Rice SDR1 gene, its encoded protein and application thereof

Abstract

The application relates to a gene SDR1 for adjusting plant height. The nucleotide sequence of the SDR1 gene is shown in the nucleotide sequence of SEQ ID NO:1 or SEQ ID NO:2, and one or more nucleotides are added, replaced, inserted or deleted to generate a mutant, allele or derivative. Through phenotype analysis, genetic analysis, gene cloning and expression analysis of the dwarf mutant screened, it is determined that the gene is involved in the regulation of rice plant height development, and a foundation is laid for further analyzing the molecular regulation network of rice stem development. The gene SDR1 has a significant effect on further adjustment of the dwarf rice plant height, and therefore has an important influence on optimization of the dwarf rice plant type.

Description

Technical Field

[0001] This invention relates to the field of plant molecular breeding, and more particularly to the rice SDR1 gene, its encoded protein, and its applications. Background Technology

[0002] Rice plant architecture is an important agronomic trait that generally affects many agronomic traits of the plant, especially yield. Among rice plant architecture traits, plant height is an important agronomic trait that has a significant impact on rice growth and development, yield, and stress resistance.

[0003] Plant height has a multifaceted impact on rice, and breeding requires comprehensive consideration of factors such as plant height and yield, stress resistance, photosynthetic efficiency, nutrient absorption, irrigation and drainage, and harvesting difficulty.

[0004] Plant height has a significant impact on the following aspects of rice: stress resistance, photosynthetic efficiency, nutrient absorption, irrigation and drainage, and harvesting difficulty.

[0005] (1) Resistance: Rice varieties with taller plants may be less resistant to pests and diseases, as tall rice is more susceptible to pests and diseases. Tall rice is also more prone to lodging in windy and rainy weather, which affects its growth and yield.

[0006] (2) Photosynthetic efficiency: Rice varieties with appropriate plant height can utilize light energy more effectively for photosynthesis, thereby accumulating more organic matter and promoting growth. Excessive plant height may cause leaves to shade each other, reducing photosynthetic efficiency.

[0007] (3) Nutrient absorption: Rice varieties with taller plant height require more nutrients to support their growth, which may place higher demands on the soil's nutrient absorption capacity. Rice varieties with suitable plant height can absorb nutrients from the soil more effectively, promoting healthy plant growth.

[0008] (4) Irrigation and drainage: Rice varieties with taller plant height require more meticulous irrigation and drainage management to prevent root hypoxia caused by prolonged water soaking. Appropriate rice plant height helps maintain suitable soil moisture, which is beneficial to root growth and plant health.

[0009] (5) Harvesting difficulty: Rice varieties with taller plants are more difficult to harvest and require more labor and time.

[0010] However, with the introduction of the rice gene sd1 (semi dwarf-1), the introduction of a plant height-related gene resolved the contradiction between high fertilization and lodging in rice cultivation, endowing rice with lodging resistance, tolerance to high fertilization, and tolerance to dense planting, thereby greatly increasing rice yield. Therefore, the discovery and cloning of rice dwarf genes is of great significance for breeding high-yielding and lodging-resistant varieties.

[0011] In recent years, numerous genes related to plant height have been discovered in rice, most of which are involved in plant hormone metabolism and signal transduction, such as gibberellin (GA), brassinosteroid (BR), strigolactone (SL), and abscisic acid (ABA). Rice OsKO2 (ent-kaureneoxidase2) encodes a kaurene oxidase that catalyzes an early step in GA biosynthesis. Reduced expression of OsKO2 affects GA biosynthesis in rice, leading to shortened internodes and dwarfing. The gene sd1 encodes a 20-oxidase in the GA biosynthesis pathway; mutations in this gene affect later steps in the GA biosynthesis pathway, thus reducing plant height. EUI encodes a cytochrome P450 monooxygenase that regulates GA content by converting active GA to inactive GA. Therefore, enhanced function or excessive accumulation of the EUI protein can lead to shortened internodes and reduced plant height in rice. GID1 (GA-insensitive dwarf mutant 1) encodes a GA signal receptor and plays an important role in regulating rice plant height by mediating GA signal transduction.

