CN108707612B - Gene related to radish late bolting character and application thereof - Google Patents
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Abstract
The invention provides a gene related to late bolting character of radish and application thereof, belonging to the technical field of genetic engineering and having a nucleotide sequence shown in SEQ ID No. 1. The gene provided by the invention can ensure that the radish shoots and blooms at night.
Description
Technical Field
The invention relates to the technical field of genetic engineering, in particular to a gene related to radish late bolting character and application thereof.
Background
The radish originates from China, is an important vegetable crop in China, and is a 'current vegetable' for urban and rural residents in China for a long time. The annual sowing area is 1600 mu, and accounts for 6 percent of the whole vegetable production in China. Radish is a long-day plant, and is transformed from vegetative growth to reproductive growth under the long-day condition after low-temperature vernalization, so that the radish is bolting and flowering. The most important influence of immature bolting and flowering on radish production is the conversion from vegetative growth to reproductive growth, and the inhibition of the expansion of fleshy roots, which leads to the reduction of yield and quality. The discovery of late bolting gene of radish and the cultivation of late bolting radish variety are the fundamental approaches to solve the problem.
Based on a high-throughput RNA sequencing technology, genes related to late bolting and flowering traits are identified in radish, and a large number of differentially expressed genes and key genes for controlling bolting and flowering, such as FT, CO, SOC1, FLC and LFY, are found. By transcriptome analysis, 3 homologous FLC genes (RsFLC1, RsFLC2 and RsFLC3) were found to be located on Rs7, Rs2 and Rs3 chromosomes, respectively (Yi et al 2014; Kitashiba et al 2014). Obvious sequence variation exists on RsFLC gene locus, but no new gene sequence related to radish late bolting character is found.
Disclosure of Invention
The invention aims to provide a gene related to the late bolting character of radish, which can ensure that the radish can bolt and flower late.
In order to achieve the above object, the present invention provides the following technical solutions:
the invention provides a gene related to the late bolting character of radish, which has a nucleotide sequence shown in SEQ ID No. 1.
The invention also provides the application of the gene in the technical scheme in identifying the bolting character of radish.
Preferably, the method for identifying the bolting character of radish comprises the following steps:
carrying out PCR amplification on the genomic DNA of the radish to be detected to obtain an amplification product, wherein primers used in the PCR amplification are 1F and 1R, the 1F has a nucleotide sequence shown in SEQ ID No.2, and the 1R has a nucleotide sequence shown in SEQ ID No. 3;
when the fragment of the amplified product is 2417bp and contains the gene in the technical scheme, the bolting character of the radish is a late bolting character;
and when the fragment of the amplified product is 790bp and does not contain the gene in the technical scheme, the bolting character of the radish is an early bolting character.
Preferably, the reaction system for PCR amplification comprises 100ng of genomic DNA, 2. mu.l of 10 × PCRbuffer, 1.6. mu.l of dNTPs, 0.4. mu.l of 1F at a concentration of 10. mu.M, 0.4. mu.l of 1R at a concentration of 10. mu.M, 1.5. mu.l of Taq enzyme, and 24.1. mu.l of ddH per 30. mu.l2O。
Preferably, the procedure of PCR amplification is: pre-denaturation at 94 ℃ for 4 min; denaturation at 94 ℃ for 30s, annealing at 60 ℃ for 1min, extension at 72 ℃ for 1.5min, and 35 cycles; extending for 10min at 72 ℃; storing at 4 ℃. The invention also provides application of the gene sequence in the technical scheme in radish breeding, and the radish breeding method comprises the following steps: and selecting the radish to be tested containing the gene in the technical scheme in the genome as a parent to breed by utilizing the steps in the technical scheme.
The invention provides a gene related to the late bolting and flowering character of radish. The radish is a two-year crop, the bolting and flowering identification time is long, when the method is used for identifying the bolting character of radish varieties and assisting in selective breeding parental application, the bolting property identification can be carried out on the varieties to be detected in the seedling stage, and the field management cost and time of the plants are saved.
The results of the embodiments of the present invention show that: the gene provided by the invention can ensure that the radish shoots and blooms at night.
Drawings
FIG. 1 shows QTL positioning information of flowering time character of bolting radish, A: bolting and flowering time is preliminarily positioned between the InDel162 and InDel170 markers; b: the partially encrypted radish R02 chromosome, wherein a candidate gene RsFLC2 is positioned between markers InDel520 and InDel 535;
FIG. 2 shows the genotyping by agarose gel electrophoresis.
