CN107916299B - Ordinary wheat SNP locus marker and application thereof in wheat related trait detection - Google Patents
Ordinary wheat SNP locus marker and application thereof in wheat related trait detection Download PDFInfo
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Abstract
The invention discloses a common wheat SNP locus marker and application thereof in wheat related trait detection. The invention provides application of a substance for detecting Ta-7A-SNP354 locus haplotype in a wheat genome in identification or auxiliary identification of thousand grain weight, ear length, plant height and/or tiller number characters of wheat. The invention uses a molecular marker method to find an SNP locus Ta-7A-SNP354 on a 7A chromosome of wheat, develops a molecular marker according to the SNP locus, and uses marker/character association analysis to find that the SNP locus is remarkably related to wheat grain weight (P <0.01) and is remarkably related to wheat ear length, plant height and tiller number (P <0.05) in wheat micro-core germplasm in China. Meanwhile, the marker is a co-dominant marker, has good repeatability and low cost, and has good application prospect in molecular marker-assisted selection and molecular design breeding for improving the wheat grain weight.
Description
Technical Field
The invention belongs to the technical field of biology, and particularly relates to a common wheat SNP locus marker and application thereof in wheat related trait detection.
Background
Wheat is a main grain crop in the world, and the search for functional genes related to high yield and molecular markers thereof has important theoretical significance and application value for future molecular breeding. The yield traits mostly belong to the quantitative traits controlled by multiple genes, and are represented by continuous variation, so that the research is difficult. In contrast, the yield constitutive factor has higher genetic force than the yield character, and the breeding requirements of different ecological regions on the constitutive factor are different, so that the research of dividing the yield character into independent factors is more feasible. Ear number, ear grain number, thousand grain weight, ear length, effective tillering, and the like are all agronomic traits that affect crop yield. The selection efficiency can be greatly improved by using the molecular marker closely linked with the gene or QTL related to the wheat yield to carry out auxiliary selection. Mapping a number of yield-related QTLs and related markers on different chromosomes of wheat (Cuthbert JL, Somers DJ, Brule-Babel AL, et AL. molecular mapping of quantitative trap loci for yield and yield compounds in spring wheat (Triticum aestivum L.). Theorappl Gene 2008,117: 595. visco. E.608; Maccalir M, Sanguinet MC, Corneti S, et AL. quantitative locus for gain and adaptation of yield wheat (Triticum durum Dessf.) acquisition of nucleic acid a range of water availability, 2008. D.G. No. 178:489, truck DJ.CA, Somers J.575. QT. Lu. J. genes 4452. for breeding genes of yield-related QTLs and yield-related markers in spring wheat, but for mapping of genes of wheat genes, found in breeding genes of 12. J. 35. J. 12. J. C. J. 12. J. 12. C. J. for breeding genes, No. 35. No. D. 35. J. No. D. J. 4452. J. D. J. ID. 1. Most of the existing molecular markers are developed based on specific genetic population and environment interaction conditions, and whether the existing molecular markers are effective or not under different genetic backgrounds is still to be evaluated; 2. the wheat genome is large, and the genetic distance between the marker and the functional gene is long; 3. the existing markers are mainly related to quality traits such as disease resistance, quality and the like, and yield trait markers which can be used for actual breeding are too few. Therefore, the deep excavation of the functional markers which can be used in the germplasm identification and breeding process has important significance.
Disclosure of Invention
The invention aims to provide application of a substance for detecting a haplotype of a Ta-7A-SNP354 locus in a wheat genome.
The invention provides an application of a substance for detecting a Ta-7A-SNP354 locus haplotype in a wheat genome in identification or auxiliary identification of any one of the following a-e traits of wheat: a. the plant height; b. the number of tillers; c. ear length; d. thousand seed weight; e. any 2 or any 3 or any 4 combinations of a-d;
the locus of the Ta-7A-SNP354 is the 354 th locus of the sequence 5.
In the application, the haplotype of the Ta-7A-SNP354 site is AA, GG or AG.
The invention also provides application of the substance for detecting the Ta-7A-SNP354 locus haplotype in the wheat genome in breeding wheat with improved thousand grain weight, spike length, plant height and/or tiller number.
