CN111118205B - C07 chromosome major QTL site of main inflorescence silique density character of brassica napus, SNP molecular marker and application - Google Patents
C07 chromosome major QTL site of main inflorescence silique density character of brassica napus, SNP molecular marker and application Download PDFInfo
- Publication number
- CN111118205B CN111118205B CN202010116274.2A CN202010116274A CN111118205B CN 111118205 B CN111118205 B CN 111118205B CN 202010116274 A CN202010116274 A CN 202010116274A CN 111118205 B CN111118205 B CN 111118205B
- Authority
- CN
- China
- Prior art keywords
- brassica napus
- molecular marker
- main inflorescence
- density
- silique density
- 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
Abstract
The invention provides a C07 chromosome major QTL locus for the silique density character of a main inflorescence of brassica napus, which is positioned between 42696564 base sites and 43484267 base sites of a C07 chromosome of the brassica napus. Preferably, the contribution rate to the silique density character of the main inflorescence of the brassica napus is 17.51%. Closely linked to the first SNP molecular marker, which is at base 42696564, either G or T, the mutation results in a polymorphism. Closely linked to the second SNP molecular marker, which is at base 43484267, either C or T, this mutation results in a polymorphism. Closely linked to the peak SNP molecular marker, which is at base 43199100, either G or T, the mutation results in a polymorphism. Also provides related SNP molecular markers and application. The C07 chromosome major QTL locus has high contribution rate to the silique density character of the main inflorescence of the brassica napus, plays a key role in regulating and controlling the silique density of the main inflorescence of the brassica napus, can be used for map 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 the silique density character of a main inflorescence of brassica napus, and specifically relates to a C07 chromosome main effect QTL locus of the silique density character of the main inflorescence of the brassica napus, an SNP molecular marker and application.
Background
The demand of edible oil in China is rigidly increased at the speed of 100 ten thousand tons per year, and the demand of vegetable oil is estimated to be 3.5-4.0 times of the current domestic production capacity by 2025 years, but the arable land resources in China are continuously reduced, so that the improvement of the unit yield of oil crops is a fundamental way for realizing the increase of the total yield of oil crops. The rape is the first large oil crop in China, the annual sowing area exceeds 1 hundred million acres, the total yield is more than 1500 ten thousand tons, and the rape seed oil accounts for more than 55 percent of the total amount of edible vegetable oil in China. At present, the planting area and the yield of rape industry in China continuously decline for years, the industrial safety degree declines year by year, and China is the largest world oil import country. The yield per unit is improved, the production cost is reduced to promote the income of farmers, and the method is a core measure for promoting the development of the rape industry in China and ensuring the safety of edible vegetable oil supply.
At present, the rape yield level in China is low, and the planting enthusiasm of farmers is influenced. The regional test yield level of the winter rape variety examined by China in 2001-2016 is 2.26-3.75 tons/hm 2 In between, the test is much lower than that of a new variety in 2013-2015 Canada for 4.06 tons/hm 2 The level of yield of (a); in recent years, the yield per unit of rape field production in China is about 1.92 tons/hm 2 And the EU is 3.12 tons/hm 2 Canada of 2.24 tons/hm 2 . Because the yield per unit of rape is low and the economic benefit is low, the enthusiasm of farmers for rape planting is influenced, and the normal development of the rape industry is restricted. In production, the need of creating new varieties of ultra-high yield rape with a yield level exceeding that of European Union and Canada is high.
The variety lack suitable for the whole-process mechanized production causes the production cost to be high. The total cost of rape production in China is up to 640 yuan/mu, wherein the labor input and management is higher than 360 yuan, and the total cost is 60-70%; and the total production cost of the rape in the European Union and Canada is less than 300 yuan/mu, wherein the labor input and management is only 7.5 yuan/mu, and the total cost is about 2.5 percent. The traditional rape varieties are high and large in lodging, branches are scattered and staggered, the maturity is inconsistent, siliques are easy to crack, great difficulty is caused to mechanized harvesting, semi-short-stalk lodging resistance, compact plant types, good maturity consistency and angle cracking resistance are urgently needed in production, and rape varieties suitable for mechanized operation are needed, but at present, mechanized breeding of rape in China just starts, and the production is extremely lack of suitable mechanized varieties.
One of the characteristics of rape varieties suitable for mechanized harvesting is that the rape varieties are suitable for close planting. Under the planting condition of 0.8-1.2 ten thousand plants/mu, the effective silique number of a single plant is a main factor influencing the yield, but under the planting condition of more than 2.6 ten thousand plants/mu, the silique density is the largest factor improving the yield, and the silique density and the yield are in positive correlation and are the key selection indexes in breeding. QTL mapping analysis indicates that silique density is genetically controlled by QTLs, primarily by additive effects. The gene for controlling the grain density has been cloned from crops such as rice and corn, and the research on the density of rape pod is very little.
