CN110551719A - Long-chain non-coding RNA gene ALEX1 and application thereof in improving bacterial leaf blight resistance of rice - Google Patents
Long-chain non-coding RNA gene ALEX1 and application thereof in improving bacterial leaf blight resistance of rice Download PDFInfo
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Abstract
The invention discloses a long-chain non-coding RNA gene ALEX1 and application thereof in improving rice bacterial leaf blight resistance. The invention clones long-chain non-coding RNA ALEX1 gene from rice, and the nucleotide sequence is shown as SEQ ID NO:1, the transcription product of the gene is induced by the bacterial blight of the leaf blight to be up-regulated and expressed. Biological function research on ALEX1 proves that activation of the expression of the gene can improve the content of the jasmonic acid in rice and obviously enhance the resistance of the rice to the bacterial blight of the rice, and the long-chain non-coding RNA ALEX1 can positively regulate the resistance of the rice to the bacterial blight of the rice. The invention provides a new strategy and genetic resources for cultivating new rice disease-resistant varieties, in particular new rice bacterial leaf blight-resistant varieties, and has very important theoretical significance and application value.
Description
Technical Field
The invention relates to the technical field of plant genetic engineering, in particular to a long-chain non-coding RNA gene ALEX1 and application thereof in improving rice bacterial leaf blight resistance.
Background
Plant diseases seriously affect the yield and quality of crops, and the cultivation of disease-resistant plants is one of the major topics for the research of crop molecular breeding. Bacterial blight of rice caused by pathogenic variant Xoo (Xanthomonas oryzae) of gram-negative bacterium Xanthomonas oryzae is one of the most common diseases in rice production, pathogenic bacteria invade through water holes or wounds of rice leaves, propagate in large quantities in the vascular bundles and secrete a large amount of polysaccharide substances to block the vascular bundles, so that the leaves are withered and even die, the photosynthesis of rice is seriously reduced, and the yield of rice is reduced and even the rice is harvested absolutely.
At present, internationally, especially Chinese scientists, have identified a plurality of genes related to the bacterial leaf blight resistance of rice, but the cloning and function research of the genes is still less. On the other hand, the bacterial leaf blight pathogenic strain is continuously mutated under the double pressure of natural selection and artificial selection, so that further deep excavation of rice genetic resources with bacterial leaf blight resistance has very important theoretical significance and application value for crop genetic improvement and solving of food safety problems.
Long non-coding RNA (lncRNA) is a non-coding RNA with the length of more than 200nt, which is widely involved in various aspects of organism development and metabolism, and is another research hotspot in the non-coding RNA research field following small-molecule RNA, and the molecular mechanism of lncRNA for regulating plant growth and development and crop agronomic traits becomes a significant scientific frontier problem in the life science field. The function of lncRNA has been reported in mammals, and it is proved that lncRNA can participate in phylogeny, immune regulation and disease occurrence and development of mammals. However, the research on lncRNA in plants is relatively less, and the application of lncRNA and the disease resistance and defense response of rice bacterial leaf blight is still blank up to now.
Disclosure of Invention
The invention aims to overcome the defects in the prior art, provides a long-chain non-coding RNA gene ALEX1 related to the disease resistance of rice bacterial leaf blight, and obviously improves the resistance of rice to bacterial blight. The invention has important application value for molecular genetic breeding of disease-resistant varieties of important grain crops such as rice and the like.
The second purpose of the invention is to provide the application of the long-chain non-coding RNA gene ALEX1 in improving the bacterial leaf blight resistance of rice.
The above object of the present invention is achieved by the following technical solutions:
A long-chain non-coding RNA ALEX1 gene has a nucleotide sequence shown in SEQ ID NO. 1, and the ALEX1 gene is a new gene.
The research of the invention finds a long-chain non-coding RNA (lncRNA) which is specifically expressed only in leaves infected by the bacterial blight bacteria and hardly expressed under normal physiological conditions, and the long-chain non-coding RNA is named ALEX 1. 5 '-RACE and 3' -RACE have proved that ALEX1 gene is located on antisense DNA chain of No. 8 rice chromosome, its gene covers the range from 22381757bp to 22382050bp, can transcribe lncRNA with length of 294nt, its nucleotide sequence is shown in SEQ ID NO. 1. The promoter sequence of the long non-coding RNA ALEX1 gene is shown as SEQ ID NO. 2.
The invention also provides a pair of primer pairs for amplifying the full-length DNA sequence of ALEX1 gene, wherein the primer pairs comprise an upstream primer and a downstream primer, and the nucleotide sequences of the upstream primer and the downstream primer are shown as SEQ ID NO. 3-4 in sequence:
F:5’-CCGGCGACAAGATTTGCAGAG-3’(SEQ ID NO:3);
R:5’-CGCCGTGACATCACCTGGCAATGG-3’(SEQ ID NO:4)。
The invention proves that the in-situ expression activation plants (ALEX1ox-1 and ALEX1ox-2) based on the ALEX1 promoter can enhance the resistance of rice to the bacterial blight. The expression of JA signal pathway related genes (such as JAZ8, MYC2, PR1a, PR1b, PR10a, RSOsPR10 and the like) in ALEX1ox-1 is found to be obviously changed; compared with WT, ALEX1ox-1 has shorter root, and gradient concentration treatment of MeJA also indicates that ALEX1ox-1 is more sensitive to MeJA, and the content measurement result of endogenous hormone shows that the expression of ALEX1 activates the content of JA and JA-Ile in plants to be obviously increased. The results show that the JA signal is activated in the rice ALEX1 high-expression plant, and the ALEX1 is suggested to be possibly involved in JA-mediated defense reaction of rice to bacterial blight.
Therefore, the invention also provides an in situ activation expression vector, which comprises necessary elements for targeting the promoter region of the ALEX1 gene and recruiting a transcription activator so as to promote the expression level of the gene per se and enhance the expression degree of the ALEX1 gene at the in situ level; the promoter sequence of the ALEX1 gene is shown as SEQ ID NO. 2.
Meanwhile, the invention constructs an ALEX1 overexpression vector UBI under the drive of a UBI promoter based on the sequence full length of ALEX1 shown in SEQ ID NO. 1, ALEX1, and the expression vector is transformed to rice callus through agrobacterium to obtain a transgenic rice plant OXALEX1 of overexpression ALEX 1. Experimental results prove that in three OXALEX1 transgenic rice