Background
Wheat is one of the most widely planted food crops worldwide, and provides the most basic ration demand for 35% -40% of the world population. In the large-area production and cultivation process of wheat, the loss of wheat yield caused by the invasion of various pathogenic microorganisms, pests and the like is difficult to measure, wherein wheat stripe rust is one of the most serious fungal diseases. Wheat stripe rust is a wheat gas-borne leaf disease caused by the specialized infection of the wheat of the rust-shaped rust bacteria, and has the advantages of wide epidemic range, high transmission speed and large hazard degree. Long-term exploration practices prove that by utilizing the disease resistance of the wheat, new disease resistance gene resources are discovered, and the reasonable layout of the resistant varieties has great effect on preventing and controlling the occurrence and transmission of wheat stripe rust. However, the promotion of resistant varieties is often accompanied by the generation and development of new physiological races of wheat stripe rust. In the 50 s of the 20 th century, the BiMA1 number of the wheat variety which is popularized and planted on a large scale in production loses disease resistance due to the occurrence of CYR1 physiological race, and after that, new wheat resistant varieties are overcome by new Rumex striolatus dominant race successively.
With the progress of modern biotechnology and the application of molecular marker technology, we have found and named a large number of stripe rust resistance genes, up to now, 83 stripe rust resistance genes (Yr 1-Yr 83) which have been formally named, and a plurality of temporary stripe rust resistance genes or QTL genetic loci. The number of the discovered disease-resistant genes is similar to 'considerable', but most of stripe rust resistance genes are lost in China, at present, only Yr5, yr15, yr50, yr61, yr69 and the like still have good seedling resistance genes, but the genes are all from wheat kindred species, and meanwhile, a plurality of 'linkage encumbrances' are likely to exist when the disease-resistant genes are introduced, so that the application of the genes in disease-resistant breeding is greatly limited. Therefore, development and utilization of new disease-resistant gene resources from common wheat materials are urgently needed, and the genetic basis of disease-resistant breeding materials is further widened. The common wheat variety dwarf 58 is a comprehensive resistant variety which is well applied in production practice at present, and is found by previous researches to carry a stripe rust resistance gene YrZH84 and has good resistance to physiological race CYR 32. Through gene localization, we find that the wheat 7B chromosome has an excellent disease resistance gene resisting CYR34, and named YrAK58, the gene is a stripe rust resistance gene in the whole growth period, the discovery can provide excellent disease resistance gene resources for wheat disease resistance breeding, and the gene can be polymerized with more durable multi-resistance genes in the adult period so that the variety maintains sufficient stripe rust resistance in the seedling period and the adult period, thereby reducing the hazard of the wheat stripe rust in the whole growth and development process. Meanwhile, the modified wheat seedling stage rust resistance agent also has great potential application value for future modification of wheat seedling stage rust resistance. Therefore, the development of the molecular marker of the stripe rust resistance gene is of great significance to the molecular assisted polymerization breeding of a plurality of disease resistance genes.
Disclosure of Invention
Therefore, the invention aims to provide a molecular marker which is obviously related to the wheat stripe rust resistance, can be used for detecting or predicting the wheat stripe rust resistance, and provides a basis for breeding excellent disease-resistant varieties.
The wheat stripe rust resistance gene YrAK58 functional molecular marker provided by the invention is Ta4417, the molecular marker and the wheat stripe rust resistance gene YrAK58 are co-located on a wheat 7B chromosome, the nucleotide sequence of the molecular marker is shown as SEQ ID NO.1, and the 24 th base from the 5' end of the nucleotide sequence is an SNP locus, wherein Y is a base C or T.
The invention also aims to provide application of the molecular marker in auxiliary breeding in detecting wheat stripe rust resistance or wheat stripe rust resistance.
Further, when the genotype of the molecular marker SNP is TT, wheat has stripe rust resistance, and when the genotype of the molecular marker SNP is CC or CT, wheat has stripe rust resistance.
Further, the primer for amplifying the molecular marker comprises an upstream primer with a nucleotide sequence shown as SEQ ID NO.2-3 and a downstream primer with a nucleotide sequence shown as SEQ ID NO. 4.
Further, the detection of the wheat stripe rust resistance comprises the following steps:
s1, extracting genome DNA of a wheat material to be detected;
s2, taking genomic DNA of the wheat material as a template, and carrying out PCR amplification by using the primer to obtain an amplification product;
s3, determining the genotype of the 24 th base from the 5' end of the amplified product, and judging that the wheat material has the stripe rust resistance property or stripe rust feeling property.
Furthermore, the amplification system of the PCR in S2 is as follows: 2.5. Mu.L of HiGeno2×Probemix B, 0.056. Mu.L of primer Mix, 50-100ng of DNA template, ddH 2 O makes up 5. Mu.L; the forward primer concentration was 12mmol/L and the reverse primer concentration was 30mmol/L.
Further, the PCR reaction procedure in S2 is: 94 ℃ for 15min;94 ℃ for 20s; 61-55deg.C for 1min, and each cycle is reduced by 0.6deg.C for 10 cycles; 94℃for 20s, 55℃for 60s, 30 cycles.
