CN118086577B - Molecular marker of wheat biological rhythm clock gene TaPRR-A1 and application thereof - Google Patents
Molecular marker of wheat biological rhythm clock gene TaPRR-A1 and application thereofInfo
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Abstract
The invention discloses a molecular marker of a wheat biological rhythm clock gene TaPRR-A1 and application thereof, belonging to the field of plant variation and genetic engineering. The molecular marker is TaPRR-A1-SNP 1432, is obtained by amplifying a primary PCR primer shown in SEQ ID NO. 1 and SEQ ID NO. 2 and a secondary PCR primer shown in SEQ ID NO. 3 and SEQ ID NO. 4, and is obtained by cutting the molecular marker by EcoRV enzyme, if the molecular marker is cut into two bands, the haplotype of the TaPRR-A1 gene is Hapl a, otherwise, the haplotype is Hapl b. The invention discovers excellent alleles of TaPRR-A1 genes from natural wheat groups, develops related functional molecular markers for identifying the plant height, the spike length and the thousand grain weight of wheat, and provides gene resources and effective approaches for genetic improvement of wheat yield traits.
Description
Technical Field
The invention relates to a molecular marker and application thereof, in particular to a molecular marker of a wheat biological rhythm clock gene TaPRR-A1 and application thereof in identifying wheat yield traits, belonging to the technical field of plant variation and genetic engineering.
Background
Wheat is one of the most important food crops worldwide, and its yield and quality improvement are particularly important. The traditional wheat breeding workload is large, the cost is high, the period is long, and the wheat molecular marker assisted breeding technology can accurately and stably select target genes in early stage, so that the wheat breeding process is accelerated, and the breeding efficiency is improved.
The biological rhythm clock is a rhythm oscillation adaptation system of 24-hour periodicity of plants, and plays an important role in the growth and development of plants. Biological clocks are capable of regulating plant flowering, photosynthesis and biological and non-biological defense processes, which are critical to crop adaptability and yield formation. The biological rhythm clock gene OsPRR of rice positively regulates the yield of rice by influencing plant height, secondary branch and stem number, grain number per ear, seed setting rate and single plant weight. The development and utilization of the functions and molecular markers of the wheat biological rhythm clock gene TaPRR are not yet reported.
Disclosure of Invention
The invention aims to provide a molecular marker of a wheat biological rhythm clock gene TaPRR-A1 and application thereof, and aims to provide gene resources and effective ways for genetic improvement of wheat yield traits.
In order to achieve the above object, the present invention adopts the following technical scheme:
The molecular marker of the wheat biological rhythm clock gene TaPRR-A1 is TaPRR-A1-SNP 1432, is CAPS molecular marker, is amplified by a primary PCR primer shown in SEQ ID NO. 1 and SEQ ID NO. 2 and a secondary PCR primer shown in SEQ ID NO. 3 and SEQ ID NO. 4, is cut by restriction enzyme EcoRV, and if the CAPS molecular marker is cut into two bands, the haplotype of the wheat biological rhythm clock gene TaPRR-A1 is Hapl a, and if the CAPS molecular marker cannot be cut, the haplotype of the wheat biological rhythm clock gene TaPRR-A1 is Hapl b.
The use of the molecular marker TaPRR-A1-SNP 1432 of the aforementioned wheat biorhythmic clock gene TaPRR-A1 for identifying the yield traits of wheat, including plant height, spike length and thousand kernel weight, which are significantly reduced, significantly increased, and significantly increased for the Hapl a type, as compared to the Hapl b type, hapl a type is the excellent genotype of the wheat biorhythmic clock gene TaPRR-A1.
The invention has the advantages that: the invention discovers the excellent allele (Hapl a type) of the wheat biological rhythm clock gene TaPRR-A1 from the natural population of wheat, develops related functional molecular markers (TaPRR 59-A1-SNP 1432) for identifying the plant height, the spike length and the thousand grain weight of the wheat, and provides gene resources and effective approaches for genetic improvement of wheat yield traits.
Drawings
FIG. 1 is a schematic diagram showing variation of the wheat biorhythmic clock gene TaPRR-A1 gene region;
FIG. 2 is a graph showing the detection result of molecular marker gel electrophoresis of a part of wheat.
Detailed Description
The present invention will be described in detail with reference to the drawings and examples. The experimental methods used in the examples are conventional methods unless specifically indicated.
