CN111118204B - A08 chromosome major QTL (quantitative trait locus) site with oleic acid content character of brassica napus seeds, SNP molecular marker and application - Google Patents
A08 chromosome major QTL (quantitative trait locus) site with oleic acid content character of brassica napus seeds, SNP molecular marker and application Download PDFInfo
- Publication number
- CN111118204B CN111118204B CN202010116243.7A CN202010116243A CN111118204B CN 111118204 B CN111118204 B CN 111118204B CN 202010116243 A CN202010116243 A CN 202010116243A CN 111118204 B CN111118204 B CN 111118204B
- Authority
- CN
- China
- Prior art keywords
- oleic acid
- brassica napus
- acid content
- molecular marker
- seeds
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Active
Links
Images
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
- C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/13—Plant traits
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Analytical Chemistry (AREA)
- Engineering & Computer Science (AREA)
- Organic Chemistry (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Health & Medical Sciences (AREA)
- Biotechnology (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Immunology (AREA)
- Mycology (AREA)
- Microbiology (AREA)
- Molecular Biology (AREA)
- Botany (AREA)
- Biophysics (AREA)
- Physics & Mathematics (AREA)
- Biochemistry (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Genetics & Genomics (AREA)
- Breeding Of Plants And Reproduction By Means Of Culturing (AREA)
Abstract
The invention provides a main effect QTL site of an A08 chromosome of an oleic acid content character of a cabbage type rape seed, which is positioned between bases 8348554 th to 11137029 th of the A08 chromosome of the cabbage type rape seed. Preferably, the contribution rate to the oleic acid content character of the brassica napus seeds is 71.84%. Closely linked to the first SNP molecular marker, which is at base 8348554, and is either A or G, the mutation results in a polymorphism. Closely linked to the second SNP molecular marker, which is located at base 11137029 and is either A or T, this mutation results in a polymorphism. Closely linked to the peak SNP molecular marker, which is at base 10194057, as C or T, the mutation results in a polymorphism. Also provides related SNP molecular markers and application. The A08 chromosome major QTL site has high contribution rate to the character of the oleic acid content of the brassica napus seeds, plays a key role in regulating and controlling the oleic acid content of the brassica napus seeds, can be used for map location cloning and molecular marker assisted selection, and is suitable for large-scale popularization and application.
Description
Technical Field
The invention relates to the technical field of molecular biology and rape breeding, in particular to the technical field of oleic acid content traits of brassica napus seeds, and specifically relates to an A08 chromosome major QTL site of the oleic acid content traits of brassica napus seeds, an SNP molecular marker and application.
Background
Rape is one of the most oil crops with the highest oil yield, and is one of the most important oil crops in the world, particularly in asia, europe and north america. Rape in China is sowed in a year by a year area of nearly 700 hectares, the total yield is more than 1200 million tons, the annual oil yield is more than 450 million tons, and the annual output value is nearly 130 million yuan (Guanchunyun, 2010). The planting area and the total yield are in the first place in the world. According to statistics data in 2009, rapeseed oil produced in China accounts for 57.2% of the yield of domestic oil crops, 42.8% of the total amount of domestic vegetable oil, and 17.4% of the total amount of domestic vegetable oil consumption. The rape industry becomes an important guarantee for the supply safety of the vegetable oil in China. In recent years, the annual actual consumption of vegetable oil in China is as high as 2473.8 ten thousand tons, but the annual yield of vegetable oil in China is only 900-1000 ten thousand tons, and the self-sufficiency rate is only 40.6%. In 2013, the total imported quantities of rapeseeds and rapeseed oil in China respectively reach 360 ten thousand tons and 148 ten thousand tons, the same-ratio increases respectively reach 19 percent and 27 percent, and oil is a large quantity of agricultural products with the largest dependence degree on the international market in China.
Meanwhile, with the improvement of the living standard of people, new requirements on the quality of the edible oil are provided. Linoleic acid is a synthetic precursor of some structural and functional lipids, including sphingolipids and eicosanolipids, and is an essential fatty acid that the human body must take in from the outside, since the animal body cannot synthesize itself. Oleic acid has the effect of lowering plasma Low Density Lipoprotein (LDL) cholesterol, which is a real risk factor for coronary artery disease, without acting on High Density Lipoprotein (HDL) cholesterol, which inhibits coronary artery disease. Therefore, the high oleic acid vegetable oil has good health care effect on the cardiovascular system of a human body. In recent years, people also find that the high oleic acid oil can be effectively methyl-esterified, which is beneficial to the production of biodiesel. The rapeseed oil has higher nutritional value than soybean oil, has oleic acid content close to that of olive oil, is commonly called as 'oriental olive oil', and is high-quality healthy edible oil which is popular with consumers. Therefore, the breeding of the new variety of the high-oleic acid health rape seed oil and the development of the high-oleic acid high-quality nutritional health rape seed oil are beneficial to ensuring the edible plant oil supply safety in China and effectively promoting the benign development of the health industry in China.
