SNP site related to corn plant height and reagent, kit for detecting the site and application

Abstract

The application provides a SNP site related to corn plant height, and a reagent, a kit for detecting the site and application. Specifically, the SNP site is located at position 96117284 of chromosome 6 by positioning with a corn genome B73v3 reference sequence genome. The SNP site is closely related to the corn plant height trait, and can be used as a powerful marker to predict the future plant height of corn. This provides a new screening method for breeding new corn varieties with high plant height, helps to speed up the breeding process and improve the breeding efficiency, and the results of the research will provide important theoretical and practical guidance for agricultural production.

Description

Technical Field

[0001] This invention relates to the field of biotechnology, specifically to a SNP locus associated with maize plant height and reagents, kits, and applications for detecting this locus. More specifically, this invention relates to uses, isolated nucleic acids, vectors, recombinant cells, transgenic maize plants, methods for producing tall maize plants, primer sets, kits, methods for identifying or assisting in the identification of maize plant height, and methods for breeding tall maize plants. Background Technology

[0002] Maize (scientific name: Zea mays) is an important food crop and one of the most important crops globally. Belonging to the Poaceae family, maize is an annual herbaceous plant. It exhibits high adaptability and wide genetic diversity. A distinctive feature of maize is its inflorescence, also called an ear, which bears ears of caryopsis (fruits). Each ear typically contains numerous kernels, called maize seeds or maize kernels, which are the main edible part of the maize plant.

[0003] Plant height refers to the distance from the ground level (root collar) to the top of the corn plant, usually measured in centimeters. Taller plants have a larger photosynthetic surface area, enabling them to absorb more sunlight and carbon dioxide, thus producing more nutrients. Therefore, there is an urgent need to develop a method for breeding taller corn plants to obtain corn varieties that better meet practical production requirements. Summary of the Invention

[0004] The present invention aims to solve at least one of the technical problems existing in the prior art.

[0005] The inventors discovered that at the genomic level, maize plant height, as a quantitative trait, is influenced by multiple genes, and its genetic basis remains unclear. To overcome this problem, the inventors applied a novel marker, single nucleotide polymorphism (SNP), to the genetic research of maize plant height, thereby selecting maize plants with taller plants and overcoming the shortcomings of conventional breeding methods, such as long breeding cycles, large workload in later screening, and low efficiency in identifying varieties or lines.

[0006] Based on this, the first aspect of the present invention proposes the use of SNP loci in the selection of tall maize plants, located on chromosome 6 at position 96117284, using the maize genome B73 v3 reference sequence. Through gene analysis of a large number of maize samples, the inventors discovered a close association between the nucleotide at position 96117284 on chromosome 6 of the maize genome B73 v3 reference sequence and the maize plant height trait. Genetic variation at this locus is closely related to differences in plant height, thus serving as a powerful marker for predicting maize plant height, overcoming the drawbacks of conventional breeding methods such as long cycles, heavy workload in later screening stages, and low efficiency in identifying varieties or lines. This provides a new screening method for breeding tall maize varieties, helping to accelerate the breeding process and improve breeding efficiency.

[0007] In a second aspect, this invention proposes the use of a reagent for detecting SNP loci in the breeding of tall maize plants. The SNP locus is located at position 96117284 on chromosome 6, using the maize genome B73 v3 reference sequence. As mentioned earlier, this SNP locus is closely associated with maize plant height. Therefore, a reagent for detecting this SNP locus can quickly and accurately predict the height of maize plants, thereby assisting in breeding and overcoming the shortcomings of conventional breeding methods, such as long cycles, heavy workload in later screening stages, and low efficiency in identifying varieties or lines. This detection reagent can provide information about maize plant height in a short time, thus accelerating the screening process.