Therefore, a main effect QTL site for the main inflorescence silique density character of the brassica napus needs to be provided, the contribution rate of the main inflorescence silique density character of the brassica napus is high, the main inflorescence silique density character of the brassica napus plays a key role in regulating and controlling the density of the main inflorescence siliques of the brassica napus, and the main effect QTL site can be used for site 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 C07 chromosome major QTL locus for the main inflorescence silique density character of the brassica napus, which has high contribution rate to the main inflorescence silique density character of the brassica napus, plays a key role in regulating and controlling the main inflorescence silique density of the brassica napus, can be used for site cloning and molecular marker assisted selection, and is suitable for large-scale popularization and application.
The invention also aims to provide an SNP molecular marker of the C07 chromosome major QTL locus of the main inflorescence silique density character of the brassica napus, which can detect the density of the main inflorescence siliques of the brassica napus, can predict the density of the main inflorescence siliques of the brassica napus, can effectively select the density of the main inflorescence siliques of the brassica napus, can be used for molecular marker-assisted breeding of the brassica napus with high main inflorescence silique density, accelerates the process of the high main inflorescence silique density breeding of the brassica napus, and is suitable for large-scale popularization and application.
The invention also aims to provide the SNP molecular marker of the C07 chromosome major QTL site of the main inflorescence silique density character of the brassica napus, 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 application of the SNP molecular marker of the C07 chromosome major QTL locus of the main inflorescence silique density character of the brassica napus, which can be used for detecting the density of the main inflorescence silique of the brassica napus, predicting the density of the main inflorescence silique of the brassica napus, effectively selecting the density of the main inflorescence silique of the brassica napus, assisting breeding by the molecular marker of the brassica napus with high main inflorescence silique density, accelerating the breeding process of the high main inflorescence silique of the brassica napus and being suitable for large-scale popularization and application.
The invention also aims to provide application of the SNP molecular marker of the C07 chromosome major QTL site of the brassica napus main inflorescence silique density character, 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 object, in a first aspect of the present invention, there is provided a C07 chromosome major QTL locus for the brassica napus major inflorescence silique density trait, characterized in that the C07 chromosome major QTL locus for the brassica napus major inflorescence silique density trait is located between bases 42696564 and bases 43484267 of the C07 chromosome of brassica napus.
Preferably, the contribution rate of the C07 chromosome major QTL locus for the main inflorescence silique density trait of Brassica napus to the main inflorescence silique density trait of Brassica napus is 17.51%.
Preferably, the C07 chromosome major QTL locus of the main inflorescence silique density trait of the Brassica napus is closely linked with a first SNP molecular marker, the first SNP molecular marker is located at 42696564 base, the 42696564 base is G or T, and the mutation causes polymorphism.
Preferably, the C07 chromosome major QTL locus of the main inflorescence silique density trait of the Brassica napus is closely linked with a second SNP molecular marker, the second SNP molecular marker is located at 43484267 base, the 43484267 base is C or T, and the mutation causes polymorphism.
Preferably, the C07 chromosome major QTL site of the brassica napus main inflorescence silique density trait is closely linked with a peak SNP molecular marker, the peak SNP molecular marker is located at the 43199100 th base, the 43199100 th base is G or T, and the mutation causes polymorphism.
In a second aspect of the invention, the SNP molecular marker of the C07 chromosome major QTL site of the main inflorescence silique density character of the brassica napus is provided, and is characterized in that the SNP molecular marker is located at the 42696564 base of the C07 chromosome of the brassica napus, the 42696564 base is G or T, and the mutation causes polymorphism.
In a third aspect of the present invention, an application of the SNP molecular marker of the C07 chromosome major QTL locus for the main inflorescence silique density trait of brassica napus in molecular marker-assisted breeding for detecting the main inflorescence silique density of brassica napus, predicting the main inflorescence silique density of brassica napus, selecting the main inflorescence silique density of brassica napus, or high-density main inflorescence silique of brassica napus is provided.
In the fourth aspect of the invention, the SNP molecular marker of the C07 chromosome major QTL site of the main inflorescence silique density character of the brassica napus is provided, and is characterized in that the SNP molecular marker is located at the 43484267 base of the C07 chromosome of the brassica napus, the 43484267 base is C or T, and the mutation causes polymorphism.