[0012] Besides glycosidic acid (GA), broiler (BR) is also a decisive factor in controlling plant height. BRD1 (BR-DEFICIENT DWARF1) encodes a BR-6 oxidase belonging to the cytochrome P450 family. This enzyme is a key enzyme in rice BR biosynthesis, and its mutants exhibit the typical BR-deficient phenotype of severe dwarfing and reduced leaf angle. Furthermore, D2 (DWARF2), D11, and OsDWARF4 also control rice plant height by regulating BR synthesis. Mutations in the rice BR signaling receptor OsBRI1 (Brassinosteroid-Insensitive1) gene also lead to semi-dwarfing, erect leaves, and BR insensitivity. After BR is captured by OsBRI1 on the cell surface, it transmits signals to transcription factors OsBZR1 (BRASSINAZOLE RESISTANT 1), BU1 (BRASSINOSTEROID UP-REGULATED 1), and DLT (DWARF AND LOW-TILLERING) via intracellular cascade phosphorylation. This alters the activity, protein stability, or subcellular localization of these transcription factors, ultimately affecting the expression of a large number of genes. Mutants of the above transcription factors all exhibit semi-dwarfing of plant height.

[0013] Mutations in genes related to the SL signaling pathway often lead to changes in tiller number and plant height. The rice D3 gene encodes a leucine-rich repeat-enriched F-box protein that forms a complex with the SL signaling receptor D14 to mediate the degradation of the downstream protein D53. Loss-of-function mutants of both D3 and D14 exhibit shorter stature and more tillers. Conversely, gain-of-function mutants of D53 show increased tiller number and decreased plant height. ABA has a negative regulatory effect on rice growth, typically antagonizing GA, thus leading to plant dwarfing. For example, the activity of rice OsSAPK1O (Stress-Activated Protein Kinase 10) is ABA-dependent; its overexpression downregulates the expression level of GA synthesis genes, reduces the content of active GA, and ultimately inhibits internode elongation and reduces plant height.

[0014] Currently, the control of rice plant height and lodging resistance is mainly based on the sd1 gene, which was discovered in the 1960s. In the new era, intensive rice production faces a series of challenges from changes in cultivation conditions, such as direct seeding, simplified cultivation, and mechanized operations, which place higher demands on rice plant architecture and lodging resistance.

[0015] Theoretically, further slight dwarfing of plant height is needed under the SD1 model to cultivate a "dwarf-to-dwarf" rice variety, thereby further improving its lodging resistance. Further dwarfing regulation of plant height in dwarf rice is a complex breeding technique, and its difficulty lies mainly in the following aspects:

[0016] (1) Precise positioning of breeding objectives

[0017] In the context of the sd1 gene, it is necessary to accurately control the degree of dwarfing to ensure that rice can meet production needs while maintaining good lodging resistance.

[0018] (2) Complex regulation of the genome

[0019] The rice genome contains numerous genes related to plant height and lodging resistance, and the interactions and regulatory mechanisms among these genes are complex. Achieving precise regulation within the sd1 gene context presents a challenge in molecular breeding research.

[0020] Because most reported rice dwarfing mutants exhibit drastic changes in plant height, severely impacting yield, they are difficult to apply in practical breeding. Furthermore, there is a severe lack of "fine-tuning genes" capable of slightly dwarfing plant height in the sd1 background.

[0021] This application identifies the genes involved in regulating rice plant height development and stem internode development through phenotypic analysis, genetic analysis, gene cloning, and expression analysis of degenerate mutants obtained from field screening. This lays the foundation for further analysis of the molecular regulatory network of rice stem development and provides gene resources for breeding applications.

[0022] Furthermore, on the one hand, there are differences in understanding among those skilled in the art; on the other hand, the applicant studied a large number of documents and patents when making this invention, but due to space limitations, not all details and contents were listed in detail. However, this does not mean that the present invention does not possess the features of these prior art. On the contrary, the present invention already possesses all the features of the prior art, and the applicant reserves the right to add relevant prior art to the background art. Summary of the Invention

[0023] This application further reduces plant height slightly under the background of sd1, and cultivates a new plant type of rice with significantly enhanced lodging resistance but no significant reduction in yield, in order to meet the needs of intensive rice production in the new era.