[0008] In a third aspect, this invention proposes the use of a reagent for mutating SNP sites in the breeding of tall maize plants. The SNP site is located at position 96117284 on chromosome 6, using the maize genome B73 v3 reference sequence. As mentioned earlier, this SNP site is closely associated with the plant height trait of maize plants. Therefore, a reagent for mutating this SNP site can transform ordinary or tall maize plants into tall maize plants, thereby breeding tall maize plants and overcoming the shortcomings of conventional breeding methods, such as long breeding cycles, large workload in later screening stages, and low efficiency in identifying varieties or lines.

[0009] In a fourth aspect, this invention proposes the use of a reagent for overexpressing a SNP site in the breeding of tall maize plants. The SNP site is located at position 96117284 on chromosome 6, using the maize genome B73 v3 reference sequence. As mentioned earlier, this SNP site is closely associated with the plant height trait of maize plants. Therefore, a reagent for overexpressing this SNP site can transform ordinary or short-height maize plants into tall-height maize plants, thereby breeding tall maize plants and overcoming the shortcomings of conventional breeding methods, such as long breeding cycles, large workload in later screening stages, and low efficiency in identifying varieties or lines.

[0010] In a fifth aspect, the present invention provides an isolated nucleic acid. According to embodiments of the present invention, the isolated nucleic acid has a nucleotide sequence as shown in SEQ ID NO:1. Through gene analysis and plant height measurement of a large number of maize samples, and using the maize genome B73 v3 reference sequence for genomic localization, the inventors found that when the nucleotide at position 96117284 of chromosome 6 is A, the maize plant has a higher plant height. This means that maize plants containing the nucleic acid isolated according to the present invention have a higher plant height.

[0011] In a sixth aspect, the present invention provides a vector. According to an embodiment of the invention, the vector carries the isolated nucleic acid described in the fifth aspect of the invention. Therefore, the vector not only inherits the function of the isolated nucleic acid in increasing the height of maize plants, but also effectively introduces the isolated nucleic acid into plant cells, ensuring the stable transmission of its expression and function. This function makes the vector a potential tool in agricultural production for increasing the height of maize plants.

[0012] In a seventh aspect, the present invention provides a recombinant cell. According to embodiments of the invention, the recombinant cell carries the isolated nucleic acid described in the fifth aspect of the invention or the vector described in the sixth aspect of the invention. Thus, the recombinant cell can increase the plant height of maize plants, providing a powerful tool for producing maize plants with taller plants.

[0013] In an eighth aspect, the present invention provides a transgenic maize plant. According to embodiments of the invention, the transgenic maize plant carries the isolated nucleic acid described in the fifth aspect of the invention or the vector described in the sixth aspect of the invention. By introducing the isolated nucleic acid into the maize plant, the plant height can be increased. Furthermore, the isolated nucleic acid can be stably present in the cells of the transgenic maize plant and continuously expressed throughout the life cycle of the maize plant. This ensures that offspring maize plants can persistently possess the tall plant height trait.

[0014] In a ninth aspect, the present invention provides a method for producing tall maize plants. According to an embodiment of the present invention, the method includes: transforming the recombinant cells described in the seventh aspect of the present invention into a maize plant to be constructed, or hybridizing the transgenic maize plant described in the eighth aspect of the present invention with the maize plant to be constructed. Using the method described in the present invention, maize plants with the trait of tall plant height can be produced, providing an effective improvement strategy for cultivating tall maize.

[0015] In a tenth aspect, the present invention provides a primer set. According to an embodiment of the invention, the primer set includes a forward primer and a reverse primer; the forward primer has the nucleotide sequence shown in SEQ ID NO:2; and the reverse primer has the nucleotide sequence shown in SEQ ID NO:3. Using the primer set of the present invention, a high degree of matching can be achieved with the DNA sequence of maize plants containing nucleotide A at position 96117284 of chromosome 6, resulting in specific amplification. This allows the primers to accurately and reliably identify the nucleotide at this site, laying the foundation for screening maize plants with tall plant height traits.

