CN111118203A - A06 chromosome major QTL site with first effective branching number character of brassica napus, SNP molecular marker and application - Google Patents
A06 chromosome major QTL site with first effective branching number character of brassica napus, SNP molecular marker and application Download PDFInfo
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Abstract
The invention provides a major QTL site of an A06 chromosome with a first effective branching number character of Brassica napus, which is positioned between 4152373 th base and 4570188 th base of an A06 chromosome of the Brassica napus. Preferably, the contribution rate to the trait of the first effective branch number of brassica napus is 12.43%. Closely linked to the first SNP molecular marker, which is located at base 4152373 and is either C or T, the mutation results in a polymorphism. Closely linked to a second SNP molecular marker, which is located at base 4570188, and is either A or T, this mutation results in a polymorphism. Closely linked to the peak SNP molecular marker, which is at base 4336568 and is either C or G, this mutation results in a polymorphism. Also provides related SNP molecular markers and application. The A06 chromosome major QTL locus has high contribution rate to the first effective branch number character of the cabbage type rape, plays a key role in regulating and controlling the first effective branch number of the cabbage type rape, can be used for site 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 first effective branch number character of cabbage type rape, and specifically relates to an A06 chromosome major QTL locus of the first effective branch number character of cabbage type rape, 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/hm2In between, the test is far lower than that of a new variety in 2013-2015 of Canada by 4.06 tons/hm2The level of yield of (a); in recent years, the yield per unit of rape field production in China is about 1.92 tons/hm2And 3.12 tons/hm in the European Union2Canada of 2.24 tons/hm2. 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 lack of varieties suitable for the whole-process mechanized production causes the production cost to be high. The total rape production cost in China is as high as 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.
The branch number is one of important plant type characters related to crop yield, namely a main factor suitable for mechanized plant type shaping and important agronomic characters influencing yield. Studies have shown that increasing the branching number of individual rape plants Can significantly increase the silique number of the whole Plant, and thus increase the yield of individual plants [ Camball D C, Kondra Z P.relationships and growth growing patterns, yield components and yield of rapeseed [ J ]. Can J Plant,1978,58(1):87-93 ]. Sheikh et al [ Sheikh F A, Rather A G, Wani S A. genetic variation and inter-relationship shift in Toria [ J ] Adv Plant Sci,1999,12(1): 139-.
The rape branch number is the quantitative character controlled by multiple genes, and is expressed as continuous variation, and is greatly influenced by the environment.
Therefore, it is required to provide a main QTL site for the first effective branching number trait of brassica napus, which has a high contribution rate to the first effective branching number trait of brassica napus, plays a key role in controlling the first effective branching number of brassica napus, and can be used for site-directed 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 A06 chromosome major QTL locus with the first-time effective branching number character of the brassica napus, which has high contribution rate to the first-time effective branching number character of the brassica napus, plays a key role in regulating and controlling the first-time effective branching number 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 the SNP molecular marker of the major QTL site of the A06 chromosome of the first effective branching number character of the cabbage type rape, which can detect the number of the first effective branches of the cabbage type rape, can predict the number of the first effective branches of the cabbage type rape, can effectively select the number of the first effective branches of the cabbage type rape, can be used for molecular marker assisted breeding of the cabbage type rape with a large number of the first effective branches, accelerates the high-yield breeding process of the cabbage type rape, and is suitable for large-scale popularization and application.
The invention also aims to provide the SNP molecular marker of the major QTL site of the A06 chromosome for the first effective branching number 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 major QTL site of the A06 chromosome of the first effective branching number character of the cabbage type rape, which can detect the number of the first effective branches of the cabbage type rape, predict the number of the first effective branches of the cabbage type rape, effectively select the number of the first effective branches of the cabbage type rape, be used for molecular marker-assisted breeding of the cabbage type rape with a large number of the first effective branches, accelerate the high-yield breeding process of the cabbage type rape and be 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 A06 chromosome for the first effective branching number 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.
In order to achieve the above object, in a first aspect of the present invention, there is provided an a06 chromosome major QTL locus for the first effective branching number trait of brassica napus, wherein the a06 chromosome major QTL locus for the first effective branching number trait of brassica napus is located between the 4152373 th base and the 4570188 th base of the a06 chromosome of brassica napus.