1. Acquisition of polymorphic site of wheat biorhythmic clock gene TaPRR-A1
The genome sequence of the wheat biological rhythm clock gene TaPRR-A1 is shown in SEQ ID NO. 15.
Specific primers are designed according to the genome sequence of the wheat biological rhythm clock gene TaPRR-A1 to carry out amplification sequencing. The designed specific primers are 5 pairs in total, and the specific primers are respectively: taPRR59-A1-1F/1R, taPRR59-A1-2F/2R, taPRR59-A1-3F/3R, taPRR59-A1-4F/4R, and TaPRR59-A1-5F/5R, the nucleotide sequences of each specific primer were as follows:
TaPRR59-A1-1F:TCCGTTCCCCTCTCTCCA(SEQ ID NO:5)
TaPRR59-A1-1R:CAGATCAATTTGAACAGCCAAA(SEQ ID NO:6)
TaPRR59-A1-2F:CTGTTCAAATTGATCTGCCAAA(SEQ ID NO:7)
TaPRR59-A1-2R:TTCATTCCCCATAACACACA(SEQ ID NO:8)
TaPRR59-A1-3F:AGTGTGTAACATGAGATGCCTTC(SEQ ID NO:9)
TaPRR59-A1-3R:CCAGTTACTTTAAATTCCCCTCT(SEQ ID NO:10)
TaPRR59-A1-4F:TCCAAGGCTACAACGGAACA(SEQ ID NO:11)
TaPRR59-A1-4R:GCAGTCTTCCCTTAGGTGCC(SEQ ID NO:12)
TaPRR59-A1-5F:GCGTGCGGAATGATGGAAAA(SEQ ID NO:13)
TaPRR59-A1-5R:TCCATACATGACAGACGGCG(SEQ ID NO:14)
The DNA of 30 parts of wheat material (all from the national germplasm resource pool) in Table 1 was PCR amplified using the above 5 pairs of specific primers (TaPRR-A1-1F/1R, taPRR-A1-2F/2R, taPRR-A1-3F/3R, taPRR-A1-4F/4R and TaPRR-A1-5F/5R), respectively.
The PCR amplification system was 50mL, and specifically: 2.0. Mu.L of DNA template, 2.0. Mu.L of upstream primer, 2.0. Mu.L of downstream primer, 25. Mu.L of 2 Xbuffer (Phanta Max Buffer), 1.0. Mu.L of dNTP mix (2.5. Mu.M each), 1.0mL of ultra-fidelity DNA Polymerase (Phanta Max Super-FIDELITY DNA Polymerase), 17.0. Mu.L of ultrapure water (ddH 2 O).
The common amplification procedure is adopted for amplification, and the steps are as follows: denaturation at 95℃for 3min; denaturation at 95℃for 40s, renaturation at 58℃for 40s, extension at 72℃for 2min,34 cycles; extending at 72 ℃ for 10min; and (5) finishing amplification and storing at 4 ℃.
TABLE 130 common wheat variety
After the PCR amplification is finished, the target fragment is subjected to gel cutting recovery, and the specific primers TaPRR A1-1F/1R, taPRR A1-2F/2R, taPRR A1-3F/3R, taPRR A1-4F/4R and TaPRR A1-5F/5R are used for respectively carrying out two-way first-generation sequencing on the recovered products.
The sequence analysis shows that the first intron region of the wheat biological rhythm clock gene TaPRR-A1 has 1 SNP site (SNP 4), and the region upstream of the gene start codon ATG has 3 SNP sites (SNP 1, SNP2 and SNP 3). As shown in FIG. 1, these 4 SNP sites have a co-segregation phenomenon, and constitute 2 haplotypes, taPRR-A1-Hapl a (hereinafter abbreviated as Hapl a) and TaPRR-A1-Hapl b (hereinafter abbreviated as Hapl b), respectively.
2. Development of molecular marker of wheat biorhythmic clock gene TaPRR-A1 and haplotype identification
1. Development of CAPS molecular markers
Two rounds of PCR primers were designed based on the SNP4 site (A/G, located 1432bp downstream of the initiation codon ATG) of the wheat biorhythmic clock gene TaPRR-A1, wherein:
the first round PCR primer is a genome specific primer, which is marked as TaPRR-59-A1-SNP 1432-1F/1R.
