CN114107547A - SNP (Single nucleotide polymorphism) marker related to length of maize ear bract and sword leaves and application thereof - Google Patents
SNP (Single nucleotide polymorphism) marker related to length of maize ear bract and sword leaves and application thereof Download PDFInfo
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- 235000002017 Zea mays subsp mays Nutrition 0.000 title claims abstract description 75
- 240000008042 Zea mays Species 0.000 title claims abstract description 70
- 235000016383 Zea mays subsp huehuetenangensis Nutrition 0.000 title claims abstract description 45
- 235000009973 maize Nutrition 0.000 title claims abstract description 45
- 239000003550 marker Substances 0.000 title claims abstract description 18
- 239000002773 nucleotide Substances 0.000 title description 3
- 125000003729 nucleotide group Chemical group 0.000 title description 3
- 210000000349 chromosome Anatomy 0.000 claims abstract description 13
- 235000005824 Zea mays ssp. parviglumis Nutrition 0.000 claims description 25
- 235000005822 corn Nutrition 0.000 claims description 25
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- 238000012163 sequencing technique Methods 0.000 claims description 4
- 238000009396 hybridization Methods 0.000 claims description 3
- 239000000523 sample Substances 0.000 claims description 3
- 238000009395 breeding Methods 0.000 claims description 2
- 230000001488 breeding effect Effects 0.000 claims description 2
- 241000482268 Zea mays subsp. mays Species 0.000 description 5
- 210000005069 ears Anatomy 0.000 description 5
- 241000196324 Embryophyta Species 0.000 description 3
- 238000012098 association analyses Methods 0.000 description 2
- 238000012986 modification Methods 0.000 description 2
- 230000004048 modification Effects 0.000 description 2
- 238000011160 research Methods 0.000 description 2
- 108020004414 DNA Proteins 0.000 description 1
- 108091029795 Intergenic region Proteins 0.000 description 1
- 240000007594 Oryza sativa Species 0.000 description 1
- 235000007164 Oryza sativa Nutrition 0.000 description 1
- 229920002472 Starch Polymers 0.000 description 1
- 241000209140 Triticum Species 0.000 description 1
- 235000021307 Triticum Nutrition 0.000 description 1
- 238000004458 analytical method Methods 0.000 description 1
- 238000012097 association analysis method Methods 0.000 description 1
- 210000004027 cell Anatomy 0.000 description 1
- 235000013339 cereals Nutrition 0.000 description 1
- 238000006243 chemical reaction Methods 0.000 description 1
- 235000009508 confectionery Nutrition 0.000 description 1
- 238000013461 design Methods 0.000 description 1
- 235000013399 edible fruits Nutrition 0.000 description 1
- 238000001914 filtration Methods 0.000 description 1
- 235000013312 flour Nutrition 0.000 description 1
- 235000013305 food Nutrition 0.000 description 1
- 230000002068 genetic effect Effects 0.000 description 1
- 238000003205 genotyping method Methods 0.000 description 1
- 238000012165 high-throughput sequencing Methods 0.000 description 1
- 239000011159 matrix material Substances 0.000 description 1
- 235000013336 milk Nutrition 0.000 description 1
- 239000008267 milk Substances 0.000 description 1
- 210000004080 milk Anatomy 0.000 description 1
- 238000012247 phenotypical assay Methods 0.000 description 1
- 108090000623 proteins and genes Proteins 0.000 description 1
- 239000002994 raw material Substances 0.000 description 1
- 230000001105 regulatory effect Effects 0.000 description 1
- 235000009566 rice Nutrition 0.000 description 1
- 235000019698 starch Nutrition 0.000 description 1
- 239000008107 starch Substances 0.000 description 1
- 238000006467 substitution reaction Methods 0.000 description 1
- 238000012360 testing method Methods 0.000 description 1
- 235000013311 vegetables Nutrition 0.000 description 1
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Abstract
The invention discloses an SNP marker related to the length of maize ear bract and sword leaves and application thereof. The inventor finds that the genotype of the 130211727bp position of the maize chromosome 3 is obviously related to the length of the maize ear bract and sword leaf of maize varieties, wherein the length of the bract and sword leaf is about 10.37cm when the SNP genotype is GG (7.23%), and the length of the bract and sword leaf is about 2.48cm when the SNP genotype is TT (92.77%), and the genotype at the position can be used as an SNP marker of the length of the maize ear bract and sword leaf. The SNP marker can be used for cultivating a maize inbred line with longer bract sword leaves.