The oleic acid content is affected by the stearic acid and linoleic acid content. There are two genes that promote oleic acid desaturation, the FAD2 gene (present in the endoplasmic reticulum) and the FAD6 gene (present in the chloroplast). The fact that the oleic acid content varies from 60% to nearly 90% also indicates that the high oleic acid trait is genetically complex. The genetic characteristic research of high oleic acid mainly has 3 viewpoints: multigene control, environmental influence and monogene control. Most studies suggest that the genetic nature of oleic acid is controlled by multiple genes.
Therefore, a main effect QTL site of the oleic acid content character of the brassica napus seeds needs to be provided, the contribution rate of the QTL site to the oleic acid content character of the brassica napus seeds is high, the key effect on the regulation and control of the oleic acid content of the brassica napus seeds is played, and the QTL site can be used for map-based cloning and molecular marker assisted selection.
Disclosure of Invention
In order to overcome the defects in the prior art, the invention aims to provide the A08 chromosome major QTL site with the oleic acid content character of the brassica napus seeds, which has high contribution rate to the oleic acid content character of the brassica napus seeds, plays a key role in regulating and controlling the oleic acid content of the brassica napus seeds, can be used for map cloning and molecular marker assisted selection, and is suitable for large-scale popularization and application.
The invention also aims to provide the SNP molecular marker of the major QTL site of the A08 chromosome of the oleic acid content character of the brassica napus seeds, which can detect the content of the oleic acid of the brassica napus seeds, can predict the content of the oleic acid of the brassica napus seeds, can effectively select the content of the oleic acid of the brassica napus seeds, can be used for molecular marker-assisted breeding of the brassica napus seeds with high content of the oleic acid, can accelerate the process of breeding of the brassica napus seeds with high content of the oleic acid, and is suitable for large-scale popularization and application.
The invention also aims to provide the SNP molecular marker of the major QTL site of the A08 chromosome with the oleic acid content character of the brassica napus seeds, which has the advantages of ingenious design, simple and quick detection, low cost, no environmental influence and suitability for large-scale popularization and application.
The invention also aims to provide the application of the SNP molecular marker of the A08 chromosome major QTL site of the character of the oleic acid content of the brassica napus seeds, which can detect the content of the oleic acid in the brassica napus seeds, can predict the content of the oleic acid in the brassica napus seeds, can effectively select the content of the oleic acid in the brassica napus seeds, can be used for molecular marker-assisted breeding of the brassica napus seeds with high oleic acid content, can accelerate the breeding process of the brassica napus seeds with high oleic acid content, and is suitable for large-scale popularization and application.
The invention also aims to provide application of the SNP molecular marker of the A08 chromosome major QTL site with the character of the oleic acid content of the brassica napus seeds, which has the advantages of ingenious design, simple and quick detection, low cost, no environmental influence and suitability for large-scale popularization and application.
In order to achieve the above objects, in a first aspect of the present invention, there is provided an a08 chromosome major QTL locus for the oleic acid content trait of brassica napus seeds, characterized in that the a08 chromosome major QTL locus for the oleic acid content trait of brassica napus seeds is located between the 8348554 th base and the 11137029 th base of the a08 chromosome of brassica napus.
Preferably, the contribution rate of the A08 chromosome major QTL site for the oleic acid content trait of the brassica napus seeds to the oleic acid content trait of the brassica napus seeds is 71.84%.
Preferably, the major QTL site of the A08 chromosome of the oleic acid content trait of the brassica napus seeds is closely linked with a first SNP molecular marker, the first SNP molecular marker is located at the 8348554 th base, and the 8348554 th base is A or G, and the mutation causes polymorphism.
Preferably, the A08 chromosome major QTL site of the oleic acid content trait of the brassica napus seeds is closely linked with a second SNP molecular marker, the second SNP molecular marker is located at the 11137029 th base, the 11137029 th base is A or T, and the mutation causes polymorphism.
Preferably, the major QTL site of the A08 chromosome of the oleic acid content trait of the brassica napus seeds is closely linked with a peak SNP molecular marker, the peak SNP molecular marker is located at the 10194057 th base of the A08 chromosome of the brassica napus, the 10194057 th base is C or T, and the mutation causes polymorphism.
In a second aspect of the invention, the SNP molecular marker of the major QTL site of the A08 chromosome of the rape seed oleic acid content trait is provided, and is characterized in that the SNP molecular marker is located at the 8348554 th base of the A08 chromosome of the cabbage rape, the 8348554 th base is A or G, and the mutation causes polymorphism.
In a third aspect of the present invention, an application of the SNP molecular marker of the major QTL locus of the a08 chromosome for the oleic acid content trait of brassica napus seeds in detecting the oleic acid content of brassica napus seeds, predicting the oleic acid content of brassica napus seeds, selecting the oleic acid content of brassica napus seeds, or assisting in breeding brassica napus with molecular markers for high oleic acid content seeds is provided.
In the fourth aspect of the invention, the SNP molecular marker of the major QTL site of the A08 chromosome of the oleic acid content character of the brassica napus seeds is provided, and is characterized in that the SNP molecular marker is positioned at the 11137029 th base of the A08 chromosome of the brassica napus, the 11137029 th base is A or T, and the mutation causes polymorphism.