[0024] This application relates to a gene SDR1 that regulates plant height. More specifically, this application also relates to a rice plant height regulating gene SDR1. The nucleotide sequence of the SDR1 gene is shown in SEQ ID NO: 1 or SEQ ID NO: 2, or a mutant, allele, or derivative can be generated by adding, substituting, inserting, or deleting one or more nucleotides in the nucleotide sequence shown in SEQ ID NO: 1 or SEQ ID NO: 2.

[0025] This application, in another aspect, relates to a protein that regulates plant height. The protein is encoded by the rice height-regulating gene SDR1, and its amino acid sequence is shown in SEQ ID NO: 3. The protein sequence of the SDR1 gene is shown in A1), A2), or A3) below:

[0026] A1)SEQ ID NO: 3;

[0027] A2) is a protein derived from rice that has more than 90% similarity to A1) protein and has the same function;

[0028] A3) is a fusion protein obtained by attaching a tag to the N-terminus and / or C-terminus of A1) or A2).

[0029] Another aspect of this application relates to a mutant gene of rice plant height regulating gene SDR1. The mutation site of rice plant height regulating gene SDR1 contains one or more 217-base and 458-base sites.

[0030] This application relates in another aspect to a protein. Preferably, the protein is encoded by a rice plant height mutant gene, the amino acid sequences of which are shown in SEQ ID NO:4 and SEQ ID NO:5, respectively. Preferably, the protein comprises a protein that regulates plant height by having one or more of the following mutation sites, the mutation sites comprising:

[0031] The glutamine at position 73 is mutated to a stop codon;

[0032] The leucine at position 153 was mutated into proline.

[0033] Another aspect of this application relates to a vector containing a gene that regulates plant height. The vector contains the rice plant height regulating gene SDR1 or a rice plant height mutant gene.

[0034] Another aspect of this application relates to the application of the rice plant height regulating gene SDR1, the rice plant height mutant gene, the vector containing the rice plant height mutant gene, or the vector containing the rice plant height regulating gene SDR1 in rice breeding.

[0035] Another aspect of this application relates to any of the following applications of a protein, including: application in increasing internode length in rice; application in reducing lodging rate in rice, wherein the protein is a protein of the following A1) or A2): A1) amino acid sequence as shown in SEQ ID NO: 3; A2) fusion protein obtained by attaching a protein tag to the N-terminus and / or C-terminus of A1).

[0036] This application relates in another aspect to any of the following applications of the SDR1 gene, including: application in increasing internode length in rice; application in reducing lodging rate in rice, wherein the SDR1 gene is a gene as follows A1) or A2): A1) nucleotide sequence as shown in SEQ ID NO: 1; A2) nucleotide sequence as shown in SEQ ID NO: 2.

[0037] Another aspect of this application relates to a non-viable or non-renewable plant product. The plant product comprises one of the following: a non-viable or non-renewable plant part and the vector involved in this application; the vector involved in this application; a protein sequence of the SDR1 gene as shown in A1), A2), or A3) below; a nucleotide sequence as shown in SEQ ID NO: 1 or SEQ ID NO: 2, or a nucleotide sequence in which one or more nucleotides are added, substituted, inserted, or deleted to generate a mutant, allele, or derivative as shown in SEQ ID NO: 1 or SEQ ID NO: 2.

[0038] Another aspect of this application relates to non-viable or non-renewable plant products made from parts of transgenic rice plants. The plant product comprises one of the following: a non-viable or non-renewable plant part and the vector involved in this application; the vector involved in this application; a protein sequence of the SDR1 gene as shown in A1), A2), or A3) below; a nucleotide sequence as shown in SEQ ID NO: 1 or SEQ ID NO: 2, or a nucleotide sequence in which one or more nucleotides are added, substituted, inserted, or deleted to generate a mutant, allele, or derivative, as shown in SEQ ID NO: 1 or SEQ ID NO: 2.

[0039] Another aspect of this application relates to the application of the rice plant height regulating gene SDR1, the rice plant height mutant gene, a vector containing the rice plant height mutant gene, or a vector containing the rice plant height regulating gene SDR1 in improving the plant height of tall rice.

[0040] Another aspect of this application relates to a gene for regulating the length of internodes in rice, the nucleotide sequence of which is shown in SEQ ID NO: 1 or SEQ ID NO: 2.