Preferably, the contribution rate of the A06 chromosome major QTL locus for the first effective branching number trait of Brassica napus to the first effective branching number trait of Brassica napus is 12.43%.
Preferably, the major QTL site of the A06 chromosome of the cabbage type rape first-time effective branching number trait is closely linked with a first SNP molecular marker, the first SNP molecular marker is located at the 4152373 th base, the 4152373 th base is C or T, and the mutation causes polymorphism.
Preferably, the A06 chromosome major QTL site of the cabbage type rape first effective branching number trait is closely linked with a second SNP molecular marker, the second SNP molecular marker is located at the 4570188 th base, the 4570188 th base is A or T, and the mutation causes polymorphism.
Preferably, the major QTL site of the A06 chromosome of the first effective branching number trait of the brassica napus is closely linked with a peak SNP molecular marker, the peak SNP molecular marker is located at the 4336568 th base of the A06 chromosome of the brassica napus, the 4336568 th base is C or G, and the mutation causes polymorphism.
In a second aspect of the invention, the SNP molecular marker of the major QTL site of the A06 chromosome of the first effective branching number trait of the cabbage type rape is provided, and is characterized in that the SNP molecular marker is located at the 4152373 th base of the A06 chromosome of the cabbage type rape, the 4152373 th base is C or T, and the mutation causes polymorphism.
In a third aspect of the present invention, the application of the SNP molecular marker of the major QTL locus of the a06 chromosome for the trait of the first effective number of branches of brassica napus is provided for detecting the number of the first effective branches of brassica napus, predicting the number of the first effective branches of brassica napus, selecting the number of the first effective branches of brassica napus, or performing molecular marker-assisted breeding on brassica napus with a large number of first effective branches.
In the fourth aspect of the invention, the SNP molecular marker of the major QTL site of the A06 chromosome of the first effective branching number trait of the cabbage type rape is provided, and is characterized in that the SNP molecular marker is positioned at the 4570188 th base of the A06 chromosome of the cabbage type rape, the 4570188 th base is A or T, and the mutation causes polymorphism.
In the fifth aspect of the present invention, the application of the SNP molecular marker of the major QTL locus of the a06 chromosome for the trait of the first effective number of branches of brassica napus described above in detecting the number of the first effective branches of brassica napus, predicting the number of the first effective branches of brassica napus, selecting the number of the first effective branches of brassica napus, or in molecular marker-assisted breeding of brassica napus with a large number of first effective branches is provided.
In the sixth aspect of the invention, the peak SNP molecular marker of the major QTL site of the A06 chromosome of the first effective branching number trait of the cabbage type rape is provided, and is characterized in that the peak SNP molecular marker is located at the 4336568 th base of the A06 chromosome of the cabbage type rape, the 4336568 th base is C or G, and the mutation causes polymorphism.
In the seventh aspect of the present invention, the application of the peak SNP molecular marker of the major QTL locus of the a06 chromosome for the trait of the first effective branching number of brassica napus in molecular marker assisted breeding is provided, wherein the peak SNP molecular marker is used for detecting the number of first effective branches of brassica napus, predicting the number of first effective branches of brassica napus, selecting the number of first effective branches of brassica napus, or performing molecular marker assisted breeding on brassica napus with a large number of first effective branches.
The invention has the following beneficial effects:
1. the A06 chromosome major QTL site of the cabbage type rape first effective branching number trait is positioned between 4152373 th base and 4570188 th base of the A06 chromosome of the cabbage type rape, has high contribution rate to the first effective branching number trait of the cabbage type rape, plays a key role in regulating and controlling the first effective branching number of the cabbage type rape, can be used for map location cloning and molecular marker assisted selection, and is suitable for large-scale popularization and application.