In a fifth aspect of the present invention, an application of the SNP molecular marker of the major QTL site of the a08 chromosome for the traits of oleic acid content of brassica napus seeds in detecting the content of oleic acid in brassica napus seeds, predicting the content of oleic acid in brassica napus seeds, selecting the content of oleic acid in brassica napus seeds, or in molecular marker-assisted breeding of brassica napus seeds with high oleic acid content is provided.
In the sixth aspect of the invention, the peak SNP molecular marker of the major QTL site of the A08 chromosome of the oleic acid content character of the brassica napus seeds is provided, and is characterized in that the peak SNP molecular marker is positioned at the 10194057 th base of the A08 chromosome of the brassica napus, the 10194057 th base is C or T, and the mutation causes polymorphism.
In the seventh aspect of the present invention, an application of the peak SNP molecular marker of the major QTL locus of the a08 chromosome for the traits of oleic acid content of brassica napus seeds in detecting the content of oleic acid in brassica napus seeds, predicting the content of oleic acid in brassica napus seeds, selecting the content of oleic acid in brassica napus seeds, or in molecular marker-assisted breeding of brassica napus seeds with high oleic acid content in seeds is provided.
The invention has the following beneficial effects:
1. the major QTL site of the A08 chromosome of the rape seed oleic acid content character is positioned between the 8348554 th base and the 11137029 th base of the A08 chromosome of the rape seed, has high contribution rate to the rape seed oleic acid content character, plays a key role in regulating and controlling the rape seed oleic acid content, can be used for map cloning and molecular marker assisted selection, and is suitable for large-scale popularization and application.
2. The SNP molecular marker of the major QTL site of the A08 chromosome of the rape seed oleic acid content character comprises an SNP molecular marker of the 8348554 th base of the A08 chromosome of the cabbage rape, an SNP molecular marker of the 11137029 th base of the A08 chromosome of the cabbage rape and a peak SNP molecular marker of the 10194057 th base of the A08 chromosome of the cabbage rape, can detect the content of the oleic acid in the cabbage rape seed, can predict the content of the oleic acid in the cabbage rape seed, can effectively select the content of the oleic acid in the cabbage rape seed, can also be used for molecular marker assisted breeding of the cabbage rape seed with high content of the oleic acid, accelerates the breeding process of the high-seed oleic acid content of the cabbage rape, and is suitable for large-scale popularization and application.
3. The SNP molecular marker of the major QTL site of the A08 chromosome of the oleic acid content character of the brassica napus seeds comprises an SNP molecular marker of the 8348554 th base of the A08 chromosome of the brassica napus, an SNP molecular marker of the 11137029 th base of the A08 chromosome of the brassica napus and a peak SNP molecular marker of the 10194057 th base of the A08 chromosome of the brassica napus.
4. The application of the SNP molecular marker of the major QTL site of the A08 chromosome of the rape seed oleic acid content character comprises the application of the SNP molecular marker of the 8348554 th base of the A08 chromosome of the cabbage rape, the application of the SNP molecular marker of the 11129 th base of the A08 chromosome of the cabbage rape and the application of the peak SNP molecular marker of the 10194057 th base of the A08 chromosome of the cabbage rape.
5. The application of the SNP molecular marker of the major QTL site of the A08 chromosome of the rape seed oleic acid content character comprises the application of the SNP molecular marker of the 8348554 th base of the A08 chromosome of the cabbage rape, the application of the SNP molecular marker of the 11137029 th base of the A08 chromosome of the cabbage rape and the application of the peak SNP molecular marker of the 10194057 th base of the A08 chromosome of the cabbage rape.
These and other objects, features and advantages of the present invention will become more fully apparent from the following detailed description, the accompanying drawings and the claims, and may be realized by means of the instrumentalities, products and combinations particularly pointed out in the appended claims.
Drawings
FIG. 1 is a diagram illustrating the distribution results of the oleic acid content trait of Brassica napus seeds according to the present invention.
FIG. 2 is a schematic diagram of allelic analysis by using peak SNP molecular markers of A08 chromosome major QTL sites of the oleic acid content trait of Brassica napus seeds in the invention.
Detailed Description
Through intensive research, the inventor firstly discloses an A08 chromosome major QTL site with the character of the oleic acid content of the cabbage type rape seeds and an SNP molecular marker thereof, and can effectively and efficiently improve the oleic acid content of the cabbage type rape seeds by utilizing the QTL site.
The main effect QTL site of the A08 chromosome of the rape seed oleic acid content character is positioned between the 8348554 th base and the 11137029 th base of the A08 chromosome of the rape seed.
Preferably, the contribution rate of the A08 chromosome major QTL site for the oleic acid content trait of the brassica napus seeds to the oleic acid content trait of the brassica napus seeds is 71.84%.
Preferably, the major QTL site of the A08 chromosome of the oleic acid content trait of the brassica napus seeds is closely linked with a first SNP molecular marker, the first SNP molecular marker is located at the 8348554 th base, and the 8348554 th base is A or G, and the mutation causes polymorphism.
Preferably, the A08 chromosome major QTL site of the oleic acid content trait of the brassica napus seeds is closely linked with a second SNP molecular marker, the second SNP molecular marker is located at the 11137029 th base, the 11137029 th base is A or T, and the mutation causes polymorphism.
