the site is base T, the rice has a small (relatively small) leaf tilt angle and a compact (relatively compact) plant type; if the site is base G, the rice has a large (relatively large) leaf tilt angle.

[0009] In one or more embodiments, if the leaf tilt angle of the rice is small, it indicates that the plant type is compact (relatively compact), and it is a densely planted and / or lodging-resistant rice.

[0010] In one or more embodiments, a large leaf tilt angle in rice indicates plant expansion (relative expansion).

[0011] In one or more embodiments, the analysis of single nucleotide polymorphisms (SNPs) or haplotypes employs methods selected from the group consisting of: sequencing, PCR amplification, probe methods, hybridization, microarray methods, restriction enzyme digestion analysis, allele polymorphism analysis, and electrophoresis.

[0012] In one or more embodiments, reagents or devices for specifically detecting single nucleotide polymorphisms or haplotypes may include: chips, probe sets, primer sets, primer-probe sets, restriction enzymes, electrophoresis reagents, and gene sequencing instruments.

[0013] In another aspect of the invention, the use of the rice sf0623501417 locus or the IAA23 gene containing that locus is provided for: serving as a target for identifying (including predicting) the rice leaf tilt phenotype; or, preparing reagents, devices, or kits for identifying (including predicting) the rice leaf tilt phenotype; wherein, during identification, the single nucleotide polymorphism or haplotype of the rice sf0623501417 locus is analyzed; or, when preparing the reagent, the reagent is targeted at the single nucleotide polymorphism or haplotype of the sf0623501417 locus.

[0014] In another aspect of the invention, the use of a reagent for specifically analyzing the rice sf0623501417 site or the IAA23 gene containing that site is provided for identifying the rice leaf tilt phenotype; wherein the reagent is targeted at the single nucleotide polymorphism or haplotype of the sf0623501417 site.

[0015] In one or more embodiments, identification is performed by analyzing the single nucleotide polymorphism or haplotype of the sf0623501417 site; if the site is base T, the rice has a small leaf inclination angle and a compact plant type (relatively small); if the site is base G, the rice has a large leaf inclination angle (relatively large).

[0016] In one or more embodiments, the rice sf0623501417 locus is used as a target for (but not limited to) predicting or analyzing the plant compactness, dense planting and / or lodging resistance, and photosynthetic efficiency of rice (population) by analyzing the rice leaf tilt angle phenotype; identifying rice germplasm resources; or conducting targeted breeding of rice.

[0017] In one or more embodiments, the reagent or device includes (but is not limited to): primers (sets), probes (sets), primer-probe sets, a chip, a restriction enzyme that distinguishes the base type of the sf0623501417 site, an electrophoresis reagent, and a gene sequencing instrument for detecting the region containing the rice sf0623501417 site.

[0018] In one or more embodiments, the nucleotide sequence of the IAA23 gene is shown in SEQ ID NO:1, wherein the base type corresponding to the sf0623501417 position (position 238) includes base T or base G.

[0019] In one or more embodiments, the amino acid sequence of the protein encoded by the IAA23 gene is shown in SEQ ID NO:1, wherein the amino acid residue (position 80) corresponding to position sf0623501417 is of type S or A.

[0020] In another aspect of the present invention, a method for optimizing rice breeding is provided, comprising: knowing a type of rice with a small leaf inclination angle (such as ZH11 or NIP variety), or analyzing and identifying the leaf inclination angle of rice by any of the methods described above, and identifying it as having a small leaf inclination angle when the sf0623501417 site is a base T; for the rice with a small leaf inclination angle, changing the T at its sf0623501417 site to a base G, thereby regulating its leaf inclination angle to increase (and thus promoting its plant type expansion and regulating its photosynthetic efficiency).

[0021] In another aspect of the present invention, a method for optimizing rice breeding is provided, comprising: knowing a type of rice with a large leaf inclination angle (such as the Yangzhou Daohuaxiang (DHY) variety), or analyzing and identifying the leaf inclination angle of rice through any of the methods described above, and identifying it as having a large leaf inclination angle when the sf0623501417 site is a base G; for the rice with a large leaf inclination angle, changing the G at its sf0623501417 site to a base T, thereby regulating its leaf inclination angle to decrease (thereby promoting its compact plant type, promoting dense planting and / or lodging resistance, and regulating its photosynthetic efficiency).