The second round of PCR primers specifically amplified a 583bp fragment containing SNP4, designated TaPRR-A1-SNP 1432-2F/2R.
The nucleotide sequences of TaPRR-A1-SNP 1432-1F/1R and TaPRR-A1-SNP 1432-2F/2R are specifically as follows:
TaPRR59-A1-SNP1432-1F:TCCGTTCCCCTCTCTCCA(SEQ ID NO:1)
TaPRR59-A1-SNP1432-1R:CAGATCAATTTGAACAGCCAAA(SEQ ID NO:2)
TaPRR59-A1-SNP1432-2F:GTGAACAAATGCCTATAAATGG(SEQ ID NO:3)
TaPRR59-A1-SNP1432-2R:CAGATCAATTTGAACAGCCAAA(SEQ ID NO:4)
The molecular marker corresponding to the above two rounds of PCR primers was designated TaPRR-A1-SNP 1432.
Since SNP4 is located in the recognition sequence (GATATC) of the restriction enzyme EcoRV, the base type of SNP4 can be judged from the cleavage band pattern of the PCR product, specifically:
If the PCR product can be cut into two bands, the base of the locus is A;
If the PCR product cannot be cut, the base at this site is G.
2. Identification of haplotypes
A natural population (Table 2) consisting of 280 parts of common hexaploid wheat is selected, and genotype identification is carried out on the natural population by utilizing the CAPS molecular marker TaPRR-A1-SNP 1432.
(1) First round PCR amplification
The primer TaPRR-A1-SNP 1432-1F/1R is used for carrying out the first round of PCR amplification on the DNA of the wheat variety to be detected.
The PCR amplification system was 10. Mu.L, and specifically: 0.4. Mu.L of DNA template, 0.4. Mu.L of upstream primer, 0.4. Mu.L of downstream primer, 5. Mu.L of 2 Xbuffer (Phanta Max Buffer), 0.2. Mu.L of dNTP mix (2.5 mM each), 0.2mL of ultra-fidelity DNA Polymerase (Phanta Max Super-FIDELITY DNA Polymerase), 3.4. Mu.L of ultra-pure water (ddH 2 O).
The common amplification procedure is adopted for amplification, and the steps are as follows: denaturation at 95℃for 3min; denaturation at 95℃for 40s, renaturation at 62℃for 40s, extension at 72℃for 2min,34 cycles; extending at 72 ℃ for 10min; and (5) finishing amplification and storing at 4 ℃.
The PCR products were detected by 1% agarose gel electrophoresis, and when a single target fragment (1761 bp) was obtained, a second round of PCR amplification was performed using the primary PCR product as a template.
(2) Second round PCR amplification
A second round of PCR amplification was performed using primer TaPRR-A1-SNP 1432-2F/2R and the primary PCR product as template.
The PCR amplification system was 10. Mu.L, and specifically: 0.4. Mu.L of DNA template, 0.4. Mu.L of upstream primer, 0.4. Mu.L of downstream primer, 5. Mu.L of 2 XGC Buffer, 1.6. Mu.L of dNTP mix (2.5 mM each), 0.1mL of LA Tap enzyme, 2.1. Mu.L of ddH 2 O.
The common amplification procedure is adopted for amplification, and the steps are as follows: denaturation at 95℃for 3min; denaturation at 95℃for 40s, renaturation at 58℃for 40s, extension at 72℃for 40s,34 cycles; extending at 72 ℃ for 10min; and (5) finishing amplification and storing at 4 ℃.
The PCR products were detected by 1.5% agarose gel electrophoresis, and when a single target fragment (583 bp) was obtained, the enzyme digestion reaction was performed using the secondary PCR product as a substrate.
(3) Enzyme digestion reaction
The restriction enzyme EcoRV is used for carrying out enzyme digestion reaction by taking the secondary PCR product as a substrate.
The enzyme digestion reaction system is 10 mu L, and specifically comprises: 3.0. Mu.L of substrate, 1.0. Mu.L of Buffer (rCutSmart ™ Buffer), 0.2. Mu.L of EcoRV enzyme, 5.8. Mu.L of ddH 2 O.
The cleaved products were detected by 2.0% agarose gel electrophoresis. If the enzyme digestion product is two bands with the sizes of 300bp and 283bp, the base of the site is A, and the haplotype of the wheat biological rhythm clock gene TaPRR-A1 is Hapl a; if the enzyme digestion product is a band with the size of 583bp, the base at the site is G, and the haplotype of the wheat biological rhythm clock gene TaPRR-A1 is Hapl b.