Detailed Description
The invention provides a gene related to the late bolting character of radish, which has a nucleotide sequence shown as SEQ ID No.1, wherein the nucleotide sequence is shown as follows:
the genes in the technical scheme are related to the bolting character of the radish, and the bolting character of the radish containing the genes in the technical scheme is expressed as a late bolting character.
The invention also provides application of the gene in the technical scheme in identifying the bolting character of radish.
In the invention, the method for identifying the bolting character of radish comprises the following steps:
carrying out PCR amplification on the genomic DNA of the radish to be detected to obtain an amplification product, wherein primers used in the PCR amplification are 1F and 1R, the 1F has a nucleotide sequence shown in SEQ ID No.2, and the 1R has a nucleotide sequence shown in SEQ ID No. 3;
when the fragment of the amplification product is 2417bp and contains the gene as claimed in claim 1, the bolting character of the radish is a late bolting character;
when the fragment of the amplification product is 790bp and does not contain the gene of claim 1, the bolting character of the radish is an early bolting character.
The method for extracting the genomic DNA of the radish to be detected is not particularly limited, and can be an extraction method which is conventionally used by a person skilled in the art, such as a CTAB method.
In the invention, the primers used for PCR amplification are 1F and 1R, wherein the 1F has a nucleotide sequence shown in SEQ ID No.2, and the specific sequences are as follows:
5’-ATGGGAAGAAAAAAACTAGAGAT-3’；
the 1R has a nucleotide sequence shown as SEQ ID No.3, and is specifically shown as follows:
5’-TGCATTAATCCGTGGTAAATT-3’。
in the present invention, the reaction system for PCR amplification preferably comprises 100ng of genomic DNA, 2. mu.l of 10 × PCR Buffer, 1.6. mu.l of dNTPs, 0.4. mu.l of 1F at a concentration of 10. mu.M, 0.4. mu.l of 1R at a concentration of 10. mu.M, 1.5. mu.l of Taq enzyme, 24.1. mu.l of ddH per 30. mu.l2And O. The source of the above-mentioned reagent is not particularly limited in the present invention, and a commercially available product conventionally selected by those skilled in the art may be used.
In the present invention, the procedure of PCR amplification is: pre-denaturation at 94 ℃ for 4 min; denaturation at 94 ℃ for 30s, annealing at 60 ℃ for 1min, extension at 72 ℃ for 1.5min, and 35 cycles; extending for 10min at 72 ℃; storing at 4 ℃. The invention also provides application of the gene in the technical scheme in radish breeding, and the radish breeding method comprises the following steps: using the steps described in the above technical scheme, breeding material comprising the genes described in the above technical scheme is selected as a parent.
The following examples are provided to describe the gene related to the radish late bolting trait and the application thereof in detail, but they should not be construed as limiting the scope of the present invention.
Example 1
Obtaining of gene sequence related to bolting resistance of radish
The invention utilizes the conventional map-based cloning method to identify and clone the related genes of bolting resistance of radish.
1. Genetic segregation population construction and phenotype identification
F containing 183 individuals was constructed using a material from Japanese late bolting, "Ninengo" and a material from Chinese early bolting, "Maer" as parents2And (4) a group. Spring to parent strain F in 20161、F2And carrying out bolting and flowering character investigation on the individual plants of the group. The investigation method comprises the following steps: individual plants were investigated every other day for budding and flowering. The bud emergence time is the days from planting to the time when the buds can be seen by naked eyes; flowering time is the number of days required from planting to the opening of the first flower. The budding time and flowering time of the late bolting material "Ninengo" were 91 days and 110 days, respectively, and the budding time and flowering time of the early bolting material "Maer" were 44 days and 66 days, respectively. The bolting time variation of the F2 group single plant is 43-105 days, and the average time is 81.27 days; the variation of the flowering time is 70-121 days, and the average day is 96.7 days; the characteristic of continuous distribution quantitative trait heredity is presented.
2. Genetic linkage map construction and Quantitative Trait Locus (QTL)
Development of InDel marker (InDel): whole genome re-sequencing of The parents "Ninengo" and "Maer" was performed using The Illumina Hiseq 2500 sequencing platform, detecting polymorphisms of The parents with reference to The ` Aokubi DH ` reference genome (The radius genome and comprehensive gene expression profile of root roots formation and evaluation, Scientific Reports (2015) 5: 10835). The method comprises the following steps of preliminarily designing 500 pairs of InDel markers, wherein the spacing distance of each marker in an 'Aokubi DH' reference genome is 300-800 kb, the annealing temperature is 58-60 ℃, the base difference between parents is 3-8 bp, and the size of an amplified fragment is 100-200 bp, so that the detection is carried out by using conventional polyacrylamide gel electrophoresis.