In a fifth aspect of the present invention, an application of the SNP molecular marker at the C07 chromosome major QTL locus for the brassica napus major inflorescence silique density trait described above in molecular marker-assisted breeding for detecting the level of the brassica napus major inflorescence silique density, predicting the level of the brassica napus major inflorescence silique density, selecting the level of the brassica napus major inflorescence silique density, or selecting the level of the major inflorescence silique density of brassica napus is provided.
In a sixth aspect of the invention, the peak SNP molecular marker of the C07 chromosome major QTL site of the main inflorescence silique density character of the brassica napus is provided, and is characterized in that the peak SNP molecular marker is located at the 43199100 base of the C07 chromosome of the brassica napus, the 43199100 base is G or T, and the mutation causes polymorphism.
In a seventh aspect of the present invention, an application of the peak SNP molecular marker for the C07 chromosome major QTL locus for the brassica napus major inflorescence silique density trait described above in molecular marker-assisted breeding for detecting the level of brassica napus major inflorescence silique density, predicting the level of brassica napus major inflorescence silique density, selecting the level of brassica napus major inflorescence silique density, or selecting the level of brassica napus major inflorescence silique density.
The invention has the following beneficial effects:
1. the main QTL site of the C07 chromosome of the main inflorescence silique density character of the brassica napus is positioned between the 42696564 base and the 43484267 base of the C07 chromosome of the brassica napus, the contribution rate of the main inflorescence silique density character of the brassica napus is high, the key role is played in the regulation and control of the main inflorescence silique density of the brassica napus, the main QTL site can be used for map bit cloning and molecular marker assisted selection, and the method is suitable for large-scale popularization and application.
2. The SNP molecular marker of the major inflorescence silique density trait C07 chromosome major QTL site of the brassica napus comprises an SNP molecular marker of 42696564 base of the C07 chromosome of the brassica napus, an SNP molecular marker of 43484267 base of the C07 chromosome of the brassica napus and a peak SNP molecular marker of 43199100 base of the C07 chromosome of the brassica napus, can detect the density of the major inflorescence silique of the brassica napus, can predict the density of the major inflorescence silique of the brassica napus, can effectively select the density of the major inflorescence silique of the brassica napus, can also be used for molecular marker assisted breeding of the brassica napus with high major inflorescence silique density, and accelerates the breeding process of the high major inflorescence silique density of the brassica napus, and is suitable for large-scale popularization and application.
3. The SNP molecular marker of the C07 chromosome major QTL site of the main inflorescence silique density character of the cabbage type rape comprises an SNP molecular marker of 42696564 base of the C07 chromosome of the cabbage type rape, an SNP molecular marker of 43484267 base of the C07 chromosome of the cabbage type rape and a peak SNP molecular marker of 43199100 base of the C07 chromosome of the cabbage type rape.
4. The application of the SNP molecular marker of the major QTL site of the C07 chromosome of the main inflorescence silique density character of the brassica napus comprises the application of the SNP molecular marker of the 42696564 base position of the C07 chromosome of the brassica napus, the application of the SNP molecular marker of the 43484267 base position of the C07 chromosome of the brassica napus and the application of the peak SNP molecular marker of the 43199100 base position of the C07 chromosome of the brassica napus.
5. The application of the SNP molecular marker of the major QTL site of the C07 chromosome of the main flowering locus silique density character of the brassica napus comprises the application of the SNP molecular marker of the 42696564 base of the C07 chromosome of the brassica napus, the application of the SNP molecular marker of the 43484267 base of the C07 chromosome of the brassica napus and the application of the peak SNP molecular marker of the 43199100 base of the C07 chromosome of the brassica napus.
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 schematic diagram of the distribution results of the pod density trait of the brassica napus main inflorescence of the present invention.
FIG. 2 is a schematic diagram of allelic analysis by using peak SNP molecular markers of C07 chromosome C07 main effect QTL sites of the main inflorescence silique density trait of Brassica napus in the present invention.
Detailed Description
Through intensive research, the inventor firstly discloses a C07 chromosome main effect QTL locus of a cabbage type rape main inflorescence silique density character and an SNP molecular marker thereof, and can effectively and efficiently improve the cabbage type rape high main inflorescence silique density by utilizing the locus.
The main inflorescence silique density character C07 chromosome major QTL locus of the brassica napus is positioned between 42696564 base and 43484267 base of the C07 chromosome of the brassica napus.
Preferably, the contribution rate of the C07 chromosome major QTL locus for the main inflorescence silique density trait of Brassica napus to the main inflorescence silique density trait of Brassica napus is 17.51%.