[0022] In one or more embodiments, the method of modification includes (but is not limited to) the following techniques: site-directed mutagenesis, gene editing (such as CRISPR / Cas technology) or homologous recombination; or regulating the expression of the rice IAA23 gene in rice, wherein the sf0623501417 site of the rice IAA23 gene is selected from base T or base G.

[0023] Other aspects of the invention will be apparent to those skilled in the art from the disclosure herein. Attached Figure Description

[0024] Figure 1 The leaf tilt angle of the gene-edited material IAA23 with ZH11 as the background (iaa23-cr / ZH11) decreased, while the leaf tilt angle of its overexpression material (IAA23-OE / ZH11) increased significantly.

[0025] Figure 2 The nucleotide sequence of IAA23 contains four SNPs that are highly correlated with leaf tilt angle.

[0026] Figure 3 The nucleotide sequence of IAA23 contains four SNPs that are highly correlated with leaf tilt angle.

[0027] Figure 4 SNPs are strongly correlated with the distribution of the maximal and minimal leaf tilt populations.

[0028] Figure 5 Phenotypic analysis of leaf tilt angle of SNP intrinsic replacement material. Detailed Implementation

[0029] Through extensive research, the inventors have for the first time revealed a single nucleotide polymorphism (SNP) or haplotype target for identifying leaf tilt angle phenotype. The SNP is located at the sf0623501417 locus in rice, belonging to the IAA23 gene, with corresponding bases of T or G. The sf0623501417 locus can be used to predict or analyze rice (population) plant compactness, dense planting and / or lodging resistance, and photosynthetic efficiency; it can also be used for rice germplasm resource identification and targeted breeding of rice. This invention provides a new direction for optimized rice breeding.

[0030] In the prior art, those skilled in the art have not had a clear understanding of which genes(s) control the rice leaf angle phenotype, and existing technologies lack gene targets for identifying the rice leaf angle phenotype. Based on the inventors' new discovery, this invention provides a single nucleotide polymorphism or haplotype target suitable for identifying the rice leaf angle phenotype, specifically located at the sf0623501417 locus in rice. This invention also provides a target gene suitable for identifying the rice leaf angle phenotype, namely IAA23.

[0031] In this invention, unless otherwise specified, IAA23 can be a gene having the nucleotide sequence shown in SEQ ID NO:1 (rice source) with the SNP present at a specific location. This invention also includes sequence variations having the same function as IAA23 (but wherein the SNP sites of interest in this invention are conserved).

[0032] According to a new discovery of the present invention, a method for identifying the leaf tilt phenotype of rice is provided, including using the single nucleotide polymorphism (SNP) or haplotype at the sf0623501417 site of the rice as a target; if the site is base T, the rice has a small leaf tilt angle and a compact plant type (relatively small); if the site is base G, the rice has a large leaf tilt angle (relatively large).

[0033] Based on the novel findings of this invention, those skilled in the art can employ any of the various techniques known in the art or under development to analyze nucleic acid sequences, and these techniques are all included in this invention. The methods described include, but are not limited to: sequencing, PCR amplification, probe methods, hybridization, restriction enzyme digestion analysis, allele polymorphism analysis (such as melting curve analysis) for nucleic acid sequence identification, etc.

[0034] Genome-wide association studies (GWAS) can also be applied to analyze the aforementioned SNP loci. GWAS is a technique that studies the association between genotype and phenotype by detecting genetic markers, such as SNPs, across the entire genome of multiple individuals, thereby identifying gene variations associated with a target trait.

[0035] The methods for obtaining DNA from the sample to be tested are well known to those skilled in the art, such as the traditional phenol / chloroform / isoamyl alcohol method, or commercially available DNA extraction kits, which are well known to those skilled in the art.

[0036] Polymerase chain reaction (PCR) is a technique well-known to those skilled in the art, and its basic principle is the in vitro enzymatic synthesis of specific DNA fragments. The method of this invention can be performed using conventional PCR techniques.