2. The SNP molecular marker of the major QTL site of the A06 chromosome of the first effective branching number character of the cabbage type rape comprises an SNP molecular marker of a 4152373 th base of an A06 chromosome of the cabbage type rape, an SNP molecular marker of a 4570188 th base of an A06 chromosome of the cabbage type rape and a peak SNP molecular marker of an 4336568 th base of an A06 chromosome of the cabbage type rape, can detect the number of the first effective branching number of the cabbage type rape, can predict the number of the first effective branching number of the cabbage type rape, can effectively select the number of the first effective branching number of the cabbage type rape, can also be used for molecular marker assisted breeding of the cabbage type rape with a large number of the first effective branching number, accelerates the high-yield breeding process of the cabbage type rape, and is suitable for large-scale popularization and application.
3. The SNP molecular marker of the major QTL site of the A06 chromosome of the first effective branching numerical trait of the cabbage type rape comprises the SNP molecular marker of the 4152373 th base of the A06 chromosome of the cabbage type rape, the SNP molecular marker of the 4570188 th base of the A06 chromosome of the cabbage type rape and the peak SNP molecular marker of the 4336568 th base of the A06 chromosome of the cabbage type rape.
4. The application of the SNP molecular marker of the major QTL site of the A06 chromosome of the first effective branching number character of the cabbage type rape comprises the application of the SNP molecular marker of the 4152373 th base of the A06 chromosome of the cabbage type rape, the application of the SNP molecular marker of the 4570188 th base of the A06 chromosome of the cabbage type rape and the application of the peak SNP molecular marker of the 4336568 th base of the A06 chromosome of the cabbage type rape.
5. The application of the SNP molecular marker of the major QTL site of the A06 chromosome with the first effective branching number character of the cabbage type rape comprises the application of the SNP molecular marker of the 4152373 th base of the A06 chromosome of the cabbage type rape, the application of the SNP molecular marker of the 4570188 th base of the A06 chromosome of the cabbage type rape and the application of the peak SNP molecular marker of the 4336568 th base of the A06 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 diagram showing the distribution results of the first effective branch number trait of Brassica napus of the present invention.
FIG. 2 is a schematic diagram of allelic analysis of the peak SNP molecular marker of the major QTL site of the A06 chromosome, which utilizes the first effective branching number trait of Brassica napus in the present invention.
Detailed Description
The inventor of the invention, through intensive research, firstly reveals an A06 chromosome major QTL locus of the first effective branch number character of the cabbage type rape and an SNP molecular marker thereof, and can effectively and efficiently improve the yield of the cabbage type rape by utilizing the locus.
The main QTL site of the A06 chromosome for the first effective branching number trait of the cabbage type rape is positioned between the 4152373 th base and the 4570188 th base of the A06 chromosome of the cabbage type rape.
Preferably, the contribution rate of the A06 chromosome major QTL locus for the first effective branching number trait of Brassica napus to the first effective branching number trait of Brassica napus is 12.43%.
Preferably, the major QTL site of the A06 chromosome of the cabbage type rape first-time effective branching number trait is closely linked with a first SNP molecular marker, the first SNP molecular marker is located at the 4152373 th base, the 4152373 th base is C or T, and the mutation causes polymorphism.
Preferably, the A06 chromosome major QTL site of the cabbage type rape first effective branching number trait is closely linked with a second SNP molecular marker, the second SNP molecular marker is located at the 4570188 th base, the 4570188 th base is A or T, and the mutation causes polymorphism.
Preferably, the major QTL site of the A06 chromosome of the first effective branching number trait of the brassica napus is closely linked with a peak SNP molecular marker, the peak SNP molecular marker is located at the 4336568 th base of the A06 chromosome of the brassica napus, the 4336568 th base is C or G, and the mutation causes polymorphism.
Also provides an SNP molecular marker of the major QTL site of the A06 chromosome of the first effective branching number trait of the cabbage type rape, which is located at the 4152373 th base of the A06 chromosome of the cabbage type rape, wherein the 4152373 th base is C or T, and the mutation causes polymorphism. Namely the first SNP molecular marker.
Also provides the application of the SNP molecular marker of the major QTL site of the A06 chromosome of the first effective branching number character of the cabbage type rape in detecting the number of the first effective branching number of the cabbage type rape, predicting the number of the first effective branching number of the cabbage type rape, selecting the number of the first effective branching number of the cabbage type rape or carrying out molecular marker assisted breeding on the cabbage type rape with a large number of the first effective branching numbers.
