CN111500756B - A05 chromosome main effect QTL site of cabbage type rape main inflorescence silique density character, SNP molecular marker and application - Google Patents
A05 chromosome main effect QTL site of cabbage type rape main inflorescence silique density character, SNP molecular marker and application Download PDFInfo
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Abstract
The invention provides a cabbage type rape main inflorescence silique density character A05 chromosome main effect QTL locus, which is positioned between 20957390 th base and 21315610 th base of a cabbage type rape A05 chromosome. Preferably, the contribution rate to the silique density character of the main inflorescence of the brassica napus is 15.36%. Closely linked to the first SNP molecular marker, which is at base 20957390 and is either A or G, this mutation results in a polymorphism. Closely linked to a second SNP molecular marker, located at base 21315610, either C or T, the mutation resulting in a polymorphism. Closely linked to the peaked SNP molecular marker, which is at base 21171737, either C or T, this mutation results in a polymorphism. Also provides related SNP molecular markers and application. The A05 chromosome major QTL site 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 an A05 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 the rape industry in China continuously decline for years, the industrial safety degree declines year by year, and China is the largest oil import country in the world. 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 The new variety test is much lower than that in 2013-2015 years of Canada by 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 2.24 tons/hm in Canada 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 the production process, the creation of a new variety of the super-high-yield rape with the unit yield level exceeding that of European Union and Canada is urgently needed.
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%; the total production cost of the rape of 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 density of the seeds of crops such as rice, corn and the like has been cloned, and the research on the density of the rape pod is 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 an A05 chromosome major QTL site 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 A05 chromosome major QTL site 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 breeding process of the high main inflorescence siliques density 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 A05 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 A05 chromosome major QTL site 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 major QTL site of the A05 chromosome of the main inflorescence silique density character of the brassica napus, which has the advantages of ingenious design, simple, convenient 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 an a05 chromosome major QTL locus for the trait of brassica napus main inflorescence silique density, characterized in that the a05 chromosome major QTL locus for the trait of brassica napus main inflorescence silique density is located between the 20957390 th base and the 21315610 th base of the a05 chromosome of brassica napus.
Preferably, the contribution rate of the A05 chromosome major QTL site of the main inflorescence silique density character of the brassica napus to the main inflorescence silique density character of the brassica napus is 15.36%.
Preferably, the A05 chromosome major QTL site of the main flowering silique density trait of the brassica napus is closely linked with a first SNP molecular marker, the first SNP molecular marker is located at the 20957390 th base, and the 20957390 th base is A or G, and the mutation causes polymorphism.
Preferably, the A05 chromosome major QTL site of the main flowering silique density trait of the brassica napus is closely linked with a second SNP molecular marker, the second SNP molecular marker is positioned at the 21315610 th base, the 21315610 th base is C or T, and the mutation causes polymorphism.
Preferably, the A05 chromosome major QTL site 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 the 21171737 base, the 21171737 base is C or T, and the mutation causes polymorphism.
In a second aspect of the invention, the SNP molecular marker of the A05 chromosome major QTL site of the cabbage type rape main inflorescence silique density character is provided, and is characterized in that the SNP molecular marker is located at the 20957390 th base of the A05 chromosome of the cabbage type rape, the 20957390 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 a05 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 major QTL site of the A05 chromosome of the main inflorescence silique density character of the cabbage type rape is provided, and is characterized in that the SNP molecular marker is positioned at the 21315610 th base of the A05 chromosome of the cabbage type rape, the 21315610 th 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 a05 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 major QTL site of the A05 chromosome of the cabbage type rape main inflorescence silique density trait is provided, and is characterized in that the peak SNP molecular marker is located at the 21171737 base of the A05 chromosome of the cabbage type rape, the 21171737 base is C or T, and polymorphism is caused by mutation.