[0041] Another aspect of this application relates to a protein that regulates the length of internodes in rice, the protein being encoded by a gene with a nucleotide sequence as shown in SEQ ID NO: 1 or SEQ ID NO: 2 and an amino acid sequence as shown in SEQ ID NO: 3.

[0042] Another aspect of this application relates to a cell or strain containing the rice plant height regulating gene SDR1.

[0043] According to a preferred embodiment, the strain is Agrobacterium or Escherichia coli.

[0044] Another aspect of this application relates to the application of the SDR1 gene in controlling plant height and lodging resistance.

[0045] This application also relates to a method for reducing rice plant height. The method includes one or more of the following:

[0046] Reduce the protein content of SDR1 gene expression in recipient rice;

[0047] Reduce or block the activity of proteins expressed by the SDR1 gene in recipient rice;

[0048] Reduce or block the proper expression of the SDR1 gene in recipient rice.

[0049] Rice with reduced plant height was obtained, among which,

[0050] The proteins expressed by the SDR1 gene are as follows: A1), A2), or A3):

[0051] A1) Proteins expressed by the SDR1 gene;

[0052] A2) is a protein derived from rice that has more than 90% similarity to A1) protein and has the same function;

[0053] A3) is a fusion protein obtained by attaching a tag to the N-terminus and / or C-terminus of A1) or A2).

[0054] Preferably, the method includes transferring a rice plant height mutant gene or a vector containing a rice plant height mutant gene into the desired improved tall rice variety.

[0055] Another aspect of this application relates to a method for improving lodging resistance in rice. The method includes the following steps: gene editing of the SDR1 gene in recipient rice to obtain gene-edited rice; compared with recipient rice, the plant height of the gene-edited rice is improved.

[0056] Another aspect of this application relates to a method for improving the plant height of tall rice or enhancing its lodging resistance. The method includes one or more of the following:

[0057] Reduce the protein content of SDR1 gene expression in recipient rice;

[0058] Reduce or block the activity of proteins expressed by the SDR1 gene in recipient rice;

[0059] Reduce or block the correct expression of the SDR1 gene in recipient rice.

[0060] Another aspect of this application relates to the application of the SDR1 gene in controlling internode length in plants.

[0061] This application also relates to a method for reducing the length of rice internodes. The method includes one or more of the following:

[0062] Reduce the protein content of SDR1 gene expression in recipient rice;

[0063] Reduce or block the activity of proteins expressed by the SDR1 gene in recipient rice;

[0064] Reduce or block the proper expression of the SDR1 gene in recipient rice.

[0065] Rice varieties with reduced internode length were obtained, among which...

[0066] The proteins expressed by the SDR1 gene are as follows: A1), A2), or A3):

[0067] A1) Proteins expressed by the SDR1 gene;

[0068] A2) is a protein derived from rice that has more than 90% similarity to A1) protein and has the same function;

[0069] A3) is a fusion protein obtained by attaching a tag to the N-terminus and / or C-terminus of A1) or A2).

[0070] Another aspect of this application relates to the application of the SDR1 gene in controlling plant stem diameter.

[0071] This application, in another aspect, relates to a method for increasing the diameter of rice stems. The method includes one or more of the following:

[0072] Reduce the protein content of SDR1 gene expression in recipient rice;

[0073] Reduce or block the activity of proteins expressed by the SDR1 gene in recipient rice;

[0074] Reduce or block the proper expression of the SDR1 gene in recipient rice.

[0075] Rice with increased stem diameter was obtained, among which,

[0076] The proteins expressed by the SDR1 gene are as follows: A1), A2), or A3):

[0077] A1) Proteins expressed by the SDR1 gene;

[0078] A2) is a protein derived from rice that has more than 90% similarity to A1) protein and has the same function;

[0079] A3) is a fusion protein obtained by attaching a tag to the N-terminus and / or C-terminus of A1) or A2).

[0080] Another aspect of this application relates to a gene or protein, SDR1, that regulates rice plant height.

[0081] Another aspect of this application relates to the inactivation and downregulation of the gene SDR1 or protein SDR1 in various forms, and to mutant strains of SDR1 (including possible forms such as knockout, RNAi, and natural variants).