Also provides an SNP molecular marker of the major QTL site of the A06 chromosome of the first effective branching number trait of the cabbage type rape, which is located at the 4570188 th base of the A06 chromosome of the cabbage type rape, wherein the 4570188 th base is A or T, and the mutation causes polymorphism. Namely the second SNP molecular marker.
Also provides the application of the SNP molecular marker of the major QTL site of the A06 chromosome of the first effective branching number character of the cabbage type rape in detecting the number of the first effective branching number of the cabbage type rape, predicting the number of the first effective branching number of the cabbage type rape, selecting the number of the first effective branching number of the cabbage type rape or carrying out molecular marker assisted breeding on the cabbage type rape with a large number of the first effective branching numbers.
Also provides a peak SNP molecular marker of the major QTL site of the A06 chromosome of the first effective branching number trait of the cabbage type rape, which is located at the 4336568 th base of the A06 chromosome of the cabbage type rape, wherein the 4336568 th base is C or G, and the mutation causes polymorphism.
Also provides application of the peak SNP molecular marker of the major QTL site of the A06 chromosome of the first effective branching number character of the cabbage type rape in detecting the number of first effective branches of the cabbage type rape, predicting the number of first effective branches of the cabbage type rape, selecting the number of first effective branches of the cabbage type rape or in molecular marker assisted breeding of the cabbage type rape with a large number of first effective branches.
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 phenotypic determination of the first effective branching number trait in Brassica napus
1. Determination of the first valid branching number phenotype of a related 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 method is divided into regions, wherein 246 parts belong to domestic and 54 parts belong to foreign sources. 3-year 2-point phenotype identification is completed on rape bases in Weiyuan village and Changxing town of Kaiyang county in Guiyang city.
(2) Direct seeding and final singling are adopted, the row spacing is 40cm, the plant spacing is 25cm, the row length is 3.5m, and 4 rows are arranged in each cell. And (4) planting protective rows around the test material field.
(3) First effective number of branches: after the plants are normally mature, 10 cabbage type rapes are taken from each cell, and the number of the first effective branches of each cabbage type rape is measured, wherein the unit is one. The tabular values for all environments were averaged for 300 parts of material and the results are summarized as follows:
TABLE 1300 materials average of first effective branch number tabulated values for all environments
The first effective branch number distribution result of the associated population shows that the first effective branch number character expression distribution is in continuous distribution and normal distribution, and the first effective branch number character is proved to belong to quantitative characters and have main effective gene loci, as shown in figure 1.
2. Acquisition of related population high quality SNP data set
The method comprises the following steps of (1) extracting total DNA of leaves by adopting a CTAB method, and extracting the total DNA of the leaves of each material of a related population, wherein 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 10 min; centrifuging at room temperature at 10000 Xg for 15 min; sucking the supernatant into a new 2mL centrifuge tube; adding equal volume of mixed solution (chloroform: isoamyl alcohol is 24: 1), mixing, standing for 5min, centrifuging for 15min at 10000 Xg, and sucking supernatant into a new centrifuge tube with a gun; adding 2 times volume of anhydrous ethanol, mixing, standing at-20 deg.C for 1 hr at 10000 Xg, centrifuging for 10min, and removing supernatant; adding 500 μ L of precooled 75% ethanol, washing the precipitate, and removing the supernatant; washing and precipitating for 2 times continuously, and then airing; adding 100 μ L RNase A solution containing 2% RNase A, standing at 37 deg.C for 1h, and standing at 4 deg.C overnight; re-extracting DNA solution with equal volume of mixed solution (chloroform: isoamyl alcohol: 24: 1), reversing, mixing, standing for 10min, 10000 Xg, centrifuging for 15 or 20min, removing RNase A, sucking supernatant (about 60 μ L), and centrifuging again for 1 min; detecting the concentration, quality and integrity of the DNA by agarose gel electrophoresis (0.8%) and an ultraviolet spectrophotometer; the ratio of the absorbance 260/280 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 Gene science and technology Co., Ltd.) performed 9 Xcoverage depth sequencing and returned data, and the sequencing quality was evaluated by using FastQC software, and then adapter and low quality reads were performed 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
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 first effective branch number phenotype and the SNP data set to obtain a P value of each site of the first effective branch number character, and when the P value is less than 5 multiplied by 10-6The 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 first effective branching number trait of the cabbage type rape is limited between the 4152373 th base and the 4570188 th base of the A06 chromosome of the cabbage type rape, the corresponding SNPs are chrA06_4152373(C/T), chrA06_4570188(A/T), and the peak SNP is: and the contribution rate of the QTL to the first effective branch number character of the cabbage type rape is 12.43 percent (the materials are grouped according to different allele types of peak SNP, the one-way variance analysis is carried out, and the percentage of the variance between groups divided by the total variance is the contribution rate).