In the above-mentioned application, the first and second substrates,
the substances for detecting the Ta-7A-SNP354 site haplotype in the wheat genome are 1) or 2):
1) the primer set comprises a single-stranded DNA molecule shown as a sequence 3 in a sequence table or a derivative thereof, and a single-stranded DNA molecule shown as a sequence 4 in the sequence table or a derivative thereof;
2) a PCR reagent or a kit containing the primer set.
In the above-mentioned application, the first and second substrates,
the primer set also comprises a primer shown as a sequence 1 in a sequence table or a derivative thereof, and a primer shown as a sequence 2 in the sequence table or a derivative thereof;
or the derivatives of the primers are as follows:
a) adding 1-10 bases to the 5' end of the primer nucleotide sequence to obtain a single-stranded DNA molecule;
b) a DNA molecule having 80% or more or 90% or more homology to the primer;
in the above-mentioned application, the first and second substrates,
the kit also comprises a primer shown as a sequence 1 in the sequence table or a derivative thereof, and a restriction enzyme corresponding to a restriction enzyme cutting site contained in an amplification product of the primer shown as a sequence 2 in the sequence table or the derivative thereof;
or, the restriction enzyme is Taq I.
The 2 nd purpose of the invention is to provide a method for identifying or assisting in identifying any one of the following a-e traits of wheat.
The method provided by the invention is used for detecting whether the Ta-7A-SNP354 site haplotype in the wheat genome is AA or GG, wherein the thousand grain weight, the ear length, the plant height and/or the tillering number of the wheat to be detected with the Ta-7A-SNP354 site haplotype as AA are larger than those with the Ta-7A-SNP354 site haplotype as GG;
the 3 rd object of the present invention is to provide a method for breeding wheat improved in any one of the following a-e traits.
In the method provided by the invention, in order to detect whether the haplotype of the Ta-7A-SNP354 locus in the wheat genome is AA or GG, the wheat with the haplotype of AA is selected for breeding to obtain target wheat;
a. the plant height; b. the number of tillers; c. ear length; d. thousand seed weight; e. any 2 or any 3 or any 4 combinations of a-d.
In the above-mentioned method, the first step of the method,
the method for detecting whether the haplotype of the Ta-7A-SNP354 locus in the wheat genome is AA or GG comprises the following steps A) or B):
A) directly sequencing or sequencing the specific fragment;
B) the method shown comprises the following steps:
1) carrying out PCR amplification on the wheat genome DNA to be detected by using the primer shown in the sequence 1 in the sequence table and the primer shown in the sequence 2 in the sequence table to obtain the specific fragment;
2) carrying out PCR amplification on the specific fragment by using a primer shown in a sequence 3 in the sequence table and a primer shown in a sequence 4 in the sequence table to obtain a PCR amplification product;
3) carrying out enzyme digestion on the PCR amplification product by using Taq I to obtain an enzyme digestion product;
detecting an enzyme digestion product:
if the size of the enzyme digestion product is 170-180bp, the haplotype of the Ta-7A-SNP354 locus of the wheat to be detected is GG;
if the size of the enzyme digestion product is 150-160bp, the haplotype of the Ta-7A-SNP354 site of the wheat to be detected is AA.
In the above-mentioned method, the first step of the method,
the enzyme digestion products are detected as follows:
if the size of the enzyme digestion product is 178bp, the haplotype of the Ta-7A-SNP354 locus of the wheat to be detected is GG;
if the size of the enzyme digestion product is 157bp, the haplotype of the Ta-7A-SNP354 site of the wheat to be detected is AA.
The 4 th purpose of the invention is to provide a substance for identifying or assisting in identifying any one of the following a-e traits of wheat.
The substance provided by the invention is the substance for detecting the Ta-7A-SNP354 locus haplotype in the wheat genome in the application:
a. the plant height; b. the number of tillers; c. ear length; d. thousand seed weight; e. any 2 or any 3 or any 4 combinations of a-d.
The invention uses a molecular marker method to find an SNP locus Ta-7A-SNP354 on a 7A chromosome fragment of wheat, develops a molecular marker according to the SNP locus, finds that the SNP locus is remarkably related to wheat grain weight (P <0.01) and is remarkably related to wheat ear length, plant height and tillering number (P <0.05) by utilizing marker/character association analysis in wheat micro-core germplasm in China, and further verifies and applies in the breeding process. Meanwhile, the marker is a co-dominant marker, has good repeatability and low cost, and has good application prospect in molecular marker assisted selection and molecular design breeding for improving the plant height, tillering number, spike length and thousand kernel weight of wheat.