Preferably, the major QTL site of the A08 chromosome of the oleic acid content trait of the brassica napus seeds is closely linked with a peak SNP molecular marker, the peak SNP molecular marker is located at the 10194057 th base of the A08 chromosome of the brassica napus, the 10194057 th base is C or T, and the mutation causes polymorphism.
Also provides an SNP molecular marker of the major QTL site of the A08 chromosome of the rape seed oleic acid content character, which is positioned at the 8348554 th base of the A08 chromosome of the cabbage rape, wherein the 8348554 th base is A or G, and the mutation causes polymorphism. Namely the first SNP molecular marker.
Also provides application of the SNP molecular marker of the A08 chromosome major QTL site of the character of the oleic acid content of the cabbage type rape seeds in detecting the content of the oleic acid of the cabbage type rape seeds, predicting the content of the oleic acid of the cabbage type rape seeds, selecting the content of the oleic acid of the cabbage type rape seeds or in molecular marker-assisted breeding of the cabbage type rape seeds with high oleic acid content.
The SNP molecular marker of the major QTL site of the A08 chromosome of the oleic acid content trait of the brassica napus seeds is also provided, the SNP molecular marker is positioned at the 11137029 th base of the A08 chromosome of the brassica napus seeds, the 11137029 th base is A or T, and the mutation causes polymorphism. Namely the second SNP molecular marker.
The application of the SNP molecular marker of the major QTL site of the A08 chromosome for the oleic acid content character of the cabbage type rape seeds in detecting the content of oleic acid in the cabbage type rape seeds, predicting the content of oleic acid in the cabbage type rape seeds, selecting the content of oleic acid in the cabbage type rape seeds or assisting in breeding by the molecular marker of the cabbage type rape with high oleic acid content in the seeds is also provided.
The peak SNP molecular marker of the major QTL site of the A08 chromosome of the oleic acid content character of the cabbage type rape seeds is also provided, the peak SNP molecular marker is positioned at the 10194057 th base of the A08 chromosome of the cabbage type rape, the 10194057 th base is C or T, and the mutation causes polymorphism.
Also provides application of the peak SNP molecular marker of the major QTL site of the A08 chromosome of the oleic acid content character of the cabbage type rape seeds in detecting the content of oleic acid in the cabbage type rape seeds, predicting the content of oleic acid in the cabbage type rape seeds, selecting the content of oleic acid in the cabbage type rape seeds or in molecular marker assisted breeding of the cabbage type rape seeds with high oleic acid content.
The invention will be further illustrated with reference to the following specific examples. It should be understood that these examples are for illustrative purposes only and are not intended to limit the scope of the present invention. The experimental procedures, for which specific conditions are not noted in the following examples, are generally performed according to conventional conditions such as those described in J. SammBrook et al, molecular cloning, A laboratory Manual, third edition, scientific Press, 2002, or according to the manufacturer's recommendations.
Example 1 determination of phenotype of the oleic acid content trait of Brassica napus seeds
1. Determination of seed oleic acid content phenotype of related populations
(1) Carrying out field seed test analysis on the agronomic and quality traits of 627 parts of core germplasm materials (from a seed bank of the oil-vegetable research institute in Guizhou province), and selecting 300 high-generation brassica napus strains from all over the world to form a natural population, wherein the natural population comprises 98 parts of resources, 110 parts of breeding materials and 92 parts of varieties or parents; the method is divided into regions, wherein 246 parts belong to domestic and 54 parts belong to foreign sources. 3-year 2-point phenotype identification is completed on rape bases in Weiyuan village and Changxing town of Kaiyang county in Guiyang city.
(2) Direct seeding and final singling are adopted, the row spacing is 40cm, the plant spacing is 25cm, the row length is 3.5m, and each cell has 4 rows. And (4) planting protective rows around the test material field.
(3) The oleic acid content of the seeds is as follows: after the plants were normally mature, 10 brassica napus plants were taken per cell and the oleic acid content in units of% was determined for each mature clean seed using a near infrared scanner. The tabular values for all environments were averaged for 300 parts of material and the results are summarized as follows:
table 1 average of seed oleic acid content profile values for all environments of 300 parts material
The distribution result of the oleic acid content of the seeds of the related population shows that the character expression distribution of the oleic acid content of the seeds is in continuous bimodal distribution, and the oleic acid content character of the seeds is proved to be controlled by two major gene loci, which are shown in figure 1.