The peak SNPs for the first effective branch number trait were: chrA06_4336568(C/G), corresponding to the first significant branch number tabular grouping: when the SNP at position chrA06_4336568 is CC, the average first effective branch number of the material is 6.98; at CG, the average first effective number of branches of the material is 7.93; GG, the average number of first effective branches of the material was 8.55, as shown in FIG. 2.
One of the border SNPs for the first effective branch number trait is: chrA06_4152373(C/T), corresponding to the first significant branch number tabular grouping: when the SNP at position chrA06_4152373 is CC, the average first effective branch number of the material is 6.98; at CT, the average first effective number of branches of the material was 7.30; at TT, the average number of first effective branches of the material was 8.58, and the contribution rate of the border SNP was 12.81%.
Another border SNP for the first effective branch number trait is: chrA06_4570188(A/T), corresponding to the first significant branch number tabular grouping: when the SNP at position chrA06_4570188 is AA, the average first effective branch number of the material is 8.54 cm; AT, the average first effective number of branches of the material is 7.22; at TT, the average number of first effective branches of the material was 7.10, and the contribution rate of the border SNP was 11.54%.
The whole genome sequence of Brassica napus has been published, see http:// www.genoscope.cns.fr/brassicianapus/. The sequences (801 bp in total) of 400bp in front and back of the sequence containing chrA 06-4152373 (C/T) are shown as SEQ ID NO:1, the sequences (801 bp in total) of 400bp in front and back of the sequence containing chrA 06-4570188 (A/T) are shown as SEQ ID NO:2, and the sequences (801 bp in total) of 400bp in front and back of the sequence containing chrA 06-4336568 (C/G) 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 detecting the number of the first effective branches of the cabbage type rape, predicting the number of the first effective branches of the cabbage type rape, effectively selecting the number of the first effective branches of the cabbage type rape, and being also used for molecular marker assisted breeding of the cabbage type rape with a large number of the first effective branches and accelerating the high-yield breeding process of the cabbage type rape.
Therefore, the invention detects a main QTL site of the first effective branch number character of the cabbage type rape on the chromosome A06 by the phenotypic analysis and the whole genome re-sequencing of the first effective branch number character and then the whole genome correlation analysis, and the contribution rate of the main QTL site to the first effective branch number character of the cabbage type rape is 12.43 percent. The main effect QTL site of the first effective branching number character of the cabbage type rape is positioned between the 4152373 th base and the 4570188 th base of the A06 chromosome of the cabbage type rape, the obvious SNP of the boundary is chrA 06-4152373 (C/T), chrA 06-4570188 (A/T), and the peak SNP is chrA 06-4336568 (C/G).
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 first effective branch number of the cabbage type rape can be predicted. The selection target is clear and is not influenced by the environment. The individual cabbage type rape with a large number of effective branches for the first time can be identified in the early growth stage of cabbage type rape, and other individual plants are eliminated.
In conclusion, the A06 chromosome major QTL site of the first effective branching number character of the brassica napus has high contribution rate to the first effective branching number character of the brassica napus, plays a key role in regulating and controlling the first effective branching number of the brassica napus, can be used for site 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.