Drawings
FIG. 1 shows the alignment of the partial sequence of the fragment in which Ta-7A-SNP354 is located.
FIG. 2 shows the Ta-7A-SNP354 labeled primers and the results of enzyme digestion detection.
FIG. 3 shows the results of genetic mapping in the Ta-7A-SNP354 genetic population.
Detailed Description
The experimental procedures used in the following examples are all conventional procedures unless otherwise specified.
Materials, reagents and the like used in the following examples are commercially available unless otherwise specified.
The wheat varieties in the examples were all obtained from the China crop germplasm information network, and the uniform numbering in Table 2 is the in-network numbering. The website is as follows: http:// www.cgris.net/query/croplist. php #
Example 1 discovery of SNP354 site and development of detection marker thereof
Discovery of SNP354 site
1. Wheat material tested
30 parts of wheat materials (No. 1-No.30) distributed in different wheat regions in China and having large differences in yield character phenotypic characters are selected as the discovery materials of polymorphic SNP sites (Table 1).
2. Sequence alignment
The genome DNA of each tested wheat material is extracted by a conventional CTAB method, 30 parts of wheat material are amplified respectively, and the adopted amplification primers are a specific primer F and a specific primer R.
A specific primer F: 5'-CTGAACAGGCAGATGACATAAA-3' (sequence 1)
A specific primer R: 5'-GAAGCAACCGGCCAATGTGAC-3' (sequence 2)
1543bp PCR amplification product is obtained.
Sequencing PCR amplification products of different tested wheat materials, wherein the nucleotide sequence is sequence 5.
MegAlign sequence alignment results are shown in FIG. 1, and it can be seen that an SNP site exists at position 354 of a PCR amplification product sequence and is named as Ta-7A-SNP354, the nucleotide sequence of the Ta-7A-SNP354 is A or G, and the haplotype of the SNP site is AA or GG or AG.
3. Relationship between SNP site haplotypes and traits
Further, statistical analysis was performed on the thousand seed weight, effective tillering, plant height and ear length of 30 parts of wheat material to be tested and the haplotype of the Ta-7A-SNP354 site, and the results are shown in table 1, and it can be seen that the mean value of the thousand seed weight of the wheat material with the Ta-7A-SNP354 site haplotype as AA was 39.38g, 9.06 effective tillering, plant height 93.23cm and ear length 9.67 cm; the thousand-grain weight average value of the wheat material with the Ta-7A-SNP354 site haplotype of GG is 33.56g, the number of effective tillers is 8.31, the plant height is 92.99cm, and the ear length is 8.50 cm.
The thousand grain weight, effective tillering, plant height and spike length of the wheat material with the Ta-7A-SNP354 site haplotype as AA are all higher than those of the wheat material with the Ta-7A-SNP354 site haplotype as GG, and the difference of the two properties of the thousand grain weight and the spike length is obvious (P is less than 0.05), so that the wheat material with the Ta-7A-SNP354 site haplotype as AA is determined to be wheat with good properties.
Table 1 shows the yield traits and SNP site haplotype statistics of 36 wheat materials for SNP discovery
Second, development of Ta-7A-SNP354 site marker and establishment of detection method
1. Development of Ta-7A-SNP354 site marker
According to the Ta-7A-SNP354 locus discovered in the step one, a base difference is further discovered between a haplotype sequence (TCCA) of a variety with a high mean value of characters and a haplotype sequence (TCCG) of a variety with a low mean value of yield characters, and a site mismatch (353G) is introduced to form a Taq I enzyme digestion site (TCGA) to distinguish two allelic variations of Ta-7A-SNP354 according to a dCAPS primer design principle.
The SNP marker primers are as follows:
SNP marker F: 5'-CCTCAAATGTCGTCGCTTCG-3'
SNP marker R: 5'-TGTTCACTGCCTCTACGAAAC-3' are provided.
2. Establishment of Ta-7A-SNP354 site haplotype detection method
1) PCR amplification of specific fragments
And (3) taking the genome of the tested wheat variety as a template, and carrying out PCR amplification by adopting a specific primer F and a specific primer R pair.