2. Acquisition of related population high quality SNP dataset
The CTAB method is adopted to extract the total DNA of the leaves, and the total DNA of the leaves of each material of the associated group is extracted, and the specific method comprises the following steps:
rinsing the young and tender leaves in 10% ethanol; then shearing 0.1-0.2g of blades, putting the blades into a grinding bowl, quickly grinding the blades into powder by using liquid nitrogen, and filling the powder into a 2mL centrifuge tube; adding 700 mu L of preheated DNA extracting solution; mixing, placing in 65 deg.C water bath for 1h, and mixing for 1 time every 10-15 min; adding 700 μ L of the mixture (phenol: chloroform: isoamyl alcohol = 25: 24: 1), and mixing by gentle inversion for 10min; centrifuging at 10000 Xg for 15min at room temperature; absorbing the supernatant into a new 2mL centrifuge tube; adding mixed solution with the same volume (chloroform: isoamylol = 24: 1), reversing and mixing uniformly, standing for 5min,10000 Xg, centrifuging for 15min, and sucking supernatant liquid into a new centrifugal tube by using a gun; adding 2 times volume of anhydrous ethanol, mixing, standing at-20 deg.C for 1h,10 000 Xg, centrifuging for 10min, and removing supernatant; adding 500 μ L of precooled 75% ethanol, washing the precipitate, and removing the supernatant; washing the precipitate for 2 times, and air drying; adding 100 μ L of RNase A solution containing 2% of RNase A, standing at 37 deg.C for 1h and then overnight at 4 deg.C; re-extracting the DNA solution with an equal volume of mixed solution (chloroform: isoamyl alcohol = 24: 1), mixing by inversion, standing for 10min,10 × g, centrifuging for 15 or 20min, removing RNase A, sucking the supernatant (about 60 μ L), and centrifuging again for 1min; detecting the concentration, quality and integrity of the DNA by agarose gel electrophoresis (0.8%) and an ultraviolet spectrophotometer; the absorbance 260/280 ratio was determined to be between 1.8-2.0 for all DNA samples. The DNA samples were then shipped on dry ice to a sequencing company (Huada science, inc.), each material having a sequencing depth of about 9X.
After obtaining high quality DNA as described above, the sequencing company (Huada science and technology Co., ltd.) performed 9 Xcoverage depth sequencing and returned data, and first performed sequencing quality evaluation using FastQC software, and then performed adapter and low quality reads filtration on the sequencing sequence. Obtaining clear data of double-end sequencing of each material, then performing mapping and GATK software for mutation detection by using bw software, performing SNP dataset quality filtration according to the minimum allele frequency of more than or equal to 0.05, the deletion rate of less than or equal to 0.1 and the heterozygosity rate of less than or equal to 0.15 after obtaining the total SNP dataset of the associated group, and finally obtaining a high-quality group SNP dataset for subsequent analysis.
3. Whole genome association analysis
Format conversion is carried out on the VCF file of the high-quality SNP data set generated in the last step by using plink software, and then the obtained seed oleic acid content phenotype is obtained by using EMMAX softwareCarrying out whole gene association analysis with the SNP data set to obtain the P value of each site of the oleic acid content character of the seeds, and when the P value is less than 5 multiplied by 10 -7 The SNP is the obvious SNP, the SNP with the minimum P value is the peak SNP, the materials are grouped by different allele types of the peak SNP in a group, variance analysis is carried out, and the percentage of the ratio of the variance between the groups to the total variance is the contribution rate of the peak SNP.
Through analysis, the interval of the main effect QTL site of the oleic acid content trait of the brassica napus seeds is limited between the 8348554 th base and the 11137029 th base of the A08 chromosome of the brassica napus, the corresponding SNPs are chrA08_8348554 (A/G), chrA08_11137029 (A/T), and the peak SNP is as follows: and chrA08_10194057 (C/T), wherein the contribution rate of the QTL to the oleic acid content character of the brassica napus seeds is 71.84% (the materials are grouped according to different allele types of peak SNP, the one-way variance analysis is carried out, and the percentage of the variance between groups divided by the total variance is the contribution rate).
The peak SNP of the seed oleic acid content character is as follows: chrA08_10194057 (C/T), corresponding to the seed oleic acid content phenotype grouping: when the SNP at the position chrA 08-10194057 is CC, the average seed oleic acid content of the material is 31.39%; at CT, the average seed oleic acid content of the material was 39.10%; at TT, the average seed oleic acid content of the material was 58.51%, as shown in figure 2.
One of the border SNPs for the seed oleic acid content trait is: chrA08_8348554 (A/G), corresponding to a phenotypic grouping of the seed oleic acid content: when the SNP at the position chrA08_8348554 is AA, the average seed oleic acid content of the material is 40.73 percent; AG, the average seed oleic acid content of the material is 50.53%; when GG is adopted, the average seed oleic acid content of the material is 58.53%, and the contribution rate of the boundary SNP is 39.85%.
Another border SNP for the seed oleic acid content trait is: chrA08_11137029 (A/T), corresponding to the seed oleic acid content phenotype grouping: when the SNP at position chrA08_11137029 is AA, the average seed oleic acid content of the material is 39.67%; AT, the average seed oleic acid content of the material was 40.54%; at TT, the average seed oleic acid content of the material was 43.75%, and the contribution of this border SNP was 57.89%.
The whole genome sequence of Brassica napus has been published, and is shown in http:// www. The sequences of 400bp (801 bp in total) before and after the sequence containing chrA08_8348554 (A/G) are shown in SEQ ID NO:1, the sequences of 400bp (801 bp in total) before and after the sequence containing chrA08_11137029 (A/T) are shown in SEQ ID NO:2, and the sequences of 400bp (801 bp in total) before and after the sequence containing chrA08_10194057 (C/T) are shown in SEQ ID NO: 3. The technicians in the field can adopt a conventional method to design a specific primer for detecting the SNP locus according to the sequence, so as to detect the genotype of the SNP locus, thereby being capable of detecting the oleic acid content of the cabbage type rape seeds, predicting the oleic acid content of the cabbage type rape seeds, effectively selecting the oleic acid content of the cabbage type rape seeds, being also capable of being used for molecular marker assisted breeding of the cabbage type rape seeds with high oleic acid content, and accelerating the process of the breeding of the cabbage type rape seeds with high oleic acid content.