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<110> Guizhou oil-saving vegetable research institute
<120> A06 chromosome major QTL locus of cabbage type rape first effective branching number trait, 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 chrA06_4152373(C/T)
<400>1
tcccggtggc agggtctagc gttgggtgga ggacgaacca gcgtgggatt atgtgcggag 60
gcaggcctaa gcacacgtag acgcacttct ccgcgtgacc catcagcgat cttgtcttgt 120
agaactccgg cgaaaccacc agcgaacgaa atctcttgga gacggcagat aacgccgctt 180
ggtccaatct ggaaacgcga gccaagcaac ttatagccac cgcatctggc aacgaatcaa 240
acgacgacga cggagacgtc tccttcttcc tccttttggc ggcggcggcg taattgtaca 300
tctcaatctg agattgattc acgattggaa gagtcaacaa cccctttgat taattaattt 360
actgaggagg aagatcgatc ttatttatat atatagaggg tacccctttt cttttttgtt 420
cataggttga aaaggaaaca cgcgattcct tattacagta actttatgtt tttccttatt 480
acagtaagac ttgactttgt gttttgtcct tttattcctc actatttggg ccgcaattag 540
gttattaggc ctattgagtt cagataaagc ccatttattt cttcccgtgg tttgcaagtt 600
attggctgtt gggatagaat ttccggaaac cctaaggcaa ctttatgatg tcatcttctg 660
tttttttttt ttttttgata accgagtgtc ctggccccac cgtggtggtc cagactagag 720
accgaaccct ttagcggcac ggacgcacac ccgtgggtgg gtcatggcca ggcaacggtc 780
ttcggtctcg ggcgccagag 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 both before and after chrA06_4570188(A/T)
<400>2
caaagcagag ttttagattt ggtagattaa gcgaagagat taagagatgg caacactagg 60
agatattgga gtagccgcaa cgatcaacat aatcactgcc atcatcttcc tgttggcgtt 120
tgcaattttg aggatccaac cttttaacga cagagtttat tttcccaaat ggtatctcaa 180
aggtataaga agcagcccgt tgcattcagg tgctcttgtc agcaagtttg tcaatgtaaa 240
cttaggctcc tacctacgtt tcttgaactg gatgcccgct gctctgaaga tgcccgagcc 300
tgagcttatt gatcatgccg gcttggattc tgccgtctac ttgaggattt acttgatagg 360
gtattaattg tttttgaacc tcttcttgct tttgcattgc atcatctata aaattatttc 420
tctgtttttt caggcttaaa atttttgtac cgatagcatt acttgcatgg tcgattcttg 480
tacctgttaa ttggacaagc gacgggctgc aactagcgaa gctacgtaac gtaacatcta 540
gtgatattga taagttatca atctctaata tcgaacgtgg atcagagagg ttttggactc 600
atctcgtgat ggcttatgcc ttcacattct ggacttgctt tgttctaatg aaagagtatg 660
agaaagtagc ttcaatgcgt ttatcctttc tccagtccga gcaaaggcgt cctgatcaat 720
tcacggtaaa gctacttact acatgatcag tttttgcctc ctgatgtaac actgctctga 780
accggttttg ctttcacagg t 801
<210>3
<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 chrA06_4336568(C/G)
<400>3
tgtttccatc tgcgcaaaaa cacagagatt ggaataacaa aaccaatgaa ggaaacatgg 60
tttgatctgg aagactaaaa ctcatcacgg ataaaacttc tcgaccaaac atataaaatt 120
ttcaagctta atggcttatc caacaaattg aacctaacaa aagaaccgcc accaacttaa 180
ctaatacaag atcaacaaaa ataacatatt ggccattaca gcttaaactc aaaagaaaca 240
gagtagtacc tgcaaagcca tgaatgcttc aggaagttct tctagttcga acaaaaactt 300
gatgtacttc tctctcttat ctttctcatc cacagccatc tcaaatagct gcccatcttg 360
agtgcccagg atgatctcct tagttgaaac tgaatccagg ggaaagacta aataaaatca 420
atatccatgt gtgaaaaaat aaaagaagac tcatcacaac accaaagcat aaccttctgt 480
tatctgttgc ctgttccaag ccaccgagtt aaccagcaaa cctttcaagc ggctcaacac 540
acgcggctta ggccatttag catgagtgta aaaagtttca gctcctccaa caccagtgac 600
cgtagcaatg caatggctac caccagggtc aacaaaaacc ttgtgaatcg attgctcccc 660
agttcgacca acagagagat caatatctat aaatccatac aaaaacaaag attactatac 720
atttaaccac tgaaaataga aacaatatga tttagtatac cataagaact cccaactcca 780
aaatcatggc ggatgatcca t 801
Claims (11)
1. A major QTL locus of the A06 chromosome for the first effective branching number trait of Brassica napus is characterized in that the major QTL locus of the A06 chromosome for the first effective branching number trait of Brassica napus is positioned between the 4152373 th base and the 4570188 th base of the A06 chromosome of Brassica napus.