A specific primer F: 5'-CTGAACAGGCAGATGACATAAA-3'
A specific primer R: 5'-GAAGCAACCGGCCAATGTGAC-3'
The PCR amplification system is as follows: 1.0 μ L of template DNA; mg (magnesium)2+1.0 μ L; 10 XPCR amplification buffer 1.5. mu.L; 1. mu.L of each of the upstream and downstream primers (10. mu.M); dNTP (25. mu.M) 0.12. mu.L; taq (5U/. mu.L); ddH2Make up to 15. mu.L of O.
The amplification procedure adopted during PCR amplification specifically comprises: 5min at 94 ℃; 30 cycles of 94 ℃ for 30s, 58 ℃ for 35s, and 72 ℃ for 1 min; 10min at 72 ℃; 10 ℃ for 1hr
2) Amplification of a fragment containing Ta-7A-SNP354 site
The PCR amplification product obtained in 1) above was diluted 50 times as a template, and the pair of SNP marker F and SNP marker R was used for amplification.
SNP marker F: 5'-CCTCAAATGTCGTCGCTTCG-3' (sequence 3)
SNP marker R: 5'-TGTTCACTGCCTCTACGAAAC-3' (sequence 4)
The PCR reaction system is as follows: 1.0 μ L of template DNA; mg (magnesium)2+1.0; 10 XPCR amplification buffer 1.5. mu.L; upstream and downstream primers (10. mu.M) each 0.5. mu.L; dNTP (25. mu.M) 0.12. mu.L; taq (5U/. mu.L); ddH2Make up to 15. mu.L of O.
The amplification procedure adopted during PCR amplification specifically comprises: 5min at 94 ℃; 30s at 94 ℃, 35s at 57 ℃, 1min at 72 ℃ and 35 cycles; 10min at 72 ℃; 10 deg.C for 1 hr.
178bpPCR amplification product was obtained.
3) Restriction enzyme Taq I digestion
The enzyme cutting system is as follows: mu.L of the PCR product obtained in 2) above, 1. mu.L of Buffer, 0.2. mu.L of restriction enzyme TaqI, ddH2O3.8 mu L; and carrying out enzyme digestion for 30min at 37 ℃ to obtain an enzyme digestion product.
And injecting restriction enzyme Taq I as a NEB product.
Detecting the enzyme digestion product by electrophoresis:
if the size of the enzyme digestion product is 178bp, the corresponding haplotype of the Ta-7A-SNP354 locus of the wheat to be tested is GG homozygous;
if the size of the enzyme digestion product is 157bp, the corresponding haplotype of the test wheat Ta-7A-SNP354 site is AA homozygous.
The result is shown in FIG. 2, and it can be seen from the electrophoretogram that the obtained 157bp corresponding test wheat Ta-7A-SNP354 locus is homozygous for AA by sequencing; the obtained 178bp corresponding Ta-7A-SNP354 locus of the wheat to be tested is sequenced, and the haplotypes are all GG homozygous.
Because wheat is a selfed crop and the proportion of the heterozygous loci of the genome is low, the experiment does not research the Ta-7A-SNP354 locus haplotype heterozygous.
The haplotype at position 354 of the Ta-7A-SNP can also be detected by direct sequencing.
Example 2 establishment of method for detecting thousand-grain weight, effective tillering, plant height and panicle length traits of wheat material at Ta-7A-SNP354 site
In this example, the basic information (105 cultivars and 157 local cultivars) of all wheat micro-core germplasm materials were subjected to corresponding phenotypic measurements in the same manner as in Henan Luo Yang, Henan Luo Yang in 2005, and Beijing in 2006 in 2002. At least 3 replicates were set for each sample and the results averaged when determining the phenotypic data.
Table 2 shows the names of 262 parts of wheat micro-core germplasm materials
1. PCR amplification of specific fragments
The genome of the wheat variety to be tested shown in Table 2 was used as a template, and PCR amplification was carried out using the specific primer F and the specific primer R.
Ta-7A-SNP354-F：5’-CTGAACAGGCAGATGACATAAA-3’
Ta-7A-SNP354-R：5’-GAAGCAACCGGCCAATGTGAC-3’
2. Amplification of a fragment containing Ta-7A-SNP354 site
The PCR amplification product obtained in 1) above was diluted 20 times as a template, and the pair of SNP marker F and SNP marker R was used for amplification.