Constructing a genetic linkage map and analyzing QTL: taking the parents and the young leaves of each individual plant of the F2 population, and extracting the total DNA by using a conventional CTAB method. Polymorphisms between the parents "Ninengo" and "Maer" were detected using the published 626-pair EST-SSR (Shirasawa K et al, An EST-SSR linking major genes of the Brassicaceae, DNASEARCH, (2011) 18: 221-. Obtaining 131 pairs of polymorphic primers for 183F by performing PCR amplification on parents and 8% polyacrylamide gel electrophoresis2And (4) marking and typing individual plants of the population. Joinmap 4.0 software is used for constructing a Chinese relic containing 9 linkage groupsAnd (6) transferring the map. The mapping method is characterized in that a bolting-resistant related gene of radish is positioned between InDel170 and InDel162 chromosomes of radish R02 by using MapQTL4.0 software, and the result is shown in FIG. 1A.
Finely positioning genes related to bolting resistance of radishes: the preliminary location interval InDel170-InDel162 was marker-encrypted according to the ` Aokubi DH ` reference Genome information (the theoretical Genome and comparative Genome expression and degradation, Scientific Reports (2015) 5: 10835) and the ` XYB36-2 ` reference Genome information (Zhang Xiaohui et al, A de novo Genome of a Chinese Radish client, Horticultural Plant Journal 2015, 1 (3): 155) for a total of 43 InDel markers, as shown in Table 1. A local encrypted linkage map was constructed, and the results are shown in FIG. 1B, and QTL analysis located bolting and flowering-time patterns of radish between R02 chromosomes InDel520 and InDel 535.
Table 143 sequences for InDel markers
3. Identification and sequence analysis of radish bolting-resistant character related gene
Identifying related candidate genes of bolting resistance of radish: according to The radish genome gene annotation (The radish genome and comprehensive gene expression profile of The root genes and The maintenance, Scientific Reports (2015) 5: 10835), RSG31600(Rs _ Scaf 675: 106, 055-.
Sequence analysis of the RsFLC2 gene: according to the disclosed RsFLC2 gene sequence (Yi et al, Identification of flower watering LOCUS C genes for conversion of mutation of L.), Hort Environ Biotechnol, 2014, 55: 548 556), primers 1F and 1R are designed, the sequence of 1F is shown as SEQ ID No.2, specifically 5'-ATGGGAAGAAAAAAACTAGAGAT-3', the sequence of 1R is shown as SEQ ID No.3, specifically 5'-TGCATTAATCCGTGGTAAATT-3', and the sequences of primers 2F and 2R, 2F are designed as SEQ ID No.90, specifically 5 '-AATTTACCACGGATTAATGCA-3, the sequence of 2R is shown as SEQ ID No.91, specifically 5'-CTAATAAAGCAGTGGGAGAGTTAC-3', the late bolting' Ninengo 'and early bolting' RsFLC2 gene sequence are respectively obtained by conventional PCR amplification, cloning and sequencing technologies, the late bolting 'Ninengo' and early bolting 'RsFLC 4692 gene sequences are shown as RsFLC 2' late 'gene sequences, the late bolting' NReID No.2 is shown as SEQ ID No.2, the method specifically comprises the following steps:
the early bolting parent 'Maer' RsFLC2 gene sequence is shown in SEQ ID No.93, and specifically comprises the following steps:
sequence alignment revealed that in 'Ninengo', a 1627bp fragment was inserted into the first intron of the RsFLC2 gene at 434bp relative to the translation initiation site.
Sequence homology analysis of the RsFLC2 gene: further, the "Ninengo" and "Maer" RsFLC2 gene sequences were aligned with the RsFLC2 gene sequence of 7 radish materials published by NCBI (KP 027027-KP 027032, KP027034, sequences from literature, Yi et al, Identification of the same flooding loci C genes for conversion of conversion in radius L), Hort Environ Biotechnol, 2014, 55: 548-556) in multiple, and the 1627bp insert sequence was not found in other materials. In addition, to identify a homologous sequence to the 1627bp insert in ` Ninengo ` RsFLC2, alignment using BLASTn (https:// blast. ncbi. nlm. nih. gov) showed that-100The 3 sequences below the threshold (from b.napus or b.oleracea) have 83-84% sequence similarity, but the coverage is only 48.7%.