In the seventh aspect of the present invention, an application of the peak SNP molecular marker of the major QTL locus of the a05 chromosome for the trait of the main inflorescence pod density of brassica napus in molecular marker-assisted breeding for detecting the main inflorescence pod density of brassica napus, predicting the main inflorescence pod density of brassica napus, selecting the main inflorescence pod density of brassica napus, or breeding brassica napus with high main pod density is provided.
The invention has the following beneficial effects:
1. the A05 chromosome major QTL site of the cabbage type rape main inflorescence silique density character is positioned between the 20957390 th base and 21315610 th base of the A05 chromosome of the cabbage type rape, the contribution rate of the QTL site to the cabbage type rape main inflorescence silique density character is high, the key role is played in the regulation and control of the cabbage type rape main inflorescence silique density, the QTL site can be used for mapping and molecular marker-assisted selection, and the method is suitable for large-scale popularization and application.
2. The SNP molecular markers of the major QTL site of the A05 chromosome of the main inflorescence silique density character of the cabbage type rape comprise a SNP molecular marker of a 20957390 th base of the A05 chromosome of the cabbage type rape, a SNP molecular marker of a 21315610 th base of the A05 chromosome of the cabbage type rape and a peak SNP molecular marker of a 21171737 th base of the A05 chromosome of the cabbage type rape.
3. The SNP molecular marker of the main flowering sequence silique density character A05 chromosome main effect QTL site of the cabbage type rape comprises an SNP molecular marker of a 20957390 th base of the A05 chromosome of the cabbage type rape, an SNP molecular marker of a 21315610 th base of the A05 chromosome of the cabbage type rape and a peak SNP molecular marker of a 21171737 th base of the A05 chromosome of the cabbage type rape.
4. The application of the SNP molecular marker of the major flowering locus QTL of the A05 chromosome of the cabbage type rape in the main flowering characteristic of the flowering locus silique of the cabbage type rape comprises the application of the SNP molecular marker of the 20957390 th base of the A05 chromosome of the cabbage type rape, the application of the SNP molecular marker of the 21315610 th base of the A05 chromosome of the cabbage type rape and the application of the peak SNP molecular marker of the 21171737 th base of the A05 chromosome of the cabbage type rape.
5. The application of the SNP molecular marker of the main flowering characteristic silique density locus of the A05 chromosome of the cabbage type rape comprises the application of the SNP molecular marker of the 20957390 th base of the A05 chromosome of the cabbage type rape, the application of the SNP molecular marker of the 21315610 th base of the A05 chromosome of the cabbage type rape and the application of the peak SNP molecular marker of the 21171737 th base of the A05 chromosome of the cabbage type 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 schematic diagram showing the distribution results of the silique density trait of the main inflorescence of Brassica napus according to the present invention.
FIG. 2 is a schematic diagram of allelic analysis by using peak SNP molecular markers of A05 chromosome A05 major QTL sites for the main inflorescence silique density trait of Brassica napus in the present invention.
Detailed Description
The inventor firstly discloses an A05 chromosome major QTL locus of a cabbage type rape main inflorescence silique density character and an SNP molecular marker thereof through deep research, and can effectively and efficiently improve the cabbage type rape high main inflorescence silique density by utilizing the locus.
The main flowering locus of A05 chromosome of the cabbage type rape pod density character is positioned between 20957390 th basic group and 21315610 th basic group of the A05 chromosome of the cabbage type rape.
Preferably, the contribution rate of the A05 chromosome major QTL site of the main inflorescence silique density character of the brassica napus to the main inflorescence silique density character of the brassica napus is 15.36%.
Preferably, the A05 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 the 20957390 th base, the 20957390 th base is A or G, and the mutation causes polymorphism.
Preferably, the A05 chromosome major QTL site 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 positioned at the 21315610 th base, the 21315610 th base is C or T, and the mutation causes polymorphism.
Preferably, the A05 chromosome major QTL site of the main flowering line silique density trait of the brassica napus is tightly linked with a peak SNP molecular marker, the peak SNP molecular marker is positioned at the 21171737 base, and the 21171737 base is C or T, and the mutation causes polymorphism.