Description
Technical Field
The invention belongs to the technical field of biology, and particularly relates to an SNP (single nucleotide polymorphism) marker related to the length of maize ear bract and sword leaves and application thereof.
Background
Corn is an important grain crop, feed and industrial raw material in China, is the first crop in China, and has total corn yield exceeding that of rice and wheat all over the world. The sweet corn is a sweet corn, the conversion of the kernel sugar into starch is hindered, so the kernel has high sugar content in the milk stage, and the sweet corn is sweet in taste and is a novel food used as both vegetable and fruit. In recent years, fresh sweet corn has become an important economic crop in our country, the planting area reaches 300 ten thousand mu, nearly billions of fresh ears (fresh bracts) are produced every year, the fresh ears are one of the largest consumption modes in sales volume, and the quality and price of the fresh ears are directly influenced by the existence and length of bract sword leaves carried on the fresh ears. The bract sword-like leaves are incomplete leaves remained in the corn ear evolution process and are usually positioned at the top of the bract of the corn ear, the bract sword-like leaves hardly grow in most corn inbred lines, and the bract sword-like leaves with different lengths are remained in only a few corn inbred lines, so that the property is also an important property for corn evolution. Therefore, digging and regulating related genes of corn ear bract sword-like leaves and developing molecular markers, and cultivating the bract sword-like leaves with proper length has important significance for improving the commodity of fresh bracts of sweet corn.
Disclosure of Invention
One objective of the present invention is to provide an SNP marker related to the length of the maize ear bract sword-like leaf, which can be used for detecting the length of the maize ear bract sword-like leaf.
An SNP marker related to the length of maize ear bract and sword leaves is positioned at 130211727bp of maize chromosome 3.
In some of these embodiments, the locus genotype of 130211727bp is GG.
In some of these embodiments, the locus genotype of 130211727bp is TT.
The invention also aims to provide a method for detecting the length of the bract and sword leaves of the corn ear.
A method for detecting the length of corn ear bract sword-like leaves is used for judging the length of the corn ear bract sword-like leaves by detecting the genotype of the 130211727bp position of a corn chromosome 3.
In some embodiments, when the locus genotype of 130211727bp is GG, the length of the corn ear bract sword-like leaf is longer.
In some embodiments, the maize ear bud flag leaf is shorter in length when the 130211727bp positional genotype is TT.
In some embodiments, the detection method is any one of direct sequencing, specific probe hybridization, specific primer extension, or PCR.
Another purpose of the invention is to provide a kit for detecting the length of the maize ear bract sword-like leaves.
A kit for detecting the length of corn ear bract sword leaves comprises a reagent for detecting the genotype of a corn chromosome 3 130211727bp position.
Preferably, the kit is applied to direct sequencing, specific probe hybridization, specific primer extension or PCR detection.
The invention also aims to provide the application of the SNP marker and the kit in detecting the length of the maize ear bract and sword leaves.
The invention also aims to provide application of the SNP marker in breeding a maize inbred line with proper length of maize bract and sword leaves.
The inventor finds that the genotype at the 130211727bp position of the maize chromosome 3 is highly related to the length of the maize ear bract sword-like leaf of maize varieties, wherein the length of the maize bract sword-like leaf is about 10.37cm when the SNP genotype is GG (7.23%), and the length of the maize bract sword-like leaf is about 2.48cm when the SNP genotype is TT (92.77%), and the genotype at the position can be used as an SNP marker for the length of the maize ear bract sword-like leaf. The SNP can be used for cultivating a maize inbred line with longer bract sword leaves.
Detailed Description
The following are specific examples of the present invention. It should be noted that these examples are only illustrative and do not limit the scope of the present invention in any way. Modifications and substitutions of the details and forms of the embodiments are within the spirit and scope of the invention.
Unless defined otherwise, technical terms used in the following examples have the same meanings as commonly understood by one of ordinary skill in the art to which the present invention belongs. 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 plants 221 parts of maize inbred line associated group germplasm resources (provided by professor laboratoria professor Lijingsheng of China agriculture university) in Wenyuan county of Shaoguan city in 2019 and 2020 respectively, adopts a random complete block design, and a test cell is 3m long and 2m wide, and is planted with 3 rows, 8 plants in each row, the plant spacing is 25cm, and the row spacing is 65 cm. 25 days after the flour is scattered, the length of the corn ear bract and sword leaves is measured by a ruler, and the whole row of corn is taken as one repetition, and the total number is three.