Further, the method of determining the genotype of the amplification product at the 24 th base from the 5' -end in S3 comprises a sequencing step.
Further, the method for determining the genotype of the 24 th base from the 5' end of the amplified product in S3 comprises the steps of using a microplate reader FAM HEX ROX beam scanning and Klumer Caller typing software to conduct typing detection on the PCR amplified product.
The invention has the following beneficial effects:
the invention provides a functional molecular marker Ta4417 of a wheat stripe rust resistance gene YrAK58, which can accurately predict the wheat stripe rust resistance gene YrAK58 and has important significance for subsequent cloning of the wheat stripe rust resistance gene YrAK 58. Meanwhile, the molecular marker and the primer thereof can be rapidly and high-throughput applied to the auxiliary breeding of wheat variety improvement molecules, thereby accelerating the breeding process of wheat at the whole genome level.
Detailed Description
The present invention will now be described in detail with reference to the drawings and specific examples, which should not be construed as limiting the invention. Unless otherwise indicated, the technical means used in the following examples are conventional means well known to those skilled in the art, and the materials, reagents, etc. used in the following examples are commercially available unless otherwise indicated.
Example 1: development of wheat stripe rust resistance gene YrAK58 functional molecular marker
1. Construction of genetic populations and genetic analysis
(1) Test wheat material: the parents used for genetic group construction are dwarf 58 and Avocet S, the disease-resistant parent dwarf 58 is a variety which is bred by the Henan sciences wheat breeding center and has seedling-stage resistance to CYR34, and the disease-resistant parent is Australian disease-resistant variety Avocet S (AvS). Hybridization with Avocet S (AvS) as female parent and disease-resistant variety dwarf 58 as male parent to obtain F 1 ,F 1 Selfing to obtain F 2 ,F 2 The single plant is continuously selfed to obtain a recombinant inbred line population (recombinant inbred line, RIL) by a single seed transmission mode, and the recombinant inbred line population is used for genetic analysis and gene positioning. The common wheat elytrigia pumila 22 is a cultivar and can be obtained from a national crop germplasm resource library as a disease control.
(2) Phenotype evaluation and phenotypic data analysis of the test population. The seedling stage resistance identification steps and the method are as follows: parental, disease-sensitive control and 133F 6 Recombinant inbred line (F) 6 RILs) were sown in a greenhouse at the university of agriculture and forestry science and technology plant pathology institute, northwest. It is subjected toThe seeds are planted into a plastic square box with 10cm multiplied by 10cm and filled with matrixes, wherein 7-8 seeds of each material are planted at 4 corners of a square basin (materials at four corners are concentrated as much as possible during sowing so as to avoid the situation that the wheat seedlings cannot be distinguished into which parent or family after growing up in the later period, and the identification of stripe rust disease in the seedling stage is not facilitated) for the parents and RIL families, and when the wheat seedlings grow to have fully extended two leaves (generally about 15 d), a powder shaking method (the wheat seedlings are subjected to CYR 34: talcum powder approximately 1:50) is adopted for inoculation (the condition that the two leaves of the seedlings are fully shaken is ensured). After inoculation, wheat seedlings are placed at 9-11 ℃ and 100% relative humidity for 24 hours in a dark place, then are placed in a greenhouse for cultivation, the temperature cycle of day and night is 18 ℃/11 ℃, the illumination intensity is 20,000lx, the light-dark period is 16 hours/8 hours, the relative humidity is about 80%, and after the infection control is fully affected (15-18 days after inoculation), avS, dwarf antibody 58 and the reaction type of offspring genetic groups are recorded. Reading of the reaction type (IT) refers to 9-level judgment standards of Line and Qayoum (1991), wherein the reaction type 0-6 level is disease-resistant type (R), and the reaction type 7-9 level is disease-sensitive type (S). Investigation was performed every 3d, and the highest response type was used as the final identification result in combination with the investigation data. According to the reaction types of the parent and offspring groups, the method of χ2 is used for detecting the suitability of the separation ratio obtained by investigation in Excel, the most suitable separation ratio is determined, the number of genes, interaction modes and disease resistance characteristics of the tested variety to specific stripe rust race resistance are determined, and then the number of stripe rust resistance genes and the correlation thereof are determined.
2. Genetic map construction and localization of stripe rust resistance gene YrAK58 and candidate gene cloning
(1) Colony isolation assay (bulked segregant analysis, BSA) in combination with wheat chip assay: and (3) collecting the 3 rd leaves of each parent and each individual plant/family after the wheat grows to about 3 leaf stage, and extracting DNA by using a CTAB method. F according to AvS ×AK58 2 The characteristic of stripe rust resistance separation of offspring group and RIL family of AvS ×AK58 is that 10 extremely disease-resistant single plants/families and 10 extremely disease-resistant single plants/families are respectively selected by adopting a cluster separation analysis method, equivalent DNA is extracted to construct two groups of anti-induction pools, and after quality inspection, the constructed anti-induction pools and the constructed anti-induction pools are subjected to quality inspectionThe parents were sent to Beijing Boao Biotechnology Co., ltd, and genotyping was performed using the wheat 660K SNP chip. And (3) primarily determining the position of the QTL locus according to the chromosome where the number of the differential SNP is located and the concentration degree of the differential SNP in the chromosome, developing an AQP marker of polymorphism, genotyping the RIL population, and drawing a genetic map by using Icimapping software, wherein the result is shown in figure 2.