Also provides an SNP molecular marker of the major QTL site of the A05 chromosome of the main inflorescence silique density character of the Brassica napus, which is positioned at the 20957390 th base of the A05 chromosome of the Brassica napus, wherein the 20957390 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 A05 chromosome major QTL site 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.
Also provides an SNP molecular marker of the major QTL site of the A05 chromosome of the main inflorescence silique density character of the cabbage type rape, the SNP molecular marker is positioned at the 21315610 th base of the A05 chromosome of the cabbage type rape, the 21315610 th base 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 A05 chromosome major QTL site 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.
Also provides a peak SNP molecular marker of the major QTL site of the A05 chromosome of the cabbage type rape main inflorescence silique density character, which is positioned at the 21171737 base of the A05 chromosome of the cabbage type rape, wherein the 21171737 base is C or T, and the mutation causes polymorphism.
Also provides application of the peak SNP molecular marker of the A05 chromosome major QTL site of the main inflorescence silique density character of the cabbage type rape in detecting the main inflorescence silique density of the cabbage type rape, predicting the main inflorescence silique density of the cabbage type rape, selecting 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 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 the Master inflorescence silique Density phenotype of the associate population
(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 food 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 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 1 hr, 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 the mixed solution with the same volume (chloroform: isoamylol = 24: 1), reversing and uniformly mixing, standing for 5min,10000 Xg, centrifuging for 15min, and sucking the supernatant 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 and precipitating for 2 times continuously, and then airing; 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 1.8-2.0 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 first performed sequencing quality evaluation using FastQC software, and then performed adapter and low quality reads filtration on the sequencing sequence. Obtaining cleardata 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. Genome-wide association analysis
Using plink software to perform format conversion on a VCF file of the high-quality SNP data set generated in the last step, then using EMMAX software to perform whole-gene association analysis on the obtained main inflorescence silique density phenotype and the SNP data set to obtain a P value of each site of the main inflorescence silique density character, 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 flowering silique density character of the cabbage type rape is limited between the 20957390 th base and 21315610 th base of the A05 chromosome of the cabbage type rape, the corresponding SNPs are chrA 05-20957390 (A/G), chrA 05-21315610 (C/T), and the peak SNP is: and chrA 05-21171737 (C/T), wherein the contribution rate of the QTL to the silique density character of the main inflorescence of the brassica napus is 15.36 percent (the materials are grouped according to different allele types of peak SNP, single-factor analysis on variance 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: chrA05_21171737 (C/T), grouped according to the main inflorescence silique density phenotype: when the SNP at the position chrA 05-21171737 is CC, the average main inflorescence silique density of the material is 1.52/cm; at CT, the average main inflorescence silique density of the material is 1.20/cm; at TT, the average major inflorescence silique density of the material was 1.13/cm, as shown in FIG. 2.
One of the border SNPs for the main inflorescence silique density trait is: chrA05_20957390 (A/G), the corresponding major inflorescence silique density phenotype was grouped as: when the SNP at position chrA 05-20957390 is AA, the average main inflorescence silique density of the material is 1.44/cm; AG, the average main inflorescence silique density of the material is 1.35 per cm; GG showed that the average major inflorescence silique density of the material was 1.13/cm, and the contribution rate of the border SNP was 11.37%.
Another border SNP for the main inflorescence silique density trait is: chrA05_21315610 (C/T), grouped as corresponding major inflorescence silique density phenotype: when the SNP at position chrA05_21315610 is CC, the average main inflorescence silique density of the material is 1.43/cm; at CT, the average main inflorescence silique density of the material is 1.26/cm; at TT, the average main inflorescence silique density of the material was 1.13/cm, and the contribution rate of this border SNP was 9.04%.