[0082] This application also relates to SDR1 gene or SDR1 protein inactivation mutants sdr in various backgrounds such as indica and japonica rice.

[0083] Another aspect of this application relates to the use of the RING-H2 finger domain of a protein encoded by the SDR1 gene in the function of internode length or plant height. Preferably, this application relates to a method for regulating internode length or plant height in plants (e.g., rice), the method comprising truncating the RING-H2 finger domain of a protein encoded by the SDR1 gene. Regulating internode length or plant height in plants (e.g., rice) refers to reducing plant height or decreasing internode length.

[0084] Another aspect of this application relates to the application of gene SDR1 or protein SDR1 or materials related to the regulation of gene SDR1 or protein SDR1 in regulating rice plant height and lodging resistance.

[0085] This application, on the other hand, relates to plasmids, strains, or plants containing any of the above-mentioned variants of the gene SDR1 or protein SDR1, and their use in regulating plant height or lodging resistance.

[0086] Another aspect of this application relates to the application of a plant in improving lodging resistance in rice, such as by crossbreeding into other backgrounds to improve lodging resistance in rice.

[0087] This invention provides a novel rice semi-dwarf gene, SDR1, and its encoded protein. By knocking out or inactivating this gene using CRISPR / Cas9 editing technology and other methods, the inventors found that this gene can moderately reduce the plant height of crops such as rice (a 20% reduction) and significantly improve the crop's lodging resistance (ZH11's maximum bending strength is 9.7 N, while sdr1-3's is 14.5 N; ZH11's lodging index is 176, while sdr1-3's is 114), thus maintaining crop yield stability. Therefore, this gene has clear application potential in the field of breeding.

[0088] By combining EMS mutagenesis with precise phenotypic identification, mutants (sdr1-1 and sdr1-2) with slight dwarfing of plant height under the sd1 background were created. Using genetic and molecular biology techniques, the "fine-tuning gene" SDR1, which can slightly dwarf plant height under the sd1 background, was cloned. Genetic techniques such as gene editing confirmed that inactivation of this gene (sdr1-3 and sdr1-4) can reduce plant height and significantly increase lodging resistance. This application screened mutants that finely tune rice plant height and successfully cloned the SDR1 gene. Knocking out this gene in japonica rice ZH11 material using CRISPR / Cas9 technology significantly reduced rice plant height and significantly enhanced lodging resistance, but had no significant impact on yield.

[0089] The rice mutants sdr1-1 and sdr1-2 provided by this invention both exhibit dwarfed plant height, providing two short-stemmed germplasm resources for rice and new gene resources for the next step of dwarfing breeding. They effectively reduce the plant height trait of tall rice varieties, enrich the genetic diversity of rice, and have broad application prospects in optimizing rice plant type. Attached Figure Description

[0090] Figure 1 Phenotypic analysis of the sdr1 mutant; A-C: Comparison of plant type between WT and sdr1 mutants; D-E: Internode trait analysis between WT and sdr1 mutants; F-H: Internode cytological analysis of mutants; I-O: Comparison of yield-related traits between WT and sdr1 mutants;

[0091] Figure 2 The process involves the cloning and validation of the SDR1 gene; A: MutMap screening for sdr1 mutation sites; B: Schematic diagram of the SDR1 gene protein structure; C-N: Observation and measurement of agronomic traits of SDR1 knockout mutants.

[0092] Figure 3 This section presents the lodging resistance and yield analysis of the SDR1 knockout mutant (sdr1-3); A-B: Lodging conditions of ZH11 and sdr1-3 in the field; C: Representative plants in the A / B diagram; D-F: Observation and measurement of stem cross-sections of ZH11 and sdr1-3; G: Maximum bending strength of ZH11 and sdr1-3 stems; H: Lodging index of ZH11 and sdr1-3; I: Comparison of actual yields of ZH11 and sdr1-3 plots. Detailed Implementation

[0093] The following is a detailed explanation with reference to the accompanying drawings.

[0094] For those skilled in the art, the specific meaning of the terms in this invention can be understood according to the specific circumstances. Unless otherwise specified, the experimental procedures described in the following embodiments are conventional procedures. Unless otherwise specified, the reagents and other materials used in the following embodiments are commercially available.