(2) Genotyping
Extracting DNA from 221 parts of maize inbred lines, performing high-throughput sequencing, filtering out joints and low-quality reads obtained by sequencing, comparing to a B73 maize reference genome (B73 RefGen _ v4) by using bwa software, and finally extracting SNP information by using GATK software to obtain the genotype of each inbred line.
(3) Whole genome Association analysis (GWAS)
And (4) calculating a kinship matrix of the genetic relationship between inbred lines by using tassel5 software. Calculating a population structure (K value is 4) by using the admixture software, and finally carrying out GWAS analysis by using a Mixed Linear Model (MLM) of tassel5 to obtain the p value of each SNP site.
2. Results of the study
(1) Maize-related group ear bract sword leaf phenotype distribution
The research of the invention totally determines the length of the bract and sword leaves of 221 parts of maize inbred line ears, the variation range is 0-28.3 cm, the average length is 3.05cm, the median is 0.75cm, and the variation coefficient is 10.4% (table 1).
TABLE 1 corn population ear bract sword leaf Length
(2) Whole genome association analysis
Combining the obtained ten million SNP markers and the phenotypic data of the ear bract length, and adopting a whole genome association analysis method, the inventor identifies that the SNP marker located at 130211727bp position of a maize 3 chromosome is significantly associated with the length of the ear bract sword leaf of a maize inbred line, the locus is located in a non-transposon area of an intergenic region, and the allelic types are GG and TT. There were 16 maize inbred lines with genotype GG, average ear bud flag leaf length of 10.37cm, 205 maize inbred lines with genotype TT, average ear bud flag leaf length of 2.48cm (table 2).
TABLE 2 statistical table of maize ear bract and sword leaf lengths of genotypes at different 130211727bp positions
| 130211727bp position genotype | Length (cm) of ear bract sword leaf | Number of inbred lines |
| GG | 10.37 | 16 |
| TT | 2.48 | 205 |
The above-mentioned embodiments are merely illustrative of the preferred embodiments of the present invention, and do not limit the scope of the present invention, and various modifications and improvements made to the technical solution of the present invention by those skilled in the art without departing from the spirit of the present invention shall fall within the protection scope defined by the claims of the present invention.
Claims (10)
1. An SNP marker related to the length of the maize ear bract and sword leaves, which is characterized in that the SNP marker is located at the position of 130211727bp of maize chromosome 3.
2. The corn ear bract and sword leaf length related SNP marker according to claim 1, wherein the genotype of the position 130211727bp of chromosome 3 of corn is GG.
3. The corn ear bract and flag leaf length related SNP marker according to claim 1, wherein the genotype at the 130211727bp position of chromosome 3 in corn is TT.
4. The method for detecting the length of the maize ear bract sword-like leaf is characterized in that the length of the maize ear bract sword-like leaf is judged by detecting the genotype of the maize chromosome 3 at the 130211727bp position.
5. The method according to claim 4, wherein when the genotype at the position 130211727bp of chromosome 3 in maize is GG, the maize ear bract and sword leaf length is longer.
6. The method of claim 4, wherein the maize ear bud flag length is shorter when the genotype at the position 130211727bp of chromosome 3 in maize is TT.
7. The detection method according to any one of claims 4 to 6, wherein the detection method comprises direct sequencing, specific probe hybridization, specific primer extension or PCR.
8. A kit for detecting the length of corn ear bract sword leaves is characterized by comprising a reagent for detecting the genotype of a corn chromosome 3 130211727bp position.
9. The use of the SNP marker of claim 1 and the kit of claim 8 for detecting the length of the bracteal leaf of an ear of corn.
10. Use of the SNP marker of claim 1 for breeding maize inbred lines with suitable length of ear bract and sword leaves.
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| CN114107547B CN114107547B (en) | 2024-02-23 |
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Cited By (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN115820897A (en) * | 2022-07-27 | 2023-03-21 | 湖南农业大学 | Molecular marker closely linked with length of maize female ear and sword leaf and application thereof |
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| US20110105347A1 (en) * | 2007-05-17 | 2011-05-05 | Monsanto Technology Llc | Corn polymorphisms and methods of genotyping |
| US20160319375A1 (en) * | 2015-04-28 | 2016-11-03 | Monsanto Technology Llc | Methods and compositions for producing brachytic corn plants |
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2021
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Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN115820897A (en) * | 2022-07-27 | 2023-03-21 | 湖南农业大学 | Molecular marker closely linked with length of maize female ear and sword leaf and application thereof |
| CN115820897B (en) * | 2022-07-27 | 2024-05-03 | 湖南农业大学 | Molecular marker closely linked with corn female spike and sword leaf length and application thereof |
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