The whole genome sequence of Brassica napus has been published, and is shown in http:// www. The sequences (801 bp) of 400bp before and after the chrA 05-20957390 (A/G) are shown in SEQ ID NO:1, the sequences (801 bp) of 400bp before and after the chrA 05-21315610 (C/T) are shown in SEQ ID NO:2, and the sequences (801 bp) of 400bp before and after the chrA 05-21171737 (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 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 method detects a main effect QTL site of the main inflorescence silique density character of the brassica napus on the chromosome A05 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 15.36 percent. The main-effect QTL site of the main inflorescence silique density character of the cabbage type rape is positioned between the 20957390 th base and the 21315610 th base of an A05 chromosome of the cabbage type rape, the obvious SNP of the boundary is chrA 05-20957390 (A/G), chrA 05-21315610 (C/T), the peak SNP is chrA 05-21171737 (C/T), and according to the SNP molecular marker tightly linked with the main-effect QTL site, the molecular marker can be used for 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, effectively selecting the height of the main inflorescence silique density of the cabbage type rape, and assisting breeding by the molecular marker of the cabbage type rape with high main inflorescence silique density, and accelerating the breeding process of the high main inflorescence silique density of the cabbage type rape.
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 A05 chromosome major QTL site of the main inflorescence silique density character of the brassica napus 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 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
<120> A05 chromosome major QTL site 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> genomic sequence comprising 400bp sequences of both before and after chrA 05-20957390 (A/G)
<400> 1
gttggattgt aacggaataa agtgaaatct gtcgggaatt ttgttcacat tctgtcggaa 60
agaggttgtc ggctggctat aaggtgcttt gagatgctca tatcttaatc tgatgggcta 120
ttgggtgatg gtaaagaaag tttgggagct tttaaagtga gattttgttg gatatggtgg 180
gctggatcat agtctctgat ctggttaggt gccactggga taaaagatct agaaagtaac 240
tgaagtggtt taaagtatac cactttaagg gaacttgaga gaggggataa aagtgccaat 300
gtctcgttgc ttcccgtttc caccaccagg atatgagaag aagaagatta gaaccgagga 360
ggctgactct ttagtaaagg ttaaactcat agaatctact gctctccttt gaaatggtga 420
tagtgatgtt tctaaggtcg tagattgaat ctgcaggaaa agcaaaagaa ggagaagaag 480
cacaaaaagg agaagaagga taaagaaaca agcaaagata gatataagga agggaaggag 540
agaaaagaga aacatagaga taagaaagac aaagaaaaga gcacgacttc tcaggacaaa 600
aataatggta atgaggagtc taagtttgtg caggacttgg caagaaggat cagcaatgaa 660
aaagaagaag ctagagagag tcaaagtgtg gggaagagta gttttccctg tggagttaca 720
gagaattttc ccatgggaaa aaggtctgaa agttcggttg gtcgagtatc ctcttggaga 780
gatcagaaag gaactgagat t 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 chrA05_21315610 (C/T)
<400> 2
cgccagtgag ctttccataa gctctcagca atatgatcca ccacaagcct gtagcagaaa 60
gttacattct cagtaaaaat gtgactgttt ctcaaagata agtggaaatg taatttattc 120
aactaaaagg aactgaaagt tgagcataat gagttaccag agtcaacggg gctaacacgt 180
ccaatagctg attcaccaaa gtctgcatct aaacactcct caaacgagcc atcattgcct 240
tcaagtgatt tcactttaaa actcgctggc attagccctg ggccagggct gtgacagtcc 300
actgttttct cccagctcta caaaaccaag tcaattagaa aacttttgca tagataagta 360
aataaaatag tacattacaa agtaaatcac ttttctaagt tccagaacct atatggcagg 420
caaggaaatg aaaagttttt aggccatgaa aaatgtaaat caatatttct aatgctcaga 480
gcgcttcacc aaagaaatat ttgaaagaaa acatttctga aagttactga ttaaaagaat 540
taagccatca actttttggg caatctgagc aaattaaaac ttaacaaagc aggcaaggag 600
aggcatcttc aagaatatca cagcacattc attctaacaa ctaaatgaca aaagtaaaca 660
aactttttgg gtctaaacaa ctaaaaacac atacctggaa ctgcaatgta caggggagag 720
atttctccaa gtcttgcctt tctccgttag gcaataaaac tcagtacaca aactagatac 780