[0095] For a long time, due to the difficulty of phenotypic research, genetic studies on rice plant height have mostly focused on dwarf mutants with drastic variations in plant height. Although many genes have been cloned, overall, these mutants exhibit excessive variations in plant height, severely impacting yield and making them difficult to apply in practical breeding.

[0096] The specific experimental methods designed in this application are as follows:

[0097] 1. Obtaining and identifying the sdr1 mutant

[0098] Screening of the R600 mutant library yielded two mutant materials, sdr1-1 and sdr1-2, with a slight decrease in plant height. Compared to the wild type (WT), both sdr1-1 and sdr1-2 showed a decrease in plant height of approximately 25%. Figure 1 As shown in A and 1B. Compared to the wild type (WT), sdr1-1 and sdr1-2 are semi-dwarfed with a slightly increased number of tillers, as shown in A and B. Figure 1 As shown in C. Anatomical analysis shows, as Figure 1 As shown in D and 1E, the decreased plant height of the mutant is due to shortened internodes. Further cytological observations indicate that, as Figure 1 As shown in F to H, the reduction in the length of intersegmental cells is the main reason for intersegmental shortening.

[0099] Furthermore, this application also investigated the yield-related traits of SDR1-1 and SDR1-2, and the results showed that, Figure 1 As shown in I to O, although the seed setting rate of these two mutants decreased slightly, their number of grains per ear, grain length, grain width, and thousand-grain weight did not change significantly compared with the wild type.

[0100] Genetic analysis showed that the traits of both the sdr1-1 and sdr1-2 mutants were controlled by a recessive single gene. It is noteworthy that, for example... Figure 1 As shown in A, the hybrid offspring of these two mutants also exhibited traits similar to their parents, indicating that the phenotypes of these two mutants may be caused by a pair of allele mutations on the same gene.

[0101] 2. Gene localization cloning and functional verification

[0102] To locate and clone the SDR1 gene, this application randomly selected 50 individuals with mutant phenotypes from the BCF2 populations of sdr1-1 and sdr1-2 for pooled sequencing. The R600 genome assembled by our team was used as a reference sequence, and analysis was performed using the MutMap method. The results showed that LOC_Os08g06090 is the SDR1 gene controlling this phenotype, and its CDS sequence is shown in SEQ ID NO.1. The amino acid sequence encoded by this gene is shown in SEQ ID NO.3, consistent with previous genetic analysis results. The amplification primers were: ATGGGGTTCCCGTCGGTG and TCAGAAGGAGGGGAGGTGG.

[0103] Furthermore, such as Figure 2 As shown in Figure A, the results indicate that two SNPs of the same candidate gene are linked to the mutant phenotypes of sdr1-1 and sdr1-2, respectively.

[0104] like Figure 2As shown in B, the candidate gene encodes a previously unreported RING-type E3 ubiquitin ligase containing a leucine zipper and a RING-H2 finger domain. The sdr1-1 mutation is located between the leucine zipper and the RING-H2 finger, as shown in Figure B. Figure 2 As shown in B, the mutation leads to premature termination of protein translation. Figure 2 As shown in Figure B, the sdr1-2 mutation is located precisely in the RING-H2 finger domain, causing the amino acid to change from leucine (Leu) to proline (Pro). Based on this result, this application confirms that the loss of function in the RING-H2 finger domain can affect the function of the candidate gene (SDR1 gene) in internode length or plant height.

[0105] This application uses a method of gene editing of candidate genes in the context of Japonica rice ZH11 using CRISPR / Cas9 technology to verify the function of candidate genes.

[0106] Sequencing results showed that, Figure 2 As shown in B, the transgenic plants sdr1-3 and sdr1-4 had deletions of 5 and 2 base pairs, respectively, at their corresponding target sites, indicating that the candidate genes were successfully knocked out in these two lines.

[0107] Through protein structure prediction and other methods, we found that the amino acids corresponding to the above-mentioned action sites belong to the key functional domains of proteins. Therefore, changes in the above-mentioned sites can be used for screening and detection of dwarf plants in actual production processes.