Preferably, the C07 chromosome major QTL locus of the main inflorescence silique density trait of the Brassica napus is closely linked with a first SNP molecular marker, the first SNP molecular marker is located at 42696564 base, the 42696564 base is G or T, and the mutation causes polymorphism.
Preferably, the C07 chromosome major QTL locus of the main inflorescence silique density trait of the Brassica napus is closely linked with a second SNP molecular marker, the second SNP molecular marker is located at 43484267 base, the 43484267 base is C or T, and the mutation causes polymorphism.
Preferably, the C07 chromosome major QTL locus of the main inflorescence silique density trait of the brassica napus is closely linked with a peak SNP molecular marker, the peak SNP molecular marker is located at 43199100 base, the 43199100 base is G or T, and the mutation causes polymorphism.
The SNP molecular marker of the C07 chromosome major QTL site of the cabbage type rape main inflorescence silique density character is also provided, the 42696564 base of the C07 chromosome of the cabbage type rape is positioned, the 42696564 base is G or T, and the mutation causes polymorphism. Namely the first SNP molecular marker.
Also provides application of the SNP molecular marker of the C07 chromosome main effect QTL locus of the main inflorescence silique density character of the cabbage type rape in detecting the height of the main inflorescence silique density of the cabbage type rape, predicting the height of the main inflorescence silique density of the cabbage type rape, selecting the height of the main inflorescence silique density of the cabbage type rape or in molecular marker-assisted breeding of the cabbage type rape with the high main inflorescence silique density.
The SNP molecular marker of the major QTL site of the C07 chromosome of the main inflorescence silique density character of the brassica napus is also provided, the base is 43484267 of the C07 chromosome of the brassica napus, the base at 43484267 is C or T, and the mutation causes polymorphism. Namely the second SNP molecular marker.
Also provides application of the SNP molecular marker of the C07 chromosome main effect QTL locus of the main inflorescence silique density character of the cabbage type rape in detecting the height of the main inflorescence silique density of the cabbage type rape, predicting the height of the main inflorescence silique density of the cabbage type rape, selecting the height of the main inflorescence silique density of the cabbage type rape or in molecular marker-assisted breeding of the cabbage type rape with the high main inflorescence silique density.
The peak SNP molecular marker of the main inflorescence silique density character C07 chromosome main effect QTL locus of the brassica napus is also provided, the peak SNP molecular marker is positioned at 43199100 base of the C07 chromosome of the brassica napus, the 43199100 base is G or T, and the mutation causes polymorphism.
Also provides application of the peak SNP molecular marker of the C07 chromosome major QTL site of the main inflorescence silique density character of the brassica napus in detecting the height of the main inflorescence silique density of the brassica napus, predicting the height of the main inflorescence silique density of the brassica napus, selecting the height of the main inflorescence silique density of the brassica napus or in molecular marker-assisted breeding of the brassica napus with the high main inflorescence silique density.
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. SammBruk et al, molecular cloning protocols, third edition, scientific Press, 2002, or according to the manufacturer's recommendations.
Example 1 determination of phenotype of Brassica napus Master inflorescence silique Density traits
1. Determination of dominant inflorescence silique density phenotype of related populations
(1) Carrying out field seed examination analysis on the agronomic and quality traits of 627 parts of core germplasm materials (from a seed bank of the oil-rape research institute in Guizhou province), and selecting 300 cabbage type rape high-generation 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 years of phenotype identification at 2 points is completed in rape bases in Qinghe village, kaiyang county, guiyang city and Weiyuan town, changshun county.
(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 4 rows are arranged in each cell. And (4) planting protective rows around the test material field.
(3) Density of main inflorescence siliques: after the plants are normally mature, measuring the length of the main inflorescence of 10 cabbage type rape in units of centimeters to be accurate to 0.1cm in each cell, counting the number of effective siliques on the main inflorescence, and then obtaining the density of the main inflorescence siliques in units of per cm by using the number (number) of the effective siliques of the main inflorescence/the length (cm) of the main inflorescence. The tabular values for all environments were averaged for 300 parts of material and the results are summarized as follows:
TABLE 1 average value of dominant inflorescence silique Density phenotype values for all environments of 300 parts of Material
The density distribution result of the main inflorescence siliques of the related population shows that the performance distribution of the density character of the main inflorescence siliques is in continuous distribution, and the density character of the main inflorescence siliques is proved to be controlled by the major gene locus, which is shown in figure 1.