[0016] In an eleventh aspect, the present invention provides a kit. According to an embodiment of the invention, the kit comprises the primer set described in the twelfth aspect of the invention. Using the kit described in this invention, a high degree of matching with the DNA sequence of a maize variety containing nucleotide A at position 96117284 on chromosome 6 is achieved, resulting in specific amplification. This enables the kit to accurately and reliably identify the nucleotide at this site, thereby screening for maize plants with the tall plant height trait.

[0017] In a twelfth aspect, the present invention provides a method for identifying or assisting in the identification of the height of a maize plant to be tested. According to an embodiment of the present invention, the method includes: performing PCR amplification on the DNA of the maize plant to be tested using the primer set described in the tenth aspect of the present invention or the kit described in the eleventh aspect of the present invention; sequencing the amplified product and locating it using the maize genome B73 v3 reference sequence to obtain the nucleotide type located at position 96117284 on chromosome 6 of the maize plant to be tested. By using the method described in the present invention, the height of the maize plant to be tested can be effectively and rapidly identified.

[0018] In a thirteenth aspect, this invention provides a method for selecting maize plants with tall plant height. According to an embodiment of the invention, the method includes: performing PCR amplification on the DNA of the maize plant to be selected using the primer set described in the tenth aspect of the invention or the kit described in the eleventh aspect of the invention; sequencing the amplified product to locate the nucleotide type at position 96117284 of chromosome 6 using the maize genome B73 v3 reference sequence. By using the method described in this invention, maize plants with tall plant height can be effectively and rapidly screened.

[0019] Additional aspects and advantages of the invention will be set forth in part in the description which follows, and in part will be obvious from the description, or may be learned by practice of the invention. Attached Figure Description

[0020] The above and / or additional aspects and advantages of this application will become apparent and readily understood from the description of the embodiments taken in conjunction with the following drawings, in which:

[0021] Figure 1 This is a diagram showing the plant height of the corn material in Example 3 of this application. Detailed Implementation

[0022] The embodiments of the present invention are described in detail below. The embodiments described below are exemplary and are only used to explain the present invention, and should not be construed as limiting the present invention.

[0023] It should be noted that the terms "first" and "second" are used for descriptive purposes only and should not be construed as indicating or implying relative importance or implicitly specifying the number of indicated technical features. Therefore, a feature defined as "first" or "second" may explicitly or implicitly include one or more of that feature. Furthermore, in the description of this invention, unless otherwise stated, "a plurality of" means two or more.

[0024] The singular forms “a,” “the,” and “the” used in the embodiments of this application and the appended claims are also intended to include the plural forms, unless the context clearly indicates otherwise.

[0025] In this document, the terms “containing,” “comprising,” or “including” are open-ended expressions, meaning they include the contents specified in this invention but do not exclude other aspects.

[0026] In this document, the terms “optionally,” “optionally,” or “optionally” generally refer to an event or condition that may, but may not, occur, and the description includes both cases in which the event or condition occurs and cases in which the event or condition does not occur.

[0027] This invention proposes the uses of SNP sites, isolated nucleic acids, vectors, recombinant cells, transgenic maize plants, methods for producing tall maize plants, primer sets, reagent kits, methods for identifying or assisting in the identification of the height of maize plants to be tested, and methods for breeding maize plants with tall plants. These will be described in detail below.

[0028] use

[0029] In a first aspect, this invention proposes the use of SNP loci in breeding tall maize plants, located on chromosome 6 at position 96117284, using the maize genome B73 v3 reference sequence. Through gene analysis and protein content determination of numerous maize samples, the inventors discovered a close association between the nucleotide at position 96117284 on chromosome 6 of the maize genome B73 v3 reference sequence and the maize plant height trait. Genetic variation at this locus is closely correlated with differences in plant height, thus serving as a powerful marker for predicting maize plant height, overcoming the drawbacks of conventional breeding methods such as long cycles, heavy workload in later screening stages, and low efficiency in identifying varieties or lines. This provides a new screening method for breeding tall maize varieties, helping to accelerate the breeding process and improve breeding efficiency.