Therefore, the method detects a major QTL site of the oleic acid content character of the brassica napus seeds on the chromosome A08 of the brassica napus through phenotype analysis and whole genome re-sequencing of the oleic acid content character of the seeds and then whole genome association analysis, and the contribution rate of the major QTL site to the oleic acid content of the brassica napus seeds is 71.84 percent. The main effect QTL site of the rape seed oleic acid content character is positioned between the 8348554 th base and the 11137029 th base of the A08 chromosome of the cabbage type rape, the obvious SNP of the boundary is chrA 08-8348554 (A/G), chrA 08-11137029 (A/T), and the peak SNP is chrA 08-10194057 (C/T), according to the SNP molecular marker tightly linked with the main effect QTL site, the method can be used for detecting the content of the oleic acid in the cabbage type rape seed, predicting the content of the oleic acid in the cabbage type rape seed, effectively selecting the content of the oleic acid in the cabbage type rape seed, assisting the breeding by the molecular marker of the cabbage type rape seed with high content of the oleic acid, and accelerating the process of the breeding of the cabbage type rape seed with high content of the oleic acid.
The SNP molecular marker disclosed by the invention is used for carrying out molecular marker-assisted selection, the identification method is simple, the selection efficiency is high, and the oleic acid content of the brassica napus seeds can be predicted. The selection target is clear and is not influenced by the environment. The individual cabbage type rape with high oleic acid content in the seeds can be identified in the early growth stage of the cabbage type rape, and other individual plants are eliminated.
In conclusion, the A08 chromosome major QTL site of the oleic acid content character of the brassica napus seeds has high contribution rate to the oleic acid content character of the brassica napus seeds, plays a key role in regulating and controlling the oleic acid content of the brassica napus seeds, can be used for map-based cloning and molecular marker-assisted selection, and is suitable for large-scale popularization and application.
It will thus be seen that the objects of the invention have been fully and effectively accomplished. The functional and structural principles of the present invention have been shown and described in the embodiments, and the embodiments may be modified without departing from the principles. Therefore, this invention includes all modifications encompassed within the spirit and scope of the claims.
Sequence listing
<110> research institute for rape in Guizhou province
<120> A08 chromosome major QTL site of cabbage type rape seed oleic acid content character, SNP molecular marker and application
<160> 3
<210> 1
<211> 801
<212> DNA
<213> Brassica napus (Brassica napus, L.)
<220>
<221> misc_feature
<222> (1)...(801)
<223> genome sequence comprising 400bp sequences before and after chrA08_8348554 (A/G)
<400> 1
tgtgagtgat ctaacttaaa accgaggaat agtgtatcat atgaaagcat tttgttgatc 60
agtggcactg tcgagtgagc tgcgagtaaa gagaaaatta gcctaaatcc tgatttgctt 120
gttgacccct cctgttttgt tctttcgcag aaacttgagt cacctttaaa ctcccaaact 180
gcaacaaaac aatatgctaa aatttgagga acttggatga atggctctct ttcacttaag 240
tacatctttt ctcatatgaa atagcactca gcttctagta gtagccttct tcattagcag 300
gcatgtcttc cctttcgctc tgtaccatta ctacttgtct attgttgttt ttgttctctc 360
aggttctgag actttgagac tgtttgttgt tggccaatct gatgtatgat taaatcacta 420
cactacactt gctttctata atgcaatacc agattctagg aaaaacctct gctacaagaa 480
cactcaaaat taagaataat tcttcaatct ctgctcctgc aatgcctcag cctgacccag 540
agttatgctt tcttctgaac aagctatcaa aaagttcaat aattacatat ggaagacctt 600
cgctgtcttg catagcttag ggcgagaacg taaacctatc aaaacaagta ttgaagactt 660
ttattatgga tgcttatcta agtctattta ctttgtatga tgtggttcca agattttatt 720
tgtgattttg ttatcagcaa gattttattt gtgtaaagtt ggcaaatgaa aaaggaatat 780
ttccactgga ctggttatca g 801
<210> 2
<211> 801
<212> DNA
<213> Brassica napus (Brassica napus, L.)
<220>
<221> misc_feature
<222> (1)...(801)
<223> genomic sequence comprising 400bp sequences of both before and after chrA 08-11137029 (A/T)
<400> 2
attgtattga tgtgaatgat tacaactctg aaggtcttaa aataccaacc gaaccagatt 60
gtccaatctg cctacaagat tttggtccta ggagcatcat caccaagttg cgctgctgcg 120
actacaattt tcacagggat tgtattctca cgtggctggg ccgcaagcct tcatgtccta 180
cttgtcgtga tgatatccac aacccccgac caaagaaatt taccccaaag atatttttag 240
gccgataaca catatatggc catgaactca aagattcaga tttttattta aatccttttc 300
cctttcatgt tgtgtctaat atgtatggct tttcttttct tttttccttt cctttttcgt 360
cttatatagt taagaattga atgaaaatat gtatcgtttc atgtaaaatt tgaatctaaa 420
tcttaaatct ttgaaggagg aacagttgac ttgaagaagc aaaccttcgg aagtgttttg 480
gttcatgtga agtttcttca gtagcacgag cagctaatga attggtgaaa gcaatctttg 540
gaggtatatc ctcgctttct tctaattaat taaacaaggg tcataatgtt ctctccatag 600
atgaaaaaac gttccatgta tgcctagaaa acatacagta caaacacaga atacaataat 660
aaaatggaat gccattctaa aagagtaaga acgtaattta ttttaacgcc aaaagtgtgc 720
taaagaaaac tattagaaaa ccatctaaca gatctcaaag tgctttcttt ttgtgcgcag 780
atcctatcaa agatcagatc c 801
<210> 3
<211> 801
<212> DNA
<213> Brassica napus (Brassica napus, L.)