2. Acquisition of related population high quality SNP data set
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 bowl mill, quickly milling the blades into powder by using liquid nitrogen, and putting 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 mixed solution (phenol: chloroform: isoamyl alcohol = 25: 24: 1), and mixing by gentle inversion for 10min; centrifuging at 10000 Xg for 15min at room temperature; sucking 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 mu L of precooled 75% ethanol, washing the precipitate, and removing supernatant; washing the precipitate for 2 times, and air drying; adding 100 μ L of 2% RNase A solution, standing at 37 deg.C for 1h, and standing overnight at 4 deg.C; re-extracting DNA solution with 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 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 and 2.0 for all DNA samples. The DNA samples were then transported on dry ice to sequencing Inc. (Huada science and technology, 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 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 using bwa software to carry out mapping and GATK software to carry out mutation detection, and after obtaining a total SNP data set of an associated group, carrying out SNP data set quality filtering 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, and finally obtaining a high-quality group SNP data set for subsequent analysis.
3. Whole genome association analysis
Performing format conversion on a VCF file of the high-quality SNP data set generated in the last step by using plink software, performing whole-gene association analysis on the obtained main inflorescence silique density phenotype and the SNP data set by using EMMAX software to obtain a P value of each site of the main inflorescence silique density trait, 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 QTL site of the main inflorescence silique density character of the brassica napus is limited between 42696564 bases to 43484267 bases of the C07 chromosome of the brassica napus, the corresponding SNPs are chrC 07-42696564 (G/T) and chrC 07-43484267 (C/T), the peak SNP is: the contribution rate of the QTL to the main inflorescence silique density character of the brassica napus is 17.51 percent (the materials are grouped according to different allele types of peak SNP, the one-way anova 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 density character of the main inflorescence silique is as follows: chrC07_43199100 (G/T), corresponding to the major inflorescence silique density phenotype were grouped as: when the SNP at the position of chrC07_43199100 is GG, the average main inflorescence silique density of the material is 1.13/cm; GT, the average major inflorescence silique density of the material is 1.22/cm; at TT, the average major inflorescence silique density of the material was 1.88/cm, as shown in FIG. 2.
One of the border SNPs for the main inflorescence silique density trait is: chrC07_42696564 (G/T), corresponding to the major inflorescence silique density phenotype were grouped as: when the SNP at the position of chrC07_42696564 is GG, the average main inflorescence silique density of the material is 1.14/cm; GT, the average major inflorescence silique density of the material is 1.19/cm; at TT, the average main inflorescence silique density of the material was 1.57/cm, and the contribution rate of this border SNP was 9.54%.
Another border SNP for the main inflorescence silique density trait is: chrC 07-43484267 (C/T), grouped corresponding to the dominant inflorescence silique density phenotype: when the SNP at the position of chrC 07-43484267 is CC, the average main inflorescence silique density of the material is 1.88/cm; at CT, the average main inflorescence silique density of the material is 1.22/cm; at TT, the average major inflorescence silique density of the material was 1.13/cm, and the contribution of this border SNP was 17.43%.
The whole genome sequence of Brassica napus has been published, see http:// www.genoscope.cns.fr/brassicana/. The sequences (801 bp) of 400bp before and after containing chrC 07-42696564 (G/T) are shown as SEQ ID NO:1, the sequences (801 bp) of 400bp before and after containing chrC 07-43484267 (C/T) are shown as SEQ ID NO:2, and the sequences (801 bp) of 400bp before and after containing chrC 07-43199100 (G/T) are shown as 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 density of the siliques of the main inflorescence of the brassica napus, predicting the density of the siliques of the main inflorescence of the brassica napus, effectively selecting the density of the siliques of the main inflorescence of the brassica napus, being also capable of being used for molecular marker assisted breeding of the brassica napus with high density of the siliques, and accelerating the process of the high-density breeding of the siliques of the brassica napus.
Therefore, the main-effect QTL site of the main-inflorescence silique density character of the brassica napus is detected on the C07 th chromosome of the brassica napus by phenotype analysis and whole-genome re-sequencing of the main-inflorescence silique density character and then whole-genome association analysis, and the contribution rate of the main-effect QTL site to the main-inflorescence silique density of the brassica napus is 17.51 percent. The main QTL site of the main inflorescence silique density character of the brassica napus is positioned between 42696564 bases to 43484267 bases of a C07 chromosome of the brassica napus, the boundary significant SNP is chrC 07-42696564 (G/T), chrC 07-43484267 (C/T), and the peak SNP is chrC 07-43199100 (G/T).
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 silique density of the main inflorescence of the brassica napus can be predicted. The selection target is clear and is not influenced by the environment. The individual cabbage type rape with high main inflorescence silique density can be identified in the early growth stage of the cabbage type rape, and other individual plants are eliminated.