[0030] According to an embodiment of the present invention, the nucleotide at position 96117284 is A, which is an indicator of the height of the maize plant.

[0031] In this invention, the term "plant height" refers to the height of a corn plant at maturity or when it has ears.

[0032] In a second aspect, this invention proposes the use of a reagent for detecting SNP loci in the breeding of tall maize plants. The SNP locus is located at position 96117284 on chromosome 6, using the maize genome B73 v3 reference sequence. As mentioned earlier, this SNP locus is closely associated with maize plant height. Therefore, a reagent for detecting this SNP locus can quickly and accurately predict the height of maize plants, thereby assisting in breeding and overcoming the shortcomings of conventional breeding methods, such as long cycles, heavy workload in later screening stages, and low efficiency in identifying varieties or lines. This detection reagent can provide information about maize plant height in a short time, thus accelerating the screening process.

[0033] According to an embodiment of the present invention, the nucleotide at position 96117284 is A, which is an indicator of the height of the maize plant.

[0034] In a third aspect, this invention proposes the use of a reagent for mutating SNP sites in the breeding of tall maize plants. The SNP site is located at position 96117284 on chromosome 6, using the maize genome B73 v3 reference sequence. As mentioned earlier, this SNP site is closely associated with the plant height trait of maize plants. Therefore, a reagent for mutating this SNP site can transform ordinary or tall maize plants into tall maize plants, thereby breeding tall maize plants and overcoming the shortcomings of conventional breeding methods, such as long breeding cycles, large workload in later screening stages, and low efficiency in identifying varieties or lines.

[0035] According to an embodiment of the present invention, the nucleotide at position 96117284 is A, which is an indicator of the height of the maize plant.

[0036] In a fourth aspect, this invention proposes the use of a reagent for overexpressing a SNP site in the breeding of tall maize plants. The SNP site is located at position 96117284 on chromosome 6, using the maize genome B73 v3 reference sequence as the genomic reference. As mentioned earlier, this SNP site is closely associated with the plant height trait of maize plants. Therefore, a reagent for overexpressing this SNP site can transform ordinary or tall maize plants into tall maize plants, thereby breeding tall maize plants and overcoming the drawbacks of conventional breeding methods, such as long breeding cycles, large workload in later screening stages, and low efficiency in identifying varieties or lines.

[0037] According to an embodiment of the present invention, the nucleotide at position 96117284 is A, which is an indicator of the height of the maize plant.

[0038] Isolated nucleic acids, vectors, recombinant cells, and transgenic maize plants

[0039] In a fifth aspect, the present invention provides an isolated nucleic acid. According to embodiments of the present invention, the isolated nucleic acid has a nucleotide sequence as shown in SEQ ID NO:1. Through gene analysis and plant height measurement of a large number of maize samples, and using the maize genome B73 v3 reference sequence for genomic localization, the inventors found that when the nucleotide at position 96117284 of chromosome 6 is A, the maize plant has a higher plant height. This means that maize plants containing the nucleic acid isolated according to the present invention have a higher plant height.

[0040] According to embodiments of the present invention, an isolated polypeptide is provided. According to embodiments of the present invention, the isolated polypeptide has the amino acid sequence shown in SEQ ID NO:4. Therefore, maize plants expressing the isolated polypeptide of the present invention have a higher plant height.

[0041] The "isolated" nucleic acid / peptide molecules described in this invention are artificially separated from their natural environment and are therefore not natural products. The isolated nucleic acid / peptide molecules can exist in purified form or in non-natural environments, such as recombinant cells or transgenic plants.

[0042] In this invention, "natural" refers to genes present in the genome of untransformed cells.

[0043] The "nucleic acid molecule" or "nucleic acid sequence" described in this invention can be a linear fragment of single- or double-stranded DNA or RNA that can be isolated from any source. In the context of this invention, preferably, the nucleic acid molecule is a DNA fragment.