atttcccgtt ttcacaaaaa 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 both the front and back of chrA05_21171737 (C/T)
<400> 3
cacttttgat ctcgcttcag ctcaggtgaa acacttattt gaattttggt gtagaagacc 60
caatatgcaa tttgatcgta ttgtgttttg tttcacagtt attcaagttg gggacagtcc 120
agttcatatg tgtatctgat gataactcag aggaggaggt tcgtaaaagt tacttacttt 180
actatattta tacttgatta tgtaatcaga atgtgtttat tttgttgcgt ttggaacaga 240
gatcgttctc taaaggagtt aatataaagt ttggaagtga gaaggatagc aaagagtttt 300
gtgattcatt cgaggagtgg agaaaggatg ctcttgttca tggtgcgtct tagactctga 360
agaaccagtt tatctctgtg catactcatt gattgttctt ttcattcttt cgtttatagg 420
atcatccaca gtttcagcta gtaaaagcaa gtttgacgat aagattgagg cgtcctctgc 480
caaaatgtat ttccattact atggacaact tctacatcag caaaacatgc ttcaagatta 540
tgtcaggaca ggtaaaatta tatgggattg tatgtatttg gttgcctagg aactggtcca 600
cttctcttgt agaggatgta aattcatcag aagaaatatc atctgtcttc ttagcacctc 660
attcatgtct tcaggtacat attatgctgc ggtgatggag aaccgttcag attttgctgg 720
tcgtgttgtg gtcgatgtgg gtgctgggag tggcattttg tctatgtttg ctgcccaggt 780
atgcattaag atgacttgtt t 801
Claims (6)
1. An SNP molecular marker of a main flowering characteristic A05 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, the 401 th base of the nucleotide sequence is A or G, and polymorphism is caused by mutation.
2. The application of the SNP molecular marker of the A05 chromosome major QTL locus for 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 the Brassica napus with high main inflorescence silique density.
3. An SNP molecular marker of a main flowering characteristic and silique density characteristic A05 chromosome major QTL locus of a cabbage type rape main inflorescence 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 polymorphism is caused by mutation.
4. The application of the SNP molecular marker of the A05 chromosome major QTL locus for 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 the Brassica napus with high main inflorescence silique density.
5. A peak SNP molecular marker of a main fruiting QTL site of an A05 chromosome of a main inflorescence pod 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 C or T, and the mutation causes polymorphism.
6. The application of the peak SNP molecular marker of the A05 chromosome major QTL site for the main inflorescence silique density trait of the Brassica napus as claimed in claim 5 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 the Brassica napus with high main inflorescence silique density.
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| CN111118205B (en) * | 2020-02-25 | 2023-04-14 | 贵州省油菜研究所 | C07 chromosome major QTL site of main inflorescence silique density character of brassica napus, SNP molecular marker and application |
| CN116716425B (en) * | 2023-01-16 | 2023-11-28 | 南京农业大学 | Molecular marker of drooping character site of cabbage type rape leaf-rolling/pod and application thereof |
Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| 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 |
| CN108728575A (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 Pod length character |
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| AU2018378789A1 (en) * | 2017-12-08 | 2020-06-11 | Seminis Vegetable Seeds, Inc. | Brassica oleracea plants with downy mildew resistant curds or heads |
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Patent Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| 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 |
| CN108728575A (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 Pod length character |
Non-Patent Citations (2)
| Title |
|---|
| Yi Yang等.High Density Linkage Map Construction and QTL Detection for Three Silique-Related Traits in Orychophragmus violaceus Derived Brassica napus Population.《Frontiers in Plant Science》.2017,第8卷第1-13页. * |
| 胡鸣等.基于高深度重测序的春性、半冬性和冬性甘蓝型油菜基因组遗传变异分析.《中国油料作物学报》.2018,第40卷第469-478页. * |
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