The molecular marker gel electrophoresis detection results of some of 280 common hexaploid wheat shown in table 2 are shown in fig. 2, and the molecular marker identification results of all wheat are shown in table 2.
TABLE 2 typing results of molecular marker TaPRR59-A1-SNP1432 in Natural populations
3. Correlation analysis of haplotypes and yield traits
The association analysis was performed on the phenotype data of the two haplotypes (Hapl a, hapl b) of the wheat biorhythm clock gene TaPRR-A1 and the three environments (smoke floor Zhifu region, laishan bath village, laishan waterfall valley) of the natural population for two years (2021, 2022) using the Tassel5.2 software GLM model.
The haplotype and yield trait correlation analysis results of wheat biorhythmic clock gene TaPRR-A1 are shown in Table 3.
TABLE 3 haplotype of wheat biorhythmic clock gene TaPRR-A1 and yield trait correlation analysis results
Note that: ** P <0.01, * P < 0.05.
As can be seen from table 3: compared with Hapl b types, hapl a types have significantly reduced plant height (P < 0.01), spike length (P < 0.05), average reduction ratio of 8.3 percent (plant height) and 5.8 percent (spike length) respectively, and Hapl a types have significantly increased thousand kernel weight (P < 0.01) and average increase ratio of 5.8 percent.
The result shows that Hapl a type is the excellent genotype of wheat biological rhythm clock gene TaPRR59-A1, and molecular marker TaPRR59-A1-SNP1432 can be applied to wheat breeding with excellent yield traits.
It should be noted that the above examples are only examples for clearly illustrating the present invention, and are not limiting to the embodiments of the present invention. Other variations or modifications of the above teachings will be apparent to those of ordinary skill in the art. Not all embodiments are exhaustive. Obvious changes and modifications which are extended by the technical proposal of the invention are still within the protection scope of the invention.
Claims (2)
1. The application of the molecular marker of the wheat biological rhythm clock gene TaPRR-59-A1 in identifying the plant height, spike length and thousand grain weight of wheat is characterized in that the molecular marker is TaPRR-A1-SNP 1432, is CAPS molecular marker, is obtained by amplifying a primary PCR primer shown in SEQ ID NO. 1 and SEQ ID NO. 2 and a secondary PCR primer shown in SEQ ID NO. 3 and SEQ ID NO. 4 to obtain a secondary PCR product, and then carrying out restriction enzyme EcoRV digestion, wherein the fragment length of the primary PCR product is 1761bp, the fragment length of the secondary PCR product is 583bp, if the digestion product is two bands, the sizes are 300bp and 283bp respectively, the corresponding haplotype of the wheat biological rhythm clock gene TaPRR-A1 at 1432bp downstream of an initiation codon ATG is Hapl a, if the digestion product is one band, the band size is still 583bp, the fragment length of the wheat biological rhythm clock gene TaPRR-A1 is corresponding to the haplotype Hapl b downstream of the initiation codon ATG of the 300 bp-283 bp.
2. The use of the molecular marker of wheat biorhythmic clock gene TaPRR-A1 according to claim 1 to identify wheat plant height, ear length and thousand kernel weight, wherein the plant height and ear length of type Hapl a are both significantly reduced and the thousand kernel weight is significantly increased relative to type Hapl b, and type Hapl a is the excellent genotype of wheat biorhythmic clock gene TaPRR 59-A1.
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CN109825639A (en) * | 2019-04-24 | 2019-05-31 | 鲁东大学 | Molecular labeling and its application with wheat grains per spike main effect QTL compact linkage |
CN112442115A (en) * | 2020-12-08 | 2021-03-05 | 中国农业科学院作物科学研究所 | Application of wheat TaPRR95-B protein or coding gene thereof in regulating and controlling plant height |
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CN109825639A (en) * | 2019-04-24 | 2019-05-31 | 鲁东大学 | Molecular labeling and its application with wheat grains per spike main effect QTL compact linkage |
CN112442115A (en) * | 2020-12-08 | 2021-03-05 | 中国农业科学院作物科学研究所 | Application of wheat TaPRR95-B protein or coding gene thereof in regulating and controlling plant height |
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