CN114107547B - SNP (Single nucleotide polymorphism) marker related to corn ear bud She Jian leaf length and application thereof - Google Patents
SNP (Single nucleotide polymorphism) marker related to corn ear bud She Jian leaf length and application thereof Download PDFInfo
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Abstract
The invention discloses a SNP marker related to the length of a corn ear bud She Jian leaf and application thereof. The inventor found that the genotype at the 130211727bp position of maize chromosome 3, which is significantly associated with the maize variety ear bud She Jian leaf length, wherein the bud She Jian leaf length is about 10.37cm when the SNP genotype is GG (7.23%), and the bud She Jian leaf length is about 2.48cm when the SNP genotype is TT (92.77%), can be used as the SNP marker of the maize ear bud leaf sisal leaf length. The SNP marker can be used for cultivating corn inbred lines of longer bract sisal leaves.
Description
Technical Field
The invention belongs to the technical field of biology, and particularly relates to a SNP (single nucleotide polymorphism) marker related to the She Jian leaf length of corn ear buds and application thereof.
Background
Corn is an important grain crop, feed and industrial raw material in China, is the first crop in China, and the total yield of corn is over that of rice and wheat worldwide. Sweet corn is a sweet corn, and the conversion of grain sugar into starch is blocked, so that the grain in the milk ripening period has higher sugar content, and the sweet corn is sweet, and is a novel food for both vegetables and fruits. In recent years, fresh sweet corn has become an important economic crop in China, the planting area reaches 300 ten thousand mu, nearly three billions of fresh ears (fresh buds) are produced each year, the fresh ears are one of the consumption modes with the largest sales amount, and the existence and the length of bract and sisal leaves carried on the fresh ears directly influence the commodity quality and price. The bract sisal leaves are incomplete leaves which are reserved in the corn ear evolution process, the bract She Dingduan is usually positioned on the corn ear, most corn inbred lines hardly grow the bract sisal leaves, only few corn inbred lines reserve the bract sisal leaves with unequal lengths, and the characteristics are important characteristics of the corn evolution. Therefore, the development of the related genes and the development of molecular markers of the corn ear bud leaf and the bud leaf with proper length is important for improving the commodity of the sweet corn fresh bud.
Disclosure of Invention
One of the purposes of the present invention is to provide a SNP marker related to the length of the corn ear bud She Jian leaves, which can be used for detecting the length of the corn ear bud She Jian leaves.
A SNP marker related to the leaf length of a maize ear bud She Jian is positioned at 130211727bp of a maize chromosome 3.
In some of these embodiments, the 130211727bp locus genotype is GG.
In some of these embodiments, the 130211727bp locus genotype is TT.
The invention further aims to provide a detection method for the length of the corn ear bud leaf and the sisal leaf.
A method for detecting the length of the leaf of the corn ear bud, the length of the leaf of the corn ear bud and the leaf of the corn leaf is judged by detecting the genotype of the 130211727bp position of a chromosome 3 of the corn.
In some of these embodiments, the length of the corn ear bud leaf is greater when the 130211727bp locus genotype is GG.
In some of these embodiments, the length of the corn ear bud leaf is shorter when the 130211727bp locus genotype is TT.
In some embodiments, the detection method is any one of direct sequencing, specific probe hybridization, specific primer extension, or PCR.
Another object of the invention is to provide a kit for detecting the length of the corn ear bud and the leaf.
A kit for detecting the length of leaves of corn ear bract and sisal leaves comprises a reagent for detecting the genotype of a 130211727bp position of a corn chromosome 3.
Preferably, the kit is used for direct sequencing, specific probe hybridization, specific primer extension or PCR detection.
Another object of the present invention is to provide the use of the above SNP markers and the above kit for detecting the length of the leaf of the corn ear bud and the leaf of the sword.
Another object of the present invention is to provide the use of the above SNP markers for breeding maize inbred lines with appropriate length of ear bud leaf and sisal leaf.
The inventors found that the genotype at the 130211727bp position of maize chromosome 3, which is highly correlated with the maize variety ear bud She Jian leaf length, wherein the bud She Jian leaf length was about 10.37cm when the SNP genotype was GG (7.23%), and the bud She Jian leaf length was about 2.48cm when the SNP genotype was TT (92.77%), was considered as SNP markers for maize ear bud sisal leaf length. The SNP can be used for cultivating corn inbred lines with longer bract and sisal leaves.
Detailed Description
The following is a specific example of the implementation of the invention. It should be noted that these examples are only exemplary and do not limit the scope of the present invention in any way. Modifications and substitutions of detail and form of embodiments within the spirit and scope of the invention are all within the scope of the invention.
Unless defined otherwise, technical terms used in the following examples have the same meaning as commonly understood by one of ordinary skill in the art to which the present invention pertains. The experimental reagents used in the following examples are all conventional biochemical reagents unless otherwise specified.
Example 1
1. Research method
(1) Phenotypic assay
The inventor respectively plants 221 corn inbred line related group germplasm resources (provided by a Lai Jincheng professor laboratory of China agricultural university) in Shaoguan city, shaoguan, china in 2019 and 2020, adopts a random complete group design, and the test cell is 3m long and 2m wide, 3 rows are planted, 8 plants in each row are planted, the plant spacing is 25cm, and the row spacing is 65cm. 25 days after powder scattering, the length of the corn ear bud leaf and the leaf is measured by using a ruler, and the whole row of corn is taken as one repetition, and three repetitions are taken as the whole row of corn.