[0044] In a sixth aspect, the present invention provides a vector. According to an embodiment of the invention, the vector carries the isolated nucleic acid described in the fifth aspect of the invention. Therefore, the vector not only inherits the function of the isolated nucleic acid in increasing the height of maize plants, but also effectively introduces the isolated nucleic acid into plant cells, ensuring the stable transmission of its expression and function. This function makes the vector a potential tool in agricultural production for increasing the height of maize plants.

[0045] The term "vector" as used in this invention refers to a transformation vector that can be used for plant transformation, which is known to those skilled in the art of plant transformation, and the nucleic acid molecules of this invention can be used in conjunction with any such vector. The selection of the vector will depend on the preferred transformation technology used for transformation and the target plant species.

[0046] The term "plant" as used in this invention can refer to any plant at any stage of development.

[0047] The "plant cell" described in this invention is a structural and physiological unit of a plant, comprising a protoplast and a cell wall. A plant cell can be an isolated single cell or a cultured cell, or as a higher organized unit, such as a plant tissue, plant organ, or part of a whole plant.

[0048] The "protoplast" described in this invention is a separated plant cell that has no cell wall or only a partial cell wall.

[0049] In a seventh aspect, the present invention provides a recombinant cell. According to embodiments of the present invention, the recombinant cell carries the isolated nucleic acid described in the fifth aspect of the present invention or the vector described in the sixth aspect of the present invention. Thus, the recombinant cell can increase the plant height of maize plants, providing a powerful tool for producing maize plants with taller plants. It should be noted that the recombinant cell described in the present invention is not particularly limited, as long as it can transform the target plant; for example, the recombinant cell can be selected from Agrobacterium.

[0050] According to an embodiment of the present invention, the recombinant cells are selected from Agrobacterium.

[0051] In an eighth aspect, the present invention provides a transgenic maize plant. According to embodiments of the invention, the transgenic maize plant carries the isolated nucleic acid described in the fifth aspect of the invention or the vector described in the sixth aspect of the invention. By introducing the isolated nucleic acid into the maize plant, the plant height can be increased. Furthermore, the isolated nucleic acid can be stably present in the cells of the transgenic maize plant and continuously expressed throughout the life cycle of the maize plant. This ensures that offspring maize plants can persistently possess the tall plant height trait.

[0052] In this invention, "transformed / genetically modified / recombinant" refers to a host organism, such as bacteria or plants, in which a heterologous nucleic acid molecule has been introduced. The nucleic acid molecule can be stably integrated into the host genome or may exist as an extrachromosomal molecule. This extrachromosomal molecule can replicate autonomously. Transformed cells, tissues, or plants are understood to include not only the final products of the transformation process but also their transgenic progeny.

[0053] Methods for producing tall maize plants

[0054] In a ninth aspect, the present invention provides a method for producing tall maize plants. According to an embodiment of the present invention, the method includes: transforming the recombinant cells described in the seventh aspect of the present invention into a maize plant to be constructed, or hybridizing the transgenic maize plant described in the eighth aspect of the present invention with the maize plant to be constructed. Using the method described in the present invention, maize plants with the trait of tall plant height can be produced, providing an effective improvement strategy for cultivating tall maize.

[0055] Primer set

[0056] In a tenth aspect, the present invention provides a primer set. According to an embodiment of the invention, the primer set includes a forward primer and a reverse primer; the forward primer has the nucleotide sequence shown in SEQ ID NO:2; and the reverse primer has the nucleotide sequence shown in SEQ ID NO:3. Using the primer set of the present invention, a high degree of matching can be achieved with the DNA sequence of maize plants containing nucleotide A at position 96117284 of chromosome 6, resulting in specific amplification. This allows the primers to accurately and reliably identify the nucleotide at this site, laying the foundation for screening maize plants with tall plant height traits.