SNP marker F: 5'-CCTCAAATGTCGTCGCTTCG-3'
SNP marker R: 5'-TGTTCACTGCCTCTACGAAAC-3'
3. Restriction enzyme Taq I digestion
The enzyme cutting system is as follows: mu.L of the PCR product obtained in 2) above, 1. mu.L of Buffer, 0.2. mu.L of restriction enzyme TaqI, ddH2O3.8 mu L; and carrying out enzyme digestion for 30min at 37 ℃ to obtain an enzyme digestion product.
Detecting the enzyme digestion product by electrophoresis:
if the size of the enzyme digestion product is 178bp, the corresponding haplotype of the Ta-7A-SNP354 locus of the wheat to be tested is GG homozygous;
if the size of the enzyme digestion product is 157bp, the corresponding haplotype of the test wheat Ta-7A-SNP354 site is AA homozygous.
The results for the 262 samples are as follows:
the average plant height of the wheat material with AA as the haplotype of the Ta-7A-SNP354 locus is 117.84cm, the average plant height of the wheat material with GG as the haplotype of the Ta-7A-SNP354 locus is 112.35cm, and the difference reaches a significant level (P < 0.05);
the average ear length of the wheat material with AA as the haplotype of the Ta-7A-SNP354 locus is 10.36cm, the average ear length of the wheat material with GG as the haplotype of the Ta-7A-SNP354 locus is 9.80cm, and the difference reaches a significant level (P < 0.05);
the average tiller number of the wheat material with AA as the haplotype of the Ta-7A-SNP354 locus is 10.97, the average tiller number of the wheat material with GG as the haplotype of the Ta-7A-SNP354 locus is 10.493, and the difference reaches a significant level (P < 0.05);
the average thousand grain weight of the wheat material with AA as the haplotype of the Ta-7A-SNP354 site is 33.35g, while the average thousand grain weight of the wheat material with GG as the haplotype of the Ta-7A-SNP354 site is 33.52g, and the difference reaches a very significant level (P < 0.01);
similarly, in the aspects of spike length, plant height and tillering traits, the wheat material with AA as the haplotype of the Ta-7A-SNP354 site is superior to the wheat material with GG as the haplotype of the Ta-7A-SNP354 site, and the difference reaches a significant level (P < 0.05).
The results were subjected to correlation analysis of the relevant traits, and the results are shown in table 3.
Table 3 is the correlation analysis of Ta-7A-SNP354 site haplotype and related traits
Note: p <0.05, P <0.01.
The results for a portion of the wheat micro-core seed material are shown in table 4 below:
table 4 shows the data of the Ta-7A-SNP354 locus haplotype and related trait partial phenotype identification of wheat micro-core seed material
Therefore, the Ta-7A-SNP354 locus can be used for detecting the grain weight, the ear length, the plant height and the tillering traits of wheat, and the specific steps are as follows:
and (3) detecting the haplotype of the Ta-7A-SNP354 locus of the wheat genome to be detected and the haplotype AA of the Ta-7A-SNP354 locus of the wheat to be detected, wherein the thousand grain weight, the ear length, the plant height and/or the tiller number of the wheat to be detected are/is higher than those of the haplotype GG of the Ta-7A-SNP354 locus.
The method for detecting the haplotype of the Ta-7A-SNP354 locus of the wheat genome to be detected can be as follows:
1) directly sequencing or sequencing the specific fragment;
the specific fragment is obtained by amplifying wheat genome DNA through a specific primer F and a specific primer R.
2) The method comprises the following steps:
firstly, amplifying wheat genome DNA by using a specific primer F and a specific primer R to obtain a specific fragment;
b, amplifying the specific fragment by using the SNP marker F and the SNP marker R to obtain a PCR amplification product;
c, using Taq I to enzyme-cut the PCR amplification product,
if the size of the enzyme digestion product is 178bp, the corresponding haplotype of the Ta-7A-SNP354 locus of the wheat to be tested is GG homozygous;
if the size of the enzyme digestion product is 157bp, the corresponding haplotype of the test wheat Ta-7A-SNP354 site is AA homozygous.
Example 3 detection of thousand-grain weight, effective tillering, plant height and panicle length traits of wheat material at Ta-7A-SNP354 site
Crossing Zhengmai 9023 with elytrigia repens No.1 for F1 generation, and selfing the F1 generation to obtain F4 generation;
DNA of 60 strains in the F4 generation was extracted, and the haplotype of the Ta-7A-SNP354 site of 60 strains in the F4 generation in the 2016-2017 year was detected according to the method of example 2.