In conclusion, the C07 chromosome major QTL locus for the main inflorescence silique density trait of the brassica napus has high contribution rate to the main inflorescence silique density trait of the brassica napus, plays a key role in regulating and controlling the main inflorescence silique density of the brassica napus, can be used for map bit 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
C07 chromosome major QTL locus of cabbage type rape main inflorescence silique density 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 of chrC07_42696564 (G/T) before and after
<400> 1
gatttgatta ttttatttga tggtagaagc atttttacgt ttttgttcat ttatttgaac 60
aagtaatata tttttaataa atgactctgt tgacaatatg gttctaaaat tcatataata 120
tgatctcaaa ctaaataatt atgtttttgg tataaaaccg aataaaccga aaaccacggt 180
atataaaccg aaccgaaccg aagtaaatat gtatttagaa tggtagttat attttactaa 240
ccgaaatacc gaaaaccgaa aaaaaccgaa cctaaaccga accgatatcc ggattgaaca 300
cccttcgtca ttagctttgc ctttactaag agctcacata gtcaataaaa aagtaacttg 360
cttagcaata acaacatcac agtttgatgc ataatgtttc gttaaatggt tctaaaagaa 420
gcaaaggatc gaagtcatgt ctctaatagt acgacccaac cacattcctt tcaaggcaaa 480
gtcttcatat gaattaaaaa aaaaagaggg aaacacaagt tcatatatca aaacgggtgg 540
gtgggttgtt tggtgattga tatcacctca ctggctgttg attgtagtga ctcttctctt 600
tcttcttctt tgcggcagcc agctttgcct tcctagcagc tgcttcttgt gcagcaactt 660
ttgcagcagc atccgtctct ttgcttgatt tcttcttctt cactgatgca atcttcttca 720
gccgttcttt gatatccatg gaagaagagg cctcctcgct ctcctgctca ccagactcac 780
ctgcagcagc atctgcgttg c 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 chrC07_43484267 (C/T) in front and rear of each
<400> 2
cacccacctc ccaagaaaaa ggcgacatac actcggatga taacaattat agccaacaag 60
tgtctctaac tcatccaaaa tctacaacat atatcacatg gtttctctag tcctctagca 120
tcatggatta tgtcataatt tataaacatg gactattctc tccatgtttc ttttcatacc 180
gtccaaaagc caaccagcaa atacattgaa atagaaagtt attctaatca atatataaat 240
gcatttacct tgtgtgttta atgcttctag atttgcgtga gagataaacg cacatgatca 300
cgtaatttca accagtagca agaacttatg gtttgacgca tgaactctat aaacattaaa 360
agattgtttg taataggaac tttaaacaag aatcatgatt ttacataaaa ggttcacgat 420
cttgaggtat aggcttaatt attttttgta agttgaggtt gaggtcttgc acggattaca 480
cgcaatactc ctaaacctat acttacttct agttctatat taaatctggc gtgtctgatt 540
cgtctgccaa tattcagtta caattaaagt gccttgtatt agtgtatcac ttataggcaa 600
ccctaagagc atatgcattc ctagttttgg agaaagattc tccaaatttg agaaattaat 660
ggatgagttt tgaatttttg agaacccatt tatatttaac tattatttat attccaatat 720
ttttttagaa cctcttttat gatgttctta ctattgaaaa tgcttttgac aaaatatagt 780
tttctataca cattaatctg t 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 of chrC07_43199100 (G/T) before and after
<400> 3
gtacatcatg tcatgtagta tttgacgaac tcagaggatg caaaaacata ccggtggttt 60
tcttgcaagt tatgtagctg tcgcttcaga atcgcagcct cattttgcca aaactataat 120
atagcagaat tattttcagg tgacggaaac tgagaaaaca agttttttac ggaattaaca 180
cttatcaagt ctagaatgga ttcttgaaaa agataatgca atataatgta tgtaatctta 240
tgttcaggtg catcttgaga ggagtcaaaa gttgaaatag gctaacgaag ctgtagcaaa 300
ctaacattat aaaaagcacc aagtaagtaa ctatctcttt gttttactat gttacttgtt 360
tggtctattc gtaattcatt tagagtatta actgcatcaa gtattcgttg aaattcatag 420
agaggactaa taaacattga accaaaagag gaataccttg atttctgaag ctgggttcat 480
ttccgaattg gtgtcacatt tggcatctct gtatctctct attaccgact tcatgctgcc 540
aaaaaaagaa gaaggttaag ttgtatatct gcaggagtga gtttggcagg taaggtaact 600
cgagcaacat caactgcatc atttctcctt acatatcttc ggtgacaaaa cttttactta 660
aactacccta agccaatttt accaacgtgg aaattaattc tctgtaccaa aaatacagat 720
tctccatact ctaaacataa catgatgttg catgaagctt aagtagagaa tgaaagaaac 780
aagaccaaac ttatgtacaa g 801
Claims (6)
1. An SNP molecular marker of a C07 chromosome major QTL site of a cabbage type rape main inflorescence silique density character is characterized in that a nucleotide sequence of the SNP molecular marker is shown as SEQ ID NO. 1, a 401 th base of the nucleotide sequence is G or T, and polymorphism is caused by mutation.