[0057] Reagent test kit

[0058] In an eleventh aspect, the present invention provides a kit. According to an embodiment of the invention, the kit comprises the primer set described in the tenth aspect of the invention. Using the kit described in this invention, a high degree of matching with the DNA sequence of a maize variety containing nucleotide A at position 96117284 on chromosome 6 is achieved, resulting in specific amplification. This enables the kit to accurately and reliably identify the nucleotide at this site, thereby screening for maize plants exhibiting the tall plant height trait.

[0059] Methods for identifying or assisting in the identification of the plant height of maize plants to be tested

[0060] In a twelfth aspect, the present invention provides a method for identifying or assisting in the identification of the height of a maize plant to be tested. According to an embodiment of the present invention, the method includes: performing PCR amplification on the DNA of the maize plant to be tested using the primer set described in the tenth aspect of the present invention or the kit described in the eleventh aspect of the present invention; sequencing the amplification product and locating it using the maize genome B73 v3 reference sequence to obtain the nucleotide type located at position 96117284 on chromosome 6 of the maize plant to be tested. By using the method described in the present invention, the height of the maize plant to be tested can be effectively and rapidly identified.

[0061] According to an embodiment of the present invention, the plant height of the maize plants to be tested with nucleotide A at position 96117284 of chromosome 6 is higher than that of the maize plants to be tested with nucleotide G at position 96117284 of chromosome 6.

[0062] According to an embodiment of the present invention, the nucleotide A at position 96117284 of chromosome 6 is an indicator that the maize plant under test has a tall plant height.

[0063] Methods for breeding tall maize plants

[0064] In a thirteenth aspect, this invention provides a method for selecting maize plants with tall plant height. According to an embodiment of the invention, the method includes: performing PCR amplification on the DNA of the maize plant to be selected using the primer set described in the tenth aspect of the invention or the kit described in the eleventh aspect of the invention; sequencing the amplified product to locate the nucleotide type at position 96117284 of chromosome 6 using the maize genome B73 v3 reference sequence. By using the method described in this invention, maize plants with tall plant height can be effectively and rapidly screened.

[0065] According to an embodiment of the present invention, the nucleotide at position 96117284 of chromosome 6 is A, which is an indicator that the maize plant to be selected has a tall plant height.

[0066] The sequences in this invention are shown in the table below:

[0067] sequence list

[0068]

[0069]

[0070] The present invention will be explained below with reference to embodiments. Those skilled in the art will understand that the following embodiments are for illustrative purposes only and should not be considered as limiting the scope of the invention. Where specific techniques or conditions are not specified in the embodiments, they are performed according to the techniques or conditions described in the literature in the field or according to the product instructions. Reagents or instruments whose manufacturers are not specified are all conventional products that can be obtained commercially.

[0071] Example 1

[0072] To study the genotypic differences between tall maize and ordinary maize, the inventors conducted gene analysis and plant height measurements on a large number of superior tall maize varieties, and screened out SNP loci closely related to plant height. The specific experimental process is as follows:

[0073] 1. Test materials

[0074] The maize materials used in this invention are all from the public germplasm resources of the Shenzhen National Gene Bank Germplasm Resource Bank. The materials and the original sequencing data are from Li C, Guan H, Jing X, Li Y, Wang B, Li Y, Liu X, Zhang D, Liu C, Xie X, Zhao H, Wang Y, Liu J, Zhang P, Hu G, Li G, Li S, Sun D, ​​Wang X, Shi Y, Song Y, Jiao C, Ross-Ibarra J, Li Y, Wang T, Wang H. Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding. NatPlants. 2022 Jul;8(7):750-763. doi:10.1038 / s41477-022-01190-2. Epub 2022 Jul18.PMID:35851624.

[0075] 2. Measurement of maize plant height

[0076] The plant height of 1600 maize samples was measured with a measuring tape at maturity. Three plants were selected from each sample, and the measurement was performed three times. The average value was taken as the plant height of each sample.