The results are as follows:
the haplotype of the Ta-7A-SNP354 site in 60 strains of the F4 generation is 26 strains of GG, the haplotype of the Ta-7A-SNP354 site is 32 strains of AA, and the haplotype of the Ta-7A-SNP354 site is two strains of AG (abandon).
And (3) performing field survey phenotype statistics on each haplotype plant, wherein the results are as follows:
the average thousand-grain weight of the wheat to be tested with the Ta-7A-SNP354 haplotype AA is 46.24g, the average ear length is 14.3cm, the average plant height is 79.2cm, and the average tillering number is 4.9; the average thousand-grain weight of wheat to be detected of the Ta-7A-SNP354 haplotype GG is 43.62g, the average ear length is 13.7cm, the average plant height is 76.3cm, and the average tillering number is 4.1; the strains of Ta-7A-SNP354 haplotype AA were all higher than the strain of Ta-7A-SNP354 haplotype GG, and the differences were significant (P < 0.05).
Example 4 functional verification and genetic mapping in the Ta-7A-SNP354 genetic population
Ta-7A-SNP354 has difference between elytrigia 1 and Neixiang 188 varieties, RIL groups constructed by the two parents are utilized, the genetic groups are scanned according to the markers developed in the example 1, and the Ta-7A-SNP354 is subjected to genetic positioning and effect analysis of chromosomes through IcMapping software. The results show (fig. 3): Ta-7A-SNP354 was located on wheat 7A chromosome between WMC83 and GWM0942 at a distance of 2.4cM and 0.9cM from these two markers, respectively; meanwhile, different haplotypes can account for 14.2% and 6.8% phenotypic variation rates of thousand kernel weight and ear length in the population, respectively.
Sequence listing
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ggaaggcctg accatctacc atgtaaagag tcatttgcag gtactacttc agggttattt 720
tcccgcttca ctgaaaatga aagcaaacat gtcttcttct tttcattgtt acttatagtt 780
tgcctgtctt tgctgaacag aagtaccgac acgcaaagta tattccagag atcaaagaag 840
gtaaacaaac cacagaagat aaatattgct cacaagtaat cggtatcggc gccttttgcg 900
attctgaatt ttgatgcatg gtgttgtctg cagaaaagaa ggcttcctcg gaccttaaga 960
aagtacaacc gggtagcagt ggaagcgatc cgttcaaaaa caagtgagct ctctgaatta 1020
ttacaccgga gtgcatgcat agcaaacacc ttgaccttag aaatttacat ctcttccctt 1080
ctccttttct taggaacttg gcagaagctc tacggatgca aatggaggtt cagaagcagc 1140
tccatgaaca gctagaggta gtctaaagct ctgaaatgca gttcactgtt gtcatgcgtg 1200
tcagaattcc gacatgtgtc tgaactctga agttcatctt agaaagttgt ctggagattg 1260
tcggttttct gatgatctgc gtgcttaatc ttggccaggt gcaaaggcag ctgcagctac 1320
gcatagaaga acacgcgaaa tacttgcaga ggatactgga agagcagcag aaggtcggca 1380
gtggcagctc gctctcactg aaaaccccga cggagccgtc cgagtcgacg tcgaaagaca 1440
gaactgaacc tgaagaggcc accacctctt cacctcagac gtccaagaac agcgaggcag 1500
ggtccccttg ttcataacag ccgtcacatt ggccggttgc ttc 1543
Claims (9)
1. The application of the substance for detecting the Ta-7A-SNP354 locus haplotype in the wheat genome in identifying or assisting in identifying any one of the following a-e traits of wheat: a. the plant height; b. the number of tillers; c. ear length; d. thousand seed weight; e. any 2 or any 3 or any 4 combinations of a-d;
the locus of the Ta-7A-SNP354 is the 354 th locus of the sequence 5.
2. Use according to claim 1, characterized in that: the haplotype of the Ta-7A-SNP354 site is AA, GG or AG.
3. The application of the substance for detecting the Ta-7A-SNP354 locus haplotype in the wheat genome in breeding wheat with the thousand grain weight, the ear length, the plant height and/or the tiller number being improved.