[0108] Subsequently, agronomic traits, including plant height, were examined in the knockout lines (SDR1-3 and SDR1-4), such as... Figure 2 As shown in C and 2F, the results indicate that the natural ZH11 strain has a plant height of 112 cm, the knockout strain sdr1-3 has a plant height of 92 cm, and the knockout strain sdr1-4 has a plant height of 91 cm. The plant height of the knockout strains also decreased by approximately 20%.

[0109] like Figure 2As shown in D and 2G, the upper internodes were also significantly shortened. The first internode of the natural ZH11 line was 42 cm, while that of the knockout line sdr1-3 was 33 cm and that of the knockout line sdr1-4 was 35 cm. The second internode of the natural ZH11 line was 20 cm, while that of the knockout lines sdr1-3 and sdr1-4 was 18 cm. The third internode of the natural ZH11 line was 17 cm, while that of the knockout lines sdr1-3 and sdr1-4 was 15 cm and 14 cm. The fourth internode of the natural ZH11 line was 13 cm, while that of the knockout lines sdr1-3 and sdr1-4 was 10 cm and 10 cm, respectively. The fifth internode length of the natural ZH11 line was 5 cm, while that of the knockout line sdr1-3 was 3 cm and that of the knockout line sdr1-4 was 4 cm. The results indicate that, compared to the wild-type ZH11, all internode lengths were shortened in the knockout lines sdr1-3 and sdr1-4.

[0110] The phenotype of the gene-silenced strains was consistent with that of the gene-mutant strains sdr1-1 and sdr1-2, both exhibiting a semi-dwarf morphology.

[0111] In addition, the investigation of yield-related agronomic traits revealed that, such as Figure 2 E and Figure 2 As shown in H-N, the knockout lines exhibited similar tiller number, seed setting rate, number of grains per panicle, grain type, and thousand-grain weight to ZH11, indicating that the functional mutation of SDR1 in the ZH11 genetic background has no adverse effect on yield. These results confirm that the gene in question is indeed SDR1, and its inactivation leads to a reduction in rice plant height.

[0112] Internode length affects a plant's lodging resistance. While longer internodes contribute to greater plant height, they may reduce the plant's mechanical strength, making rice more susceptible to lodging from external factors such as wind and rain. Therefore, compared to the wild type, SDR1-1, SDR1-2, SDR1-3, and SDR1-4 exhibit stronger lodging resistance (especially under harsh natural conditions) and more stable growth. In particular, by comparing the internode lengths of mutant plants, gene-edited plants, and wild-type plants, the applicant found that SDR1 had the greatest impact on the first stem node of rice, shortening it by 7-9 cm compared to other stem nodes (2-3 cm shorter). This shortening of the first stem node lowers the rice's center of gravity, increasing the risk of lodging in both morphology and height.

[0113] Meanwhile, the length of the xylem and phloem distributed in the internodes of rice also affects nutrient transport. Xylem is responsible for the transport of water and minerals, typically moving upwards along the stem from the roots. Phloem is responsible for the transport of organic nutrients, from the photosynthetic sites to other parts of the plant. Shortened internodes in mutants mean a shorter nutrient transport pathway (shorter nutrient transport time), but also that the regulation of nutrient transport in the internodes can be regulated more quickly. Therefore, compared to the wild type, sdr1-1, sdr1-2, sdr1-3, and sdr1-4 can also respond more quickly to stress resistance, helping rice to more rapidly report its abnormalities to growers through phenotypic changes.

[0114] 3. Lodging resistance assessment of SDR1

[0115] Lodging is a significant factor limiting rice production. During production practice, the inventors discovered that ZH11, due to its large panicle weight, experienced lodging when planted in the Chengdu Plain. Therefore, this application further obtained observational data related to the lodging resistance of the SDR1 knockout mutant (sdr1-3). The results showed that in the natural field conditions of Wenjiang, Chengdu, the parental ZH11 experienced severe lodging in the summers of 2022 and 2023 (with 2-3 severe storms and heavy rains during the maturity period), while sdr1-3 planted at the same time and of the same size did not exhibit any lodging. Figure 3 (A~C). The results of observation and measurement of stem diameter and stem wall thickness show that, Figure 3 As shown in D and 3E, the stem diameter of ZH11 is 6.6 mm, and the stem diameter of sdr1-3 is 7.1 mm. Figure 3 As shown in Figure F, the stem wall thickness of ZH11 is 1.2 mm, while that of sdr1-3 is 1.6 mm. The results indicate that the stems of sdr1-3 are thicker than those of ZH11.