Example 2
Application of 1627bp insertion sequence in RsFLC2 in identification of radish late bolting and early bolting materials
1. Identification of 1627bp insertion sequence in RsFLC2 in late bolting and early bolting radish
1) DNA extraction
The conventional CTAB method is used for respectively extracting the genomic DNA of 183 radish materials to be detected in the table 2, wherein the 183 radish materials to be detected in the table 2 are F1 generations obtained by hybridization of parent Ninengo and Maer, and F2 single plants obtained by selfing of F1.
2) PCR amplification and detection
PCR amplification is carried out on the radish material to be detected by using 1F (5'-ATGGGAAGAAAAAAACTAGAGAT-3') and 1R (5'-TGCATTAATCCGTGGTAAATT-3') primers.
PCR reaction system containing 100ng of genomic DNA, 2. mu.l of 10 × PCR Buffer, 1.6. mu.l of dNTPs, 0.4. mu.l (10. mu.M) of each of the above upstream and downstream primers, 1.5UTaq enzyme, and ddH2O to 30. mu.l. The PCR amplification procedure was: pre-denaturation at 94 ℃ for 4 min; denaturation at 94 ℃ for 30s, annealing at 60 ℃ for 1min, extension at 72 ℃ for 1.5min, and 35 cycles; extending for 10min at 72 ℃; storing at 4 ℃. After the amplification, the genotyping was performed by 1.5% agarose gel electrophoresis, and the results are shown in FIG. 2.
As can be seen from FIG. 2, 2417bp fragments are obtained by amplifying the late bolting materials in the F2 population, wherein 1627bp insertion fragments are contained, and 790bp fragments are obtained by amplifying the early bolting materials.
2. Radish bolting character identification
The budding time is used as the index of the early and late bolting of the radish, the investigation standard is the days from the permanent planting to the visual bud observation, and the result is shown in table 2.
The classification criteria for the survey were as follows:
early bolting: the budding time is 43 days to 69 days;
middle bolting: the budding time is 70 to 91 days;
late bolting: the budding time is 92 days to 105 days.
TABLE 2183 statistical tables of RsFLC2 genotyping and disease index
As can be seen from Table 2, the molecular marker was identified as a homozygous 790bp amplified fragment in 31 field-tested early bolting materials; in 31 parts of field material detected as late bolting, the molecular marker is identified as homozygous 2417bp amplified fragment, and the identification accuracy of the method is 100%.
The above examples show that the gene related to radish late bolting provided by the invention can enable radish late bolting and flowering.
The foregoing is only a preferred embodiment of the present invention, and it should be noted that, for those skilled in the art, various modifications and decorations can be made without departing from the principle of the present invention, and these modifications and decorations should also be regarded as the protection scope of the present invention.
Claims (6)
1. A gene related to the late bolting character of radish has a nucleotide sequence shown in SEQ ID No. 1.
2. The use of the gene of claim 1 in identifying early bolting or late bolting traits in radish.
3. The use of claim 2, wherein the method for identifying the bolting trait of radish comprises the following steps:
carrying out PCR amplification on the genomic DNA of the radish to be detected to obtain an amplification product, wherein primers used for the PCR amplification are 1F and 1R, the nucleotide sequence of 1F is shown as SEQ ID No.2, and the nucleotide sequence of 1R is shown as SEQ ID No. 3;
when the fragment of the amplification product is 2417bp and contains the gene as claimed in claim 1, the bolting character of the radish is a late bolting character;
when the fragment of the amplification product is 790bp and does not contain the gene of claim 1, the bolting character of the radish is an early bolting character.
4. The use of claim 3, wherein the reaction system for PCR amplification comprises 100ng of genomic DNA, 2. mu.L of 10 × PCR Buffer, 1.6. mu.L of dNTPs, 1F at a concentration of 10. mu.M at 0.4. mu.L, 1R at a concentration of 10. mu.M at 0.4. mu.L, 1.5. mu.L of Taq enzyme, 24.1. mu.L of ddH per 30. mu.L2O。
5. The use according to claim 3 or 4, wherein the PCR amplification procedure is: pre-denaturation at 94 ℃ for 4 min; denaturation at 94 ℃ for 30s, annealing at 60 ℃ for 1min, extension at 72 ℃ for 1.5min, and 35 cycles; extension at 72 ℃ for l0 min; storing at 4 ℃.
6. The use of the gene of claim 1 in radish breeding by a method comprising: using the steps of claim 3, selecting a test radish whose genome includes the gene of claim 1 as a parent for breeding.
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