4. Use according to any one of claims 1 to 3, characterized in that:
the substances for detecting the Ta-7A-SNP354 site haplotype in the wheat genome are 1) or 2):
1) the primer set is a primer set, and the primer set comprises a single-stranded DNA molecule shown as a sequence 3 in a sequence table and a single-stranded DNA molecule shown as a sequence 4 in the sequence table;
2) a PCR reagent or a kit containing the primer set.
5. Use according to claim 4, characterized in that:
the primer set also comprises a primer shown as a sequence 1 in a sequence table and a primer shown as a sequence 2 in the sequence table.
6. Use according to claim 4 or 5, characterized in that:
the kit also comprises a primer shown as a sequence 1 in the sequence table and a restriction enzyme corresponding to a restriction enzyme cutting site contained in a primer amplification product shown as a sequence 2 in the sequence table;
or, the restriction enzyme is Taq I.
7. A method for identifying or assisting in identifying any one of the following traits a-e of wheat is characterized in that the thousand grain weight, the ear length, the plant height and/or the tillering number of wheat to be detected are/is larger than those of the wheat to be detected with the Ta-7A-SNP354 site haplotype being GG, and the Ta-7A-SNP354 site haplotype being AA or GG in the wheat genome;
or a method for breeding wheat with any one of the following a-e characters improved, in order to detect whether the haplotype of the Ta-7A-SNP354 locus in the genome of the wheat is AA or GG, selecting the wheat with the haplotype of AA to breed and obtain the target wheat;
a. the plant height; b. the number of tillers; c. ear length; d. thousand seed weight; e. any 2 or any 3 or any 4 combinations of a-d.
8. The method of claim 7, wherein:
the method for detecting whether the haplotype of the Ta-7A-SNP354 locus in the wheat genome is AA or GG comprises the following steps A) or B):
A) directly sequencing or sequencing the specific fragment;
B) the method shown comprises the following steps:
1) carrying out PCR amplification on the wheat genome DNA to be detected by using the primer shown in the sequence 1 in the sequence table and the primer shown in the sequence 2 in the sequence table to obtain the specific fragment;
2) carrying out PCR amplification on the specific fragment by using a primer shown in a sequence 3 in the sequence table and a primer shown in a sequence 4 in the sequence table to obtain a PCR amplification product;
3) carrying out enzyme digestion on the PCR amplification product by using Taq I to obtain an enzyme digestion product;
detecting an enzyme digestion product:
if the size of the enzyme digestion product is 170-180bp, the haplotype of the Ta-7A-SNP354 locus of the wheat to be detected is GG;
if the size of the enzyme digestion product is 150-160bp, the haplotype of the Ta-7A-SNP354 site of the wheat to be detected is AA.
9. The method of claim 8, wherein:
the enzyme digestion products are detected as follows:
if the size of the enzyme digestion product is 178bp, the haplotype of the Ta-7A-SNP354 locus of the wheat to be detected is GG;
if the size of the enzyme digestion product is 157bp, the haplotype of the Ta-7A-SNP354 site of the wheat to be detected is AA.
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| CN109735648B (en) * | 2019-01-21 | 2022-05-03 | 中国农业科学院作物科学研究所 | Method for screening wheat with different thousand grain weights and special kit thereof |
| CN110106273B (en) * | 2019-05-01 | 2022-07-19 | 山东省农业科学院作物研究所 | Major QTL influencing thousand-grain weight of wheat and application thereof |
| CN111187852B (en) * | 2020-01-16 | 2021-09-21 | 中国科学院遗传与发育生物学研究所 | SNP (single nucleotide polymorphism) site related to wheat yield and application thereof |
| CN113699269B (en) * | 2021-09-02 | 2022-09-30 | 河北师范大学 | SNP (single nucleotide polymorphism) site related to small spike number per spike and spike grain number characters of wheat and application thereof |
| CN116769961B (en) * | 2023-07-28 | 2024-01-26 | 四川农业大学 | Wheat spike number per spike QTL linkage molecular marker developed by multi-sieve-mixing-determining four-step method and application |
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| JF951946.1;Zhang L.等;《GenBank》;20120209 * |
| Overexpression of a wheat MYB transcription factor gene, TaMYB56-B, enhances tolerances to freezing and salt stresses in transgenic Arabidopsi.crdownload.pdf;Lichao Zhang;《Gene》;20120525;第505卷;100-107 * |
| 小麦株高相关性状与SNP标记全基因组关联分析;陈广凤等;《作物学报》;20151231;第41卷(第10期);1500-1509 * |
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