2. The application of the SNP molecular marker of the C07 chromosome major QTL locus of the main inflorescence silique density trait of the Brassica napus as claimed in claim 1 in detection of the main inflorescence silique density of the Brassica napus, prediction of the main inflorescence silique density of the Brassica napus, selection of the main inflorescence silique density of the Brassica napus or molecular marker-assisted breeding of Brassica napus with high main inflorescence silique density.
3. An SNP molecular marker of a C07 chromosome major QTL site of a main inflorescence silique density character of a cabbage type rape is characterized in that a nucleotide sequence of the SNP molecular marker is shown as SEQ ID NO. 2, the 401 th base of the nucleotide sequence is C or T, and the mutation causes polymorphism.
4. The application of the SNP molecular marker of the C07 chromosome major QTL locus of the main inflorescence silique density trait of the Brassica napus as claimed in claim 3 in detection of the main inflorescence silique density of the Brassica napus, prediction of the main inflorescence silique density of the Brassica napus, selection of the main inflorescence silique density of the Brassica napus or molecular marker-assisted breeding of Brassica napus with high main inflorescence silique density.
5. A peak SNP molecular marker of a C07 chromosome major QTL site of a main inflorescence silique density character of a cabbage type rape is characterized in that a nucleotide sequence of the peak SNP molecular marker is shown as SEQ ID NO. 3, the 401 th base of the nucleotide sequence is G or T, and the mutation causes polymorphism.
6. The application of the peak SNP molecular marker of the C07 chromosome major QTL site for the main inflorescence silique density trait of the Brassica napus according to claim 5 in detecting the main inflorescence silique density of the Brassica napus, predicting the main inflorescence silique density of the Brassica napus, selecting the main inflorescence silique density of the Brassica napus or performing molecular marker assisted breeding of the Brassica napus with the high main inflorescence silique density.
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN202010116274.2A CN111118205B (en) | 2020-02-25 | 2020-02-25 | C07 chromosome major QTL site of main inflorescence silique density character of brassica napus, SNP molecular marker and application |
Applications Claiming Priority (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN202010116274.2A CN111118205B (en) | 2020-02-25 | 2020-02-25 | C07 chromosome major QTL site of main inflorescence silique density character of brassica napus, SNP molecular marker and application |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CN111118205A CN111118205A (en) | 2020-05-08 |
| CN111118205B true CN111118205B (en) | 2023-04-14 |
Family
ID=70493115
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CN202010116274.2A Active CN111118205B (en) | 2020-02-25 | 2020-02-25 | C07 chromosome major QTL site of main inflorescence silique density character of brassica napus, SNP molecular marker and application |
Country Status (1)
| Country | Link |
|---|---|
| CN (1) | CN111118205B (en) |
Citations (6)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN104805080A (en) * | 2014-10-30 | 2015-07-29 | 中国农业科学院油料作物研究所 | Rapeseed pod number major QTL molecular marker and application thereof |
| CN105766621A (en) * | 2015-12-01 | 2016-07-20 | 贵州省油菜研究所 | Breeding method of rape with high-density siliques on main inflorescence and application |
| CN108504773A (en) * | 2018-06-27 | 2018-09-07 | 中国农业科学院油料作物研究所 | Molecular labeling and its application of cabbage type rape grain weight and Pod length main effect QTL site |
| CN109762926A (en) * | 2019-03-20 | 2019-05-17 | 中国农业科学院油料作物研究所 | A kind of and the associated molecular labeling primer of siliqua of oilseed rape number and application |
| CN110358854A (en) * | 2019-06-17 | 2019-10-22 | 中国农业科学院油料作物研究所 | Main effect QTL site, SNP marker exploitation and the application of one cabbage type rape main inflorescence silique number character |
| CN111500756A (en) * | 2020-02-25 | 2020-08-07 | 贵州省油菜研究所 | A05 chromosome main effect QT L locus of brassica napus main inflorescence silique density character, SNP molecular marker and application |