[0037] Based on the above, the present invention also relates to a kit for identifying the rice leaf tilt phenotype, said kit containing reagents specifically for detecting the SNP of interest described above or a specific gene containing that SNP site. In some alternative embodiments, the kit may further include a restriction endonuclease capable of recognizing changes in the location of said SNP site. It should be understood that the reagents that can be used for identification according to the disclosure of the present invention are not limited thereto.

[0038] In addition, the kit may also include an instruction manual and / or standard operating procedures for identification. The kit enables rapid and batch detection of rice leaf tilt phenotypes.

[0039] This invention overcomes the current lack of tools for identifying rice leaf tilt phenotypes. Based on the target provided by this invention and combined with existing knowledge in the field, a simple and effective identification method and its preferred primers can be designed, thus providing a feasible method for early or rapid identification of rice leaf tilt phenotypes and a powerful tool for plant breeding and screening.

[0040] Identifying the leaf tilt phenotype of rice early in the planting process or even before planting can greatly facilitate plant breeding work.

[0041] Knowing the role of the sf0623501417 site or IAA23 containing this key site, it can be used as a molecular marker for targeted plant screening. This new discovery can also be used to screen for substances or potential substances that can target and regulate rice leaf tilt phenotypes by altering / regulating proteins at this key site in IAA23.

[0042] Methods for screening substances that act on genes or proteins or specific regions thereof as targets are well known to those skilled in the art, and these methods can all be used in this invention. The candidate substances can be selected from: peptides, polymeric peptides, peptide-like substances, non-peptide compounds, carbohydrates, lipids, antibodies or antibody fragments, ligands, small organic molecules, small inorganic molecules, and nucleic acid sequences, etc. Depending on the type of substance to be screened, those skilled in the art will understand how to select an appropriate screening method.

[0043] Through large-scale screening of the SNPs or specific genes of interest disclosed in this invention, a class of potential substances that specifically act on the IAA23 gene or protein and regulate the rice leaf tilt phenotype can be obtained.

[0044] This invention also provides a method for optimizing rice breeding. In a preferred embodiment, for a type of rice with a relatively small leaf inclination angle (such as the NIP variety), the T at the sf0623501417 site is mutated to the base G, thereby regulating the increase of its leaf inclination angle, which in turn promotes the expansion of its plant type, regulates its photosynthetic efficiency, and achieves more efficient production.

[0045] As another preferred embodiment of the present invention, the leaf tilt angle of rice is analyzed and identified by any of the methods described above. When the sf0623501417 site is a base T, it is identified as having a small leaf tilt angle. The T at the sf0623501417 site is mutated to a base G, thereby regulating the increase of its leaf tilt angle, which is beneficial to promoting the expansion of its plant type, regulating its photosynthetic efficiency, and achieving more efficient production.

[0046] As another preferred embodiment of the present invention, for a type of rice with a relatively large leaf inclination angle (such as the Yangzhou (DHY) rice variety), the G at the sf0623501417 site is mutated to the base T, thereby regulating the reduction of its leaf inclination angle, thereby promoting its compact plant type, promoting dense planting and / or lodging resistance, regulating its photosynthetic efficiency, and achieving more efficient production.

[0047] As another preferred embodiment of the present invention, the leaf tilt angle of rice is analyzed and identified using any of the methods described above. When the sf0623501417 site is a base G, it is identified as having a large leaf tilt angle. The G at the sf0623501417 site is mutated to a base T, thereby regulating the leaf tilt angle to decrease, which in turn promotes compact plant type, promotes dense planting and / or lodging resistance, regulates photosynthetic efficiency, and achieves more efficient production.

[0048] It is understood that any method applicable to targeted base / amino acid mutations can be used in this invention. For example, techniques including but not limited to site-directed mutagenesis, gene editing (such as CRISPR / Cas technology), or homologous recombination can be employed. As a preferred approach, after identifying the key regulatory genes and their key sites for rice plant architecture traits such as leaf angle, gene editing technology is preferably used to precisely modify specific genes or sites to more efficiently and accurately improve plant architecture traits such as leaf angle in rice.

[0049] In this invention, the aforementioned modification can also be implemented using the full-length or functional fragments of the IAA23 gene, including regulating the expression of the rice IAA23 gene in rice.