<220>
<221> misc_feature
<222> (1)...(801)
<223> genome sequence comprising 400bp sequences before and after chrA08_10194057 (C/T)
<400> 3
aggttctact gtacatacat ttacccaatt gatttttctt ttaccgaata gtaaaggata 60
taagaagagc aagtcttctg gaacatggag gactaaccat atttacaaac caatccaccg 120
gttcttatga gatcagagat ctatcttaac aggatatcta tggatgcaat gttcccaagg 180
attcttaacc gatggctcga catccctaag agccacccaa accgcgctgt tacacttaaa 240
cccgcttcca aaagcaatct gccaaacccg gttccctttc ctcattcttc ctttagcttc 300
cgtataagcc aactcatacc atatagaact cgatgaagtg ttaccaaatc tatgcaacgt 360
cattctcgac gcttccacat gtttcggcaa aagccttaaa ttcttctcca gctcgtcgat 420
caccgctcta cctcccgcgt gtatacagaa atgatcaaac gcaagcttga aatccggcat 480
gtaaggcttc atcttcttct tagcattaaa cagtttattc acaagataag tcgcaaagaa 540
gagaatctgc tcgctcatgg gaagaacgag aggacccaaa gtggttatat tcgtcttaag 600
agcttctcca gctatagaca tcaggtcttt agacaaagaa acacctgttt tcaaagtctc 660
gtcttgttct tgatacacgc agttgaatgc tttctcatca gatcctttat gagtccttac 720
cgtgtgaaca agtttatact tggaacgttt acgatcacaa ctcttgttgg agagcagaac 780
cgcggatcca ccaatcctaa a 801
Claims (4)
1. An SNP molecular marker of an A08 chromosome major QTL site with the character of the oleic acid content of cabbage type rape seeds is characterized in that the nucleotide sequence of the SNP molecular marker is shown as SEQ ID NO:1, the 401 th base of the nucleotide sequence is A or G, and the mutation causes polymorphism.
2. The application of the SNP molecular marker of A08 chromosome major QTL site for oleic acid content traits of Brassica napus seeds as claimed in claim 1 in detecting the content of oleic acid in Brassica napus seeds, predicting the content of oleic acid in Brassica napus seeds, selecting the content of oleic acid in Brassica napus seeds, or molecular marker-assisted breeding of Brassica napus seeds with high oleic acid content.
3. An SNP molecular marker of an A08 chromosome major QTL site with the character of the oleic acid content of cabbage type rape seeds is characterized in that the nucleotide sequence of the SNP molecular marker is shown as SEQ ID NO. 2, the 401 th base of the nucleotide sequence is A or T, and the mutation causes polymorphism.
4. The application of the SNP molecular marker of A08 chromosome major QTL site for oleic acid content traits of Brassica napus seeds as claimed in claim 3 in detecting the content of oleic acid in Brassica napus seeds, predicting the content of oleic acid in Brassica napus seeds, selecting the content of oleic acid in Brassica napus seeds, or molecular marker-assisted breeding of Brassica napus seeds with high oleic acid content.