Family Cites Families (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| AU2003271381B8 (en) * | 2003-12-24 | 2010-11-18 | BASF Agricultural Solutions Seed US LLC | Brassica plant resistant to the fungus Leptosphaeria maculans (blackleg) |
| EP2016821A1 (en) * | 2007-06-13 | 2009-01-21 | Syngeta Participations AG | New hybrid system for Brassica napus |
-
2020
- 2020-02-25 CN CN202010116274.2A patent/CN111118205B/en active Active
Patent Citations (6)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN104805080A (en) * | 2014-10-30 | 2015-07-29 | 中国农业科学院油料作物研究所 | Rapeseed pod number major QTL molecular marker and application thereof |
| CN105766621A (en) * | 2015-12-01 | 2016-07-20 | 贵州省油菜研究所 | Breeding method of rape with high-density siliques on main inflorescence and application |
| CN108504773A (en) * | 2018-06-27 | 2018-09-07 | 中国农业科学院油料作物研究所 | Molecular labeling and its application of cabbage type rape grain weight and Pod length main effect QTL site |
| CN109762926A (en) * | 2019-03-20 | 2019-05-17 | 中国农业科学院油料作物研究所 | A kind of and the associated molecular labeling primer of siliqua of oilseed rape number and application |
| CN110358854A (en) * | 2019-06-17 | 2019-10-22 | 中国农业科学院油料作物研究所 | Main effect QTL site, SNP marker exploitation and the application of one cabbage type rape main inflorescence silique number character |
| CN111500756A (en) * | 2020-02-25 | 2020-08-07 | 贵州省油菜研究所 | A05 chromosome main effect QT L locus of brassica napus main inflorescence silique density character, SNP molecular marker and application |
Non-Patent Citations (3)
| Title |
|---|
| Jiang Ye.An integrated analysis of QTL mapping and RNA sequencing provides further insights and promising candidates for pod number variation in rapeseed (Brassica napus L.).《BMC Genomics》.2017,第18卷(第71期),第1-14页. * |
| 向阳.甘蓝型油菜双主茎YD4899的选育及表型性状比较分析.《种子》.2021,第40卷(第7期),第125-129,134,149页. * |
| 王会等.利用甘蓝型油菜高密度SNP遗传图谱定位角果相关性状QTL位点.《2014中国作物学会学术年会论文集》.2014,第44页. * |
Also Published As
| Publication number | Publication date |
|---|---|
| CN111118205A (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 | |
| CN110117673B (en) | Molecular marker of brassica napus dwarf trait locus and application thereof | |
| CN110592251B (en) | Main effect QTL locus of flowering phase character of brassica napus, SNP molecular marker development and application | |
| CN108300801B (en) | Molecular marker closely related to rape grain weight and silique length and application | |
| CN114736986B (en) | SNP molecular marker related detection primer or probe of major QTL locus of oil content character of brassica napus seeds and application | |
| CN111500756B (en) | A05 chromosome main effect QTL site of cabbage type rape main inflorescence silique density character, SNP molecular marker and application | |
| CN114854894A (en) | SNP molecular marker of main effect QTL site of thousand grain weight trait of brassica napus, related detection primer or probe and application | |
| CN110894542A (en) | Primer for identifying types of GS5 gene and GLW7 gene of rice and application of primer | |
| CN110747288A (en) | Rice large grain gene function 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 | |
| CN111100950B (en) | A02 chromosome major QTL locus of cabbage type rape oil content character, SNP molecular marker and application | |
| CN111118203B (en) | A06 chromosome major QTL site with first effective branching number 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 | |
| CN111100951B (en) | A09 chromosome major QTL locus of cabbage type rape oil content character, SNP molecular marker and application | |
| CN110862444A (en) | Maize bm1 gene mutant and molecular marker and application thereof | |
| CN112176082A (en) | SNP molecular marker of wheat grain weight related gene and application thereof | |
| CN111500757B (en) | A02 chromosome major QTL (quantitative trait locus) site of main inflorescence length character of brassica napus, SNP molecular marker and application | |
| CN111172315B (en) | A01 chromosome major QTL site with main inflorescence grain weight 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 | |
| CN111118204B (en) | A08 chromosome major QTL (quantitative trait locus) site with oleic acid content character of brassica napus seeds, SNP molecular marker and application | |
| CN117106802B (en) | Cabbage type rape high-dehiscence-angle resistance gene and identification and application thereof | |
| CN112430682B (en) | InDel molecular marker coseparated with maize fragile gene 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 |