(2) Genotyping
DNA is extracted from 221 maize inbred lines, high-throughput sequencing is carried out, joints of reads obtained by sequencing and low-quality reads are filtered, the joints and the low-quality reads are compared with a B73 maize reference genome (B73 RefGen_v4) by using bwa software, and SNP information is extracted by using GATK software, so that genotypes of each inbred line are obtained.
(3) Whole genome association analysis (GWAS)
And calculating a kinship matrix of the inbred line by using tassel5 software. And calculating a group structure (K value is 4) by using admix software, and finally, performing GWAS analysis by using a Mixed Linear Model (MLM) of tassel5 to obtain a p value of each SNP locus.
2. Results of the study
(1) Corn association population spike and bud sisal leaf phenotype distribution
The present study measured a total of 221 maize inbred line ear bud She Jian leaves length, ranging from 0 to 28.3cm, an average length of 3.05cm, and a median of 0.75cm, with a coefficient of variation of 10.4% (Table 1).
TABLE 1 maize population ear bud She Jian leaf Length
(2) Whole genome association analysis
By combining the obtained tens of millions of SNP markers and the obtained phenotype data of the length of the ear bracts, and adopting a whole genome association analysis method, the inventor identifies that the SNP marker positioned at 130211727bp of a corn chromosome 3 is obviously associated with the length of the ear bracts She Jian of the corn inbred line, the locus is positioned in a non-transposon region of an intergenic region, and the allelic types are GG and TT. Among them, 16 maize inbred lines with genotype GG had an average length of 10.37cm for the leaves of the ear bud, and 205 maize inbred lines with genotype TT had an average length of 2.48cm for the leaves of the ear bud (Table 2).
TABLE 2 statistical Table of maize ear bud She Jian leaf lengths for genotypes at different 130211727bp positions
| 130211727bp position genotype | Leaf length (cm) of ear bud She Jian | Number of inbred lines |
| GG | 10.37 | 16 |
| TT | 2.48 | 205 |
The above examples are only illustrative of the preferred embodiments of the present invention and are not intended to limit the scope of the present invention, and various modifications and improvements made by those skilled in the art to the technical solution of the present invention should fall within the scope of protection defined by the claims of the present invention without departing from the spirit of the present invention.
Claims (4)
1. A detection method of the length of corn ear bud leaf and sisal leaf is characterized in that the length of the corn ear bud leaf and sisal leaf is judged by detecting the genotype of a 130211727bp position of a corn chromosome 3; when the genotype of the 130211727bp position of the corn chromosome 3 is GG, the length of the corn ear bud She Jian leaves is longer; when the genotype of the 130211727bp position of the corn chromosome 3 is TT, the length of the corn ear bud leaf and the corn leaf is short.
2. The method of claim 1, wherein the method of detection comprises direct sequencing, specific probe hybridization, specific primer extension, or PCR.
3. Application of SNP markers related to corn ear bud She Jian leaf length in detecting corn ear bud leaf sisal leaf length; the SNP marker is positioned at a 130211727bp position of a corn chromosome 3, and the genotype is GG or TT; when the genotype of the 130211727bp position of the corn chromosome 3 is GG, the length of the corn ear bud She Jian leaves is longer; when the genotype of the 130211727bp position of the corn chromosome 3 is TT, the length of the corn ear bud leaf and the corn leaf is short.
4. Application of SNP markers related to the length of corn ear bud She Jian leaves in cultivation of corn inbred lines with suitable length of ear bud leaves and sisal leaves; the SNP marker is positioned at a 130211727bp position of a corn chromosome 3, and the genotype is GG or TT; when the genotype of the 130211727bp position of the corn chromosome 3 is GG, the length of the corn ear bud She Jian leaves is longer; when the genotype of the 130211727bp position of the corn chromosome 3 is TT, the length of the corn ear bud leaf and the corn leaf is short.
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| CN112029897A (en) * | 2020-10-14 | 2020-12-04 | 江苏省农业科学院 | SNP marker closely linked with continuous multi-leaf-position leaf width main effect QTL under corn tassel and application thereof |
| CN112646925A (en) * | 2021-01-18 | 2021-04-13 | 吉林大学 | Corn ear position high-correlation ZmRzf gene SNP molecular marker and application |
| CN113528691A (en) * | 2021-03-31 | 2021-10-22 | 广东省科学院生物工程研究所 | SNP marker related to cadmium content of corn grains and application thereof |
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| BRPI0812335A2 (en) * | 2007-05-17 | 2015-01-27 | Monsanto Technology Llc | CORN POLYMORPHISMS AND GENOTYPING METHODS. |
| PL3289087T3 (en) * | 2015-04-28 | 2021-11-02 | Monsanto Technology Llc | Methods and compositions for producing brachytic corn plants |
| CN111088382B (en) * | 2019-11-28 | 2023-01-31 | 北京市农林科学院 | Corn whole genome SNP chip and application thereof |
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| CN112029897A (en) * | 2020-10-14 | 2020-12-04 | 江苏省农业科学院 | SNP marker closely linked with continuous multi-leaf-position leaf width main effect QTL under corn tassel and application thereof |
| CN112646925A (en) * | 2021-01-18 | 2021-04-13 | 吉林大学 | Corn ear position high-correlation ZmRzf gene SNP molecular marker and application |
| CN113528691A (en) * | 2021-03-31 | 2021-10-22 | 广东省科学院生物工程研究所 | SNP marker related to cadmium content of corn grains and application thereof |
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