[0077] 3. WGS (Whole Genome Sequencing) Library Construction and Resequencing

[0078] Fresh young leaves (0.5g each) were harvested from 1600 maize samples collected in step 2. Genomic DNA was extracted from each sample using the CTAB (hexadecyltrimethylammonium bromide) method and its quality was assessed. Sequencing libraries were generated using the TruSeq NanoDNAHT Sample Preparation Kit (Illumina USA), and indexes were added to each sample. The genomic DNA samples were fragmented to approximately 350 base pairs (bp) using sonication. The DNA fragments were then end-repaired, A-tailed, ligated with full-length adapters, and further amplified by PCR. The PCR products were then purified (using the AMPure XP bead system), and the size distribution of the libraries was analyzed using an Agilent 2100 bioanalyzer. Quantification was performed using real-time quantitative PCR. Subsequently, sequencing was performed using the Illumina HiSeq X platform, yielding raw sequences with paired-end reads of 150 bp.

[0079] 4. Mutation detection

[0080] Variation detection used the maize B73 reference genome v3 version. Quality control, alignment, deduplication, and variation detection were performed using the Mega BOLT full workflow developed by BGI Genomics Co., Ltd. Genotype files for each sample were obtained and merged to obtain a total file containing SNP variation information from all 1600 materials. Plink (v1.9) was used to filter SNP sites with a minor allele frequency less than 0.01 and a deletion rate greater than 0.6.

[0081] 5. Genome-wide association analysis of maize plant height

[0082] Genome-wide association analysis (GEMMA) was performed using genotype files from 1600 maize materials as input. First, the G matrix of the 1600 materials was calculated using the `-gk 2` command. Then, GEMMA was used with the G matrix as a covariate to eliminate errors caused by kinship. Finally, the `-lmm 1` model was used to perform the GEMMA analysis on the 1600 maize materials.

[0083] 6. Gene screening and mining

[0084] Using 0.05 / number of valid SNPs as the significance threshold and 0.01 / number of valid SNPs as the highly significant threshold, the p_wald values ​​in the genome-wide association analysis output files were screened. The results showed that the SNP site located on chromosome 6 of the maize B73 reference genome, POS96117284, with a mutation to G / A, was highly significantly associated with maize plant height.

[0085] Table 1

[0086] chromosome Location Alleles P_wald Gene annotation 6 96117284 G / A <![CDATA[5.0594e -08 ]]> -

[0087] Example 2

[0088] Using samtools (v1.3.1), a fAI index file was created for the FASTA file corresponding to the maize B73 reference genome v3 version, and sequences of 250 bp upstream and downstream of the target SNP, i.e., positions 96117034 to 96117534 on chromosome 6, were extracted. The extracted sequences were imported into Primer Premier 5 software to design primers, setting the primer amplification result fragment to include the target SNP at position 251, and selecting the primer pair with the highest score and the fewest hairpin and other special structures in the software design.

[0089] Example 3

[0090] VCFtools (v0.1.16) was used to extract the SNP types at position 96117284 on chromosome 6 from 1600 maize material variation detection files. Undetected types and heterozygotes were ignored. The plant height phenotype of samples homozygous at position 96117284 on chromosome 6 (i.e., all nucleotides are A or all are G) was statistically analyzed and plotted as follows: Figure 1 As shown, the height of the sample with nucleotide type G at position 96117284 on chromosome 6 is lower than that of the sample with nucleotide type A.

[0091] In the description of this specification, the references to terms such as "one embodiment," "some embodiments," "example," "specific example," or "some examples," etc., indicate that a specific feature, structure, material, or characteristic described in connection with that embodiment or example is included in at least one embodiment or example of the present invention. In this specification, the illustrative expressions of the above terms do not necessarily refer to the same embodiment or example. Furthermore, the specific features, structures, materials, or characteristics described may be combined in any suitable manner in one or more embodiments or examples. Moreover, without contradiction, those skilled in the art can combine and integrate the different embodiments or examples described in this specification, as well as the features of different embodiments or examples.