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN202010116243.7A CN111118204B (en) | 2020-02-25 | 2020-02-25 | A08 chromosome major QTL (quantitative trait locus) site with oleic acid content character of brassica napus seeds, SNP molecular marker and application |
Applications Claiming Priority (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN202010116243.7A CN111118204B (en) | 2020-02-25 | 2020-02-25 | A08 chromosome major QTL (quantitative trait locus) site with oleic acid content character of brassica napus seeds, SNP molecular marker and application |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CN111118204A CN111118204A (en) | 2020-05-08 |
| CN111118204B true CN111118204B (en) | 2023-04-14 |
Family
ID=70493058
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CN202010116243.7A Active CN111118204B (en) | 2020-02-25 | 2020-02-25 | A08 chromosome major QTL (quantitative trait locus) site with oleic acid content character of brassica napus seeds, SNP molecular marker and application |
Country Status (1)
| Country | Link |
|---|---|
| CN (1) | CN111118204B (en) |
Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2013049356A2 (en) * | 2011-09-27 | 2013-04-04 | Dow Agrosciences Llc | Ho/ll canola with resistance to clubroot disease |
| CN108728574A (en) * | 2018-06-21 | 2018-11-02 | 贵州省油菜研究所 | Main effect QTL site, SNP marker and the application of cabbage type rape seed density character |
| CN110527738A (en) * | 2019-08-28 | 2019-12-03 | 中国农业科学院油料作物研究所 | Main effect QTL site, SNP marker and its application of cabbage type rape seed oleic acid content |
-
2020
- 2020-02-25 CN CN202010116243.7A patent/CN111118204B/en active Active
Patent Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2013049356A2 (en) * | 2011-09-27 | 2013-04-04 | Dow Agrosciences Llc | Ho/ll canola with resistance to clubroot disease |
| CN108728574A (en) * | 2018-06-21 | 2018-11-02 | 贵州省油菜研究所 | Main effect QTL site, SNP marker and the application of cabbage type rape seed density character |
| CN110527738A (en) * | 2019-08-28 | 2019-12-03 | 中国农业科学院油料作物研究所 | Main effect QTL site, SNP marker and its application of cabbage type rape seed oleic acid content |
Non-Patent Citations (2)
| Title |
|---|
| Ruijuan Li等.Integrated QTL and eQTL Mapping Provides Insights and Candidate Genes for Fatty Acid Composition, Flowering Time, and Growth Traits in a F2 Population of a Novel Synthetic Allopolyploid Brassica napus.《Frontiers in Plant Science》.2018,第9卷补充表8中cis _coding工作表的第4行. * |
| 戴祥来等.甘蓝型优质杂交油菜品质性状与单株产量及群体产量的关系.《种子》.2018,第37卷第90-93页. * |
Also Published As
| Publication number | Publication date |
|---|---|
| CN111118204A (en) | 2020-05-08 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| CN108728575B (en) | Major QTL site of brassica napus silique length character, SNP molecular marker and application | |
| CN108754011B (en) | Major QTL (quantitative trait locus) site for thousand grain weight trait of brassica napus, SNP (Single nucleotide polymorphism) molecular marker and application | |
| CN108728574B (en) | Major QTL (quantitative trait locus) site for cabbage type rape grain density character, SNP (Single nucleotide polymorphism) molecular marker and application | |
| CN110527738B (en) | Major QTL (quantitative trait loci) site and SNP (single nucleotide polymorphism) molecular marker for oleic acid content of brassica napus seeds and application of major QTL site and SNP molecular marker | |
| CN108239674B (en) | Cabbage type rape high oleic acid QTL and molecular marker closely linked with same | |
| CN110592251B (en) | Main effect QTL locus of flowering phase character of brassica napus, SNP molecular marker development and application | |
| CN111500756B (en) | A05 chromosome main effect QTL site of cabbage type rape main inflorescence silique density character, SNP molecular marker and application | |
| CN110358854B (en) | Main effect QTL locus of main inflorescence pod number character of brassica napus, SNP molecular marker development and application | |
| CN110079629B (en) | SNP (Single nucleotide polymorphism) marker tightly linked with watermelon short vines, detection method and application | |
| CN114736986A (en) | SNP molecular marker related detection primer or probe of main effect QTL site of oil content character of cabbage type rape seed and application | |
| CN111100950B (en) | A02 chromosome major QTL locus of cabbage type rape oil content character, SNP molecular marker and application | |
| CN112602589B (en) | Method for rapid and accurate breeding of semi-waxy japonica rice restorer | |
| CN114350655B (en) | Exogenous radish fragment specific marker and preparation method and application thereof | |
| CN111118204B (en) | A08 chromosome major QTL (quantitative trait locus) site with oleic acid content character of brassica napus seeds, SNP molecular marker and application | |
| CN110527739B (en) | Major QTL (quantitative trait locus) site of glucosinolate content of brassica napus seeds, SNP (Single nucleotide polymorphism) molecular marker and application thereof | |
| CN109504798B (en) | SNP marker for identifying pear kernel size based on high resolution dissolution curve and application thereof | |
| CN111118203B (en) | A06 chromosome major QTL site with first effective branching number character of brassica napus, SNP molecular marker and application | |
| CN111118202B (en) | C03 chromosome major QTL (quantitative trait locus) site with oleic acid content character of brassica napus seeds, SNP (single nucleotide polymorphism) molecular marker and application | |
| CN111100951B (en) | A09 chromosome major QTL locus of cabbage type rape oil content character, SNP molecular marker and application | |
| CN114731949A (en) | High-oleic acid soybean mutant and detection method thereof | |
| CN111172315B (en) | A01 chromosome major QTL site with main inflorescence grain weight character of brassica napus, SNP molecular marker and application | |
| CN111118205B (en) | C07 chromosome major QTL site of main inflorescence silique density character of brassica napus, SNP molecular marker and application | |
| CN111500757B (en) | A02 chromosome major QTL (quantitative trait locus) site of main inflorescence length character of brassica napus, SNP molecular marker and application | |
| Jourdren et al. | Selection on pollen for linolenic acid content in rapeseed, Brassica napus L. | |
| CN116716425B (en) | Molecular marker of drooping character site of cabbage type rape leaf-rolling/pod and application thereof |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| PB01 | Publication | ||
| PB01 | Publication | ||
| SE01 | Entry into force of request for substantive examination | ||
| SE01 | Entry into force of request for substantive examination | ||
| GR01 | Patent grant | ||
| GR01 | Patent grant |