(2) Localization and cloning of YrAK 58: QTL analysis was performed on the seedling resistance phenotype of this population using icmapping v4.1 (Inclusive Composite Interval Mapping) software, the LOD threshold was set to 2.5, and the effect of the localized QTL was described by phenotypic variation interpretation PVE. The colony is positioned to a new stripe rust resistance gene, named YrAK58, further subjected to fine positioning, candidate gene screening and mutant verification, and preliminarily proved that TraesCS7B01G441700 is an important candidate gene of YrAK58, and according to the sequence difference of the candidate gene in an anti-disease material, an AQP molecular marker Ta4417 (the nucleotide sequence is shown as SEQ ID NO.1, 5' -cggagatggttgttctctagctaYcaaaaaa gtctcatacgagatta-3', the 24 th base of the nucleotide sequence from the 5' end is an SNP locus, wherein Y is a base C or T, the SNP locus is positioned at 7068136756 th chromosome of wheat 7B), and the specificity and the robustness of the gene are verified in a natural colony, so that the gene is used for auxiliary selective breeding of wheat molecular markers.
The PCR specific amplification primer was designed using the obtained sequence of the molecular marker Ta4417 as a template, and the primer of the molecular marker Ta4417 (synthesized by Shanghai Co., ltd.) comprises:
forward sequence 1:5'-gaaggtgaccaagttcatgctcggagatggttgttctctagctat-3' as shown in SEQ ID NO. 2;
forward sequence 2:5'-gaaggtcggagtcaacggattcggagatggttgttctctagctac-3' as shown in SEQ ID NO. 3;
reverse sequence 3:5'-tgcttgctaacagactggct-3' as shown in SEQ ID NO. 4.
Wherein 5'-gaaggtgaccaagttcatgct-3' is FAM fluorescent universal primer, and FAM fluorescent group is observed and read under the wavelength of 485nm of excitation light and 520nm of emission light; 5'-gaaggtcggagtcaacggatt-3' is HEX fluorescent universal primer, and HEX fluorescent group is observed at wavelength of 535nm of excitation light and 556nm of emission light.
The primer is used for detecting genotypes of the disease-resistant parent, the disease-resistant parent and the F6 recombinant inbred line population, and the specific steps are as follows:
s1, extracting genome DNA of a wheat material to be detected by a conventional method (CTAB method);
s2, respectively carrying out PCR amplification by using a primer group of an AQP molecular marker Ta 4417;
wherein, the amplification systems are: 2.5. Mu.L of HiGeno2×Probemix B, 0.056. Mu.L of primer Mix, 50-100ng of DNA template, ddH 2 O makes up 5. Mu.L; each forward primer had a concentration of 12mmol/L and each reverse primer had a concentration of 30mmol/L.
The amplification procedures were all: 94 ℃ for 15min;94 ℃ for 20s; 61-55deg.C for 1min, and each cycle is reduced by 0.6deg.C for 10 cycles; 94 ℃ for 20s, 55 ℃ for 60s and 30 cycles;
s3, respectively carrying out parting detection on the PCR amplification product by using FAM HEX ROX light beam scanning and Kmaster cavity parting software through an enzyme-labeled instrument; if the genotype of the target SNP is 'TT' homozygote, the wheat to be detected is candidate wheat with stripe rust resistance; if the genotype of the target SNP is CC homozygous or CT heterozygous, the wheat to be tested is candidate wheat with stripe rust feeling property. Disease-resistant parent, disease-susceptible parent, F 6 The amplified typing scatter plot of the recombinant inbred population is shown in FIG. 2.
Example 2: practicality verification of molecular marker Ta4417
The genotype of the molecular marker Ta4417 of 155 wheat varieties to be tested was examined by the method of example 1 to determine whether the wheat varieties were resistant to stripe rust (stripe rust may specifically be stripe rust caused by the current stripe rust epidemic race species CYR32, CYR33 and CYR 34), and the DNA concentration was 100 ng/. Mu.l of the template solution.
The amplified typing scatter plots of the antipathogenic parent, the susceptible parent, 155 wheat cultivars are shown in FIG. 3, and the genotypes and stripe rust phenotypes of 155 wheat cultivars are shown in Table 1.
TABLE 1 genotype and response of 155 wheat cultivars
While preferred embodiments of the present invention have been described, additional variations and modifications in those embodiments may occur to those skilled in the art once they learn of the basic inventive concepts. It is therefore intended that the following claims be interpreted as including the preferred embodiments and all such alterations and modifications as fall within the scope of the invention.
It will be apparent to those skilled in the art that various modifications and variations can be made to the present invention without departing from the spirit or scope of the invention. Thus, it is intended that the present invention also include such modifications and alterations insofar as they come within the scope of the appended claims or the equivalents thereof.