[0116] Stem diameter and wall thickness are important indicators of a plant's resistance to lodging and structural strength. SDR1-3 stems not only have a larger diameter but also thicker walls, indicating a more stable and robust structure. This characteristic makes SDR1-3 stems more resistant to external forces such as wind and rain, reducing the risk of lodging. Furthermore, thicker stems may also signify better nutrient and water transport capabilities, thus supporting the overall growth and development of the plant.

[0117] Further analysis of maximum flexural strength and lodging index showed that, Figure 3 As shown in G, the maximum flexural strength of ZH11 is 9.7 N, while the maximum flexural strength of SDR1-3 is 14.5 N. Figure 3 As shown in Figure H, the lodging index of ZH11 is 176, while that of SDR1-3 is 114. The results show that SDR1-3 has significantly enhanced lodging resistance.

[0118] Furthermore, combined with the above-mentioned measured stem wall thickness, the data results of the flexural strength tested in this application also demonstrate that the gene-inactivated rice plants obtained based on the above-mentioned site mutations have significant effects on reducing damage to rice during transportation and storage and improving the operability of rice during mechanized harvesting.

[0119] It is worth noting that, such as Figure 3 As shown in Figure I, the yield measurement results from a small-scale trial showed that the yield of SDR1-3 was not significantly different from that of ZH11, indicating that functional mutations in the SDR1 gene under the ZH11 genetic background do not lead to yield loss. Therefore, SDR1 is of great significance for dwarfing and lodging-resistant breeding.

[0120] The sequence is shown in Table 1.

[0121] Table 1

[0122]

[0123]

[0124]

[0125] It should be noted that the specific embodiments described above are exemplary. Those skilled in the art can devise various solutions inspired by the disclosure of this invention, and these solutions all fall within the scope of this invention and its protection. Those skilled in the art should understand that this specification and its accompanying drawings are illustrative and do not constitute a limitation on the claims. The scope of protection of this invention is defined by the claims and their equivalents. This specification contains multiple inventive concepts; phrases such as "preferredly" and "according to a preferred embodiment" indicate that the corresponding paragraph discloses an independent concept. The applicant reserves the right to file divisional applications based on each inventive concept. Throughout the text, the feature introduced by "preferredly" is only an optional mode and should not be construed as mandatory. Therefore, the applicant reserves the right to abandon or delete relevant preferred features at any time.

Claims

1. A method for improving plant height, reducing internode length, or improving resistance to lodging in a high-stalk rice plant, the method comprising, Comprising reducing or blocking the correct expression of SDR1 gene in the recipient rice, wherein the SDR1 gene is rice LOC_Os08g06090 gene.

2. The method of claim 1, wherein, The SDR1 gene is the gene of A1) or A2) as follows: A1) the nucleotide sequence shown as SEQ ID NO: 1; A2) the nucleotide sequence shown as SEQ ID NO:

2.

3. The method of claim 2, wherein, The reducing or blocking the correct expression of SDR1 gene in the recipient rice refers to mutating base C at position 217 to T and / or mutating base T at position 458 to C of SEQ ID NO:

2.

4. A method for improving plant height, reducing internode length, or improving resistance to lodging in a high-stalk rice plant, the method comprising introducing into a high-stalk rice plant a nucleic acid encoding a polypeptide having the amino acid sequence of SEQ ID NO: 2, wherein the nucleic acid is operably linked to a promoter that drives expression in a high-stalk rice plant. Comprising: reducing the content of the protein expressed by SDR1 gene in the recipient rice; and / or reducing or blocking the activity of the protein expressed by SDR1 gene in the recipient rice; wherein the SDR1 gene is rice LOC_Os08g06090 gene.

5. The method of claim 4, wherein, The protein is the protein as follows: the amino acid sequence shown as SEQ ID NO:

3.

6. The method of claim 5, wherein, The reducing or blocking the activity of the protein expressed by SDR1 gene in the recipient rice refers to mutating glutamine at position 73 to a stop codon and / or mutating leucine at position 153 to proline of SEQ ID NO: 3.

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