2. The A06 chromosomal major QTL site for the first effective branching number trait of Brassica napus according to claim 1, wherein the A06 chromosomal major QTL site for the first effective branching number trait of Brassica napus contributes 12.43% to the first effective branching number trait of Brassica napus.
3. The A06 chromosome major QTL locus for the cabbage type rape first effective branching number trait of claim 1 wherein the A06 chromosome major QTL locus for the cabbage type rape first effective branching number trait is closely linked to a first SNP molecular marker at the 4152373 th base, wherein the 4152373 th base is C or T, and wherein the mutation results in polymorphism.
4. The A06 chromosomal major QTL locus for the cabbage type rape first effective branching number trait of claim 1, wherein the A06 chromosomal major QTL locus for the cabbage type rape first effective branching number trait is closely linked to a second SNP molecular marker at position 4570188, said position 4570188 base being A or T, which mutation results in polymorphism.
5. The A06 chromosome major QTL locus for the cabbage type rape first effective branching number trait of claim 1, wherein the A06 chromosome major QTL locus for the cabbage type rape first effective branching number trait is closely linked to a peak SNP molecular marker, the peak SNP molecular marker is located at the 4336568 th base of the A06 chromosome of the cabbage type rape, the 4336568 th base is C or G, and the mutation causes polymorphism.
6. An SNP molecular marker of a major QTL site of the A06 chromosome of the first effective branching number trait of Brassica napus, which is characterized in that the SNP molecular marker is positioned at the 4152373 th base of the A06 chromosome of the Brassica napus, the 4152373 th base is C or T, and the mutation causes polymorphism.
7. The application of the SNP molecular marker of A06 chromosome major QTL locus for the trait of the first effective branching number of Brassica napus according to claim 6 in detecting the number of first effective branches of Brassica napus, predicting the number of first effective branches of Brassica napus, selecting the number of first effective branches of Brassica napus or in molecular marker assisted breeding of Brassica napus with a large number of first effective branches.
8. An SNP molecular marker of a major QTL site of the A06 chromosome of the first effective branching number trait of Brassica napus, which is characterized in that the SNP molecular marker is positioned at the 4570188 th base of the A06 chromosome of the Brassica napus, the 4570188 th base is A or T, and the mutation causes polymorphism.
9. The application of the SNP molecular marker of A06 chromosome major QTL locus for the trait of the first effective branching number of Brassica napus according to claim 8 in detecting the number of first effective branches of Brassica napus, predicting the number of first effective branches of Brassica napus, selecting the number of first effective branches of Brassica napus or in molecular marker assisted breeding of Brassica napus with a large number of first effective branches.
10. A peak SNP molecular marker of an A06 chromosome major QTL site of a cabbage type rape effective branching number trait for the first time is characterized in that the peak SNP molecular marker is located at the 4336568 th base of the A06 chromosome of the cabbage type rape, the 4336568 th base is C or G, and the mutation causes polymorphism.
11. The application of the peak SNP molecular marker of the major QTL site of the A06 chromosome for the trait of the first effective branching number of brassica napus according to claim 10 to detection of the number of first effective branches of brassica napus, prediction of the number of first effective branches of brassica napus, selection of the number of first effective branches of brassica napus or molecular marker assisted breeding of brassica napus with a large number of first effective branches.
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| CN111560461A (en) * | 2020-06-08 | 2020-08-21 | 中国农业科学院油料作物研究所 | Main effect QTL (quantitative trait locus) site closely related to first branch height traits of brassica napus, SNP (Single nucleotide polymorphism) molecular marker and application |
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