[0092] Although embodiments of the present invention have been shown and described above, it is understood that the above embodiments are exemplary and should not be construed as limiting the present invention. Those skilled in the art can make changes, modifications, substitutions and variations to the above embodiments within the scope of the present invention.

Claims

1. The use of SNP loci in breeding tall maize plants, with the SNP locus located at position 96117284 on chromosome 6, based on the maize genome B73 v3 reference sequence.

2. The use according to claim 1, characterized in that, The nucleotide at position 96117284 is A, which is an indicator that the maize plant has a tall plant height.

3. The use of reagents for detecting SNP sites in the selection of tall maize plants, using the maize genome B73 v3 reference sequence for genomic localization, the SNP site is located at position 96117284 on chromosome 6; Optionally, the nucleotide at position 96117284 is A, which is an indicator that the maize plant has a tall plant height.

4. The use of reagents for mutating SNP sites in the selection of tall maize plants, with the SNP site located at position 96117284 on chromosome 6 using the maize genome B73 v3 reference sequence. Optionally, the nucleotide at position 96117284 is A, which is an indicator that the maize plant has a tall plant height.

5. The use of reagents that overexpress SNP sites in the selection of tall maize plants, with the SNP site located at position 96117284 on chromosome 6 using the maize genome B73 v3 reference sequence. Optionally, the nucleotide at position 96117284 is A, which is an indicator that the maize plant has a tall plant height.

6. An isolated nucleic acid, characterized in that, The isolated nucleic acid has a nucleotide sequence as shown in SEQ ID NO:

1.

7. A carrier, characterized in that, Carrying the isolated nucleic acid as described in claim 6.

8. A recombinant cell, characterized in that, Carrying the isolated nucleic acid as described in claim 6 or the vector as described in claim 7; Optionally, the recombinant cells are selected from Agrobacterium.

9. A transgenic maize plant, characterized in that, Carrying the isolated nucleic acid as described in claim 6 or the vector as described in claim 7.

10. A method for producing tall maize plants, characterized in that, include: The recombinant cells described in claim 8 are transformed into the maize plant to be constructed, or the transgenic maize plant described in claim 9 is hybridized with the maize plant to be constructed.

11. A primer set, characterized in that, Including forward primers and reverse primers; The forward primer has the nucleotide sequence shown in SEQ ID NO:2; The reverse primer has the nucleotide sequence shown in SEQ ID NO:

3.

12. A reagent kit, characterized in that, include: The primer set as described in claim 11; Optionally, the kit further comprises at least one of the following components: dNTPs, Taq enzyme, and PCR reaction buffer.

13. A method for identifying or assisting in the identification of the plant height of a maize plant, characterized in that, include: The DNA of the maize plant to be tested was amplified by PCR using the primer set described in claim 11 or the kit described in claim 12. The amplification product was sequenced and located using the B73 v3 reference sequence of the maize genome to obtain the nucleotide type located at position 96117284 on chromosome 6 in the maize plant to be tested.

14. The method according to claim 13, characterized in that, The plant height of the maize plants tested with nucleotide A at position 96117284 on chromosome 6 was higher than that of the maize plants tested with nucleotide G at position 96117284 on chromosome 6. Optionally, the nucleotide at position 96117284 of chromosome 6 being A is an indicator that the maize plant being tested has a tall plant height.

15. A method for breeding maize plants with tall stems, characterized in that, include: The DNA of the maize plants to be selected was amplified by PCR using the primer set described in claim 11 or the kit described in claim 12. The amplified product was sequenced and located using the maize genome B73 v3 reference sequence to obtain the nucleotide type at position 96117284 on chromosome 6. Optionally, the nucleotide at position 96117284 of chromosome 6 is A, which is an indicator that the maize plant to be selected has a tall plant height.

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