[0050] As a preferred embodiment of the present invention, when the sf0623501417 site of the rice IAA23 gene is a base T (encoding an amino acid with an amino acid residue of S at the corresponding site) and the leaf tilt angle of the rice needs to be increased, the expression of the IAA23 gene with a base G at the sf0623501417 site (encoding an amino acid residue of A at the corresponding site) can be regulated (e.g., by gene editing replacement) in the rice.

[0051] As another preferred embodiment of the present invention, when the sf0623501417 site of the rice IAA23 gene is base G (encoding amino acid residue A at the corresponding site) and the leaf tilt angle of the rice needs to be reduced, the expression of the IAA23 gene with base T at the sf0623501417 site (encoding amino acid residue S at the corresponding site) can be regulated (e.g., by gene editing replacement) in the rice.

[0052] In summary, the SNP markers associated with plant architecture traits such as rice leaf angle of this invention can promote marker-assisted selection of rice leaf angle, effectively accelerate the rice breeding process, and improve breeding efficiency, which is of great significance to rice breeding. This invention also shows promise for applications in molecular design breeding of rice leaf angle phenotypes and in crop variety improvement using genetic engineering technology.

[0053] The present invention will be further illustrated below with reference to specific embodiments. It should be understood that these embodiments are for illustrative purposes only and are not intended to limit the scope of the invention. Experimental methods in the following embodiments that do not specify specific conditions are generally performed according to conventional conditions such as those described in J. Sambrook et al., Molecular Cloning: A Laboratory Manual, Science Press, or according to the manufacturer's recommendations.

[0054] Example 1: Target gene screening

[0055] Through extensive screening, genomic analysis, and experimental analysis, the inventors identified a candidate gene, IAA23, related to rice leaf inclination angle. The gene sequence and amino acid sequence are as follows:

[0056] The gene sequence of IAA23 (T at position 238) (SEQ ID NO:1):

[0057] ATGTCGACGAGCTCCGGCGCCGACTCGTCCCCGCCCGTCTCGGGCCTCGACTACGACGACCGCCCTCACCCTCGCCCTCCCCGGCTCCTCCTCCTCCTCCTCCTCCACCGCCGACCCCGAACGCAAGCGCCGCCCACGCCGACCACGCCGACGCCAAGCCGCCTTCCCCAAAGGCGCGGGCGGTGGGGTGGCCGCCGGTGAGGGCGTACAGGCGGAACGCCTGCGGGAGGAC T CCGCGAGGGCGAAGCTGGTCAAGGTGGCCGTGGACGGCGCGCCGTACCTGCGCAAGGTGGACCTCGCGGCGCACGCCGGCTACGCGCCCCTCCTCCGCGCTCCACGCATGTTCGCCTCCTGCCTCGCCGTCCGCGGCGGCGGCGGCGGCGACGGCGAGGGTACAAAGCT CGTCGACTTGGTCACCGGCGCCGAGTACGTGCCCACCTACGAGGACAAGGACGGCGACTGGATGCTCGTCGGCGACGTCCCCTGGAAGATGTTCGTCGAGTCCTGCAAGCGGATCCGTCTCATGAAGAGCTCCGAGGCCGTCAACTTATCGCCAAGACGATCATCCAGATAA

[0058] The amino acid sequence of IAA23 (S at position 80) (SEQ ID NO:2):

[0059] MSTSSGADSSPPVSGLDYDDTALTLALPGSSSSSSSTADPERKRAAHADHADAKPPSPKARAVGWPPVRAYRRNALRED S ARAKLVKVAVDGAPYLRKVDLAAHAGYAPLLRALHGMFASCLAVRGGGGGDGEGTKLVDLVTGAEYVPTYEDKDGDWMLVGDVPWKMFVESCKRIRLMKSSEAVNLSPRRSSR*

[0060] IAA23 gene editing vector: Using CRISPR / Cas9 gene editing technology, gRNA is introduced into a CRISPR / Cas9 vector to obtain a recombinant vector for gene editing.

[0061] gRNA sequence: CCCCGGCTCCTCCTCCTCCTCCT (SEQ ID NO: 3)

[0062] IAA23 gene overexpression vector: The IAA23 gene sequence was introduced into the pCAmbia 1300 vector to obtain a recombinant vector for overexpression.

[0063] Using rice ZH11 as a background, transgenic materials were constructed using the aforementioned expression vectors, resulting in IAA23 knockout gene-edited material (iaa23-cr / ZH11) and IAA23 overexpression material (IAA23-OE / ZH11). Rice was then planted, and genetic phenotypes were observed and analyzed.

[0064] The results showed that the leaf tilt angle of the IAA23 gene-edited material with ZH11 as the background (iaa23-cr / ZH11) was significantly reduced. Conversely, the leaf tilt angle of the IAA23 overexpression material (IAA23-OE / ZH11) was significantly increased. Figure 1 ).

[0065] Therefore, it is clear that the IAA23 gene is involved in the regulation of rice leaf tilt angle.

[0066] Example 2: Analysis of Single Nucleotide Polymorphisms (SNPs) Related to Leaf Inclination Angle in IAA23 Rice

[0067] Considering the potential role of IAA23 in rice plant type domestication and differentiation between indica and japonica rice, we analyzed the single nucleotide polymorphism (SNP) of IAA23 related to rice leaf tilt angle.

[0068] Bioinformatics analysis revealed that four SNPs were likely highly correlated with leaf tilt angle: sf0623501049, sf0623501417, sf0623501964, and sf0623502256. Figure 2 As shown.

[0069] Further analysis revealed that the four SNPs exhibited significant differentiation in both indica and japonica rice, such as... Figure 2 As shown.

[0070] Two of the SNPs are located in the exon region of the gene and involve changes in amino acids. Figure 3 The details are as follows:

[0071] sf0623501417S80->A;

[0072] sf0623501964I->R。

[0073] IAA23 A The gene sequence of IAA23 (the 238th position is G) (SEQ ID NO:4):

[0074] ATGTCGACGAGCTCCGGCGCCGACTCGTCCCCGCCCGTCTCGGGCCTCGACTACGACGACACCGCCCTCACCCTCGCCCTCCCCGGCTCCTCCTCCTCCTCCTCCTCCACCGCCGACCCCGAACGCAAGCGCGCCGCCCACGCCGACCACGCCGACGCCAAGCCGCCTTCCCCAAAGGCGCGGGCGGTGGGGTGGCCGCCGGTGAGGGCGTACAGGCGGAACGCGCTGCGGGAGGAC<0​​​​​​​​​​ARAKLVKVAVDGAPYLRKVDLAAHAGYAPLLRALHGMFASCLAVRGGGGGDGEGTKLVDLVTGAEYVPTYEDKDGDWMLVGDVPWKMFVESCKRIRLMKSSEAVNLSPRRSSR*

[0077] Example 3: Relationship between SNPs or haplotypes of IAA23 and rice leaf inclination angle

[0078] The inventors further compared and analyzed the SNPs of IAA23 with the leaf inclination angles and sequences of 378 japonica rice accessions, and found that it had a strong correlation with the haplotype distribution in the maximum and minimum leaf inclination angle populations. Figure 4 ).

[0079] Sequence determination and analysis of some varieties revealed a significant distribution pattern for the second SNP (sf0623501417S80->A). Specifically, the second SNP was G (approximately 100%) in the maximum leaf angle population and T (approximately 100%) in the minimum leaf angle population. Figure 4 As shown.

[0080] Example 4: Functional Verification of the SNP of IAA23

[0081] To further verify the function of the second SNP, the inventors selected small-leaved tilted material (Nipponbare, NIP) and large-leaved tilted material (Daohuaxiang Yangzhou, DHY) as transformation backgrounds. The second SNP underwent inner circle substitution in both strains: in NIP, T was replaced with G; and in DHY, G was replaced with T. Based on the target gene and the SNP site to be substituted, gRNA sequences related to endogenous substitution were designed, ensuring high specificity and avoiding off-target effects. The designed gRNA sequences were obtained through gene synthesis technology and cloned into a specific CRISPR vector.

[0082] gRNA sequence: CCCCGGCTCCTCCTCCTCCTCCT (SEQ ID NO: 3)

[0083] After vector construction, the CRISPR system and gRNA vector were transformed into rice recipient cells using Agrobacterium-mediated transformation to target and modify the target gene. Following transformation, the gene editing effect was verified using PCR and sequencing to ensure the mutation or knockout of the target gene. By culturing and screening rice seedlings, successfully edited plants were selected for further sequence analysis to obtain gene-edited material with correctly replaced SNPs.

[0084] The successfully edited rice was planted in the field, and plant type traits such as leaf inclination angle were measured and analyzed. The results showed that in the NIP with a small inclination angle, replacing T with G increased the leaf inclination angle.

[0085] In DHYs with large tilt angles, replacing G with T also shows a significant trend towards a smaller blade tilt angle, such as... Figure 5 As shown.

[0086] Therefore, by comparing the changes in leaf tilt angle phenotype before and after editing, it can be clearly seen that the SNPs of IAA23 have a regulatory effect on rice plant type traits.

[0087] Summarize:

[0088] This invention successfully improved the plant architecture of rice by precisely regulating key genes related to leaf tilt angle. By controlling the leaf tilt angle, rice can better utilize light energy, improve photosynthetic efficiency, and thus increase yield. Furthermore, by improving the plant architecture, the lodging resistance of rice is enhanced, and its adaptability is strengthened. The method of this invention has high efficiency, accuracy, and operability, and has broad application prospects.

[0089] This invention is applicable to rice breeding and improvement, and has significant application value, particularly in increasing rice yield, optimizing rice cultivation methods, and enhancing rice lodging resistance. This technology can be widely applied in rice breeding enterprises, agricultural research institutions, and agricultural production.

[0090] The embodiments described above are merely illustrative of several implementations of the present invention, and while the descriptions are relatively specific and detailed, they should not be construed as limiting the scope of the present invention. It should be noted that those skilled in the art can make various modifications and improvements without departing from the concept of the present invention, and these all fall within the scope of protection of the present invention. Therefore, the scope of protection of this patent should be determined by the appended claims. Furthermore, all documents mentioned in this invention are incorporated herein by reference as if each document were individually incorporated by reference.

Claims

1. A method for identifying the leaf tilt angle phenotype of rice, comprising targeting the single nucleotide polymorphism at the sf0623501417 site of rice; if the site is a base T, the rice has a small leaf tilt angle and a compact plant type; if the site is a base G, the rice has a large leaf tilt angle; wherein the sf0623501417 site is located at position 238 in the sequence shown in SEQ ID NO:

1.

2. The method as described in claim 1, characterized in that, If the leaf inclination angle of rice is small, it indicates that the plant type is compact and it is a densely planted and / or lodging-resistant type of rice; if the leaf inclination angle of rice is large, it indicates that the plant type is expanded.

3. The method as described in claim 1, characterized in that, The analysis of single nucleotide polymorphisms employed methods selected from the group consisting of: sequencing, PCR amplification, probe methods, hybridization, microarray methods, restriction enzyme digestion analysis, allele polymorphism analysis, and electrophoresis. or Reagents or devices for the specific detection of single nucleotide polymorphisms may include: chips, probe sets, primer sets, primer-probe sets, restriction enzymes, electrophoresis reagents, and gene sequencing instruments.

4. Specific detection of the sf0623501417 locus in rice or rice containing this locus. IAA23 The reagents used to identify the leaf tilt angle phenotype in rice; among them, The reagent is used to detect the single nucleotide polymorphism at the sf0623501417 site; The rice variety is identified by detecting the single nucleotide polymorphism at the sf0623501417 site. If the site contains the base T, the rice has a small leaf inclination angle and a compact plant type; if the site contains the base G, the rice has a large leaf inclination angle. The IAA23 The nucleotide sequence of the gene is shown in SEQ ID NO: 1, where the base type corresponding to the sf0623501417 position includes either a T base or a G base; wherein the sf0623501417 position is located at position 238 of the SEQ ID NO: 1 sequence; The IAA23 The amino acid sequence of the gene-encoded protein is shown in SEQ ID NO: 2, wherein the amino acid residue corresponding to the sf0623501417 position is located at position 80 of the SEQ ID NO: 2 sequence, and its type includes S or A.

5. The use as described in claim 4, characterized in that, Using the rice sf0623501417 locus as a target, the rice plant compactness, dense planting and / or lodging resistance can be predicted or analyzed by analyzing the rice leaf tilt angle phenotype.

6. The use as described in claim 4, characterized in that, The reagent or device includes primers and probes for detecting regions containing the rice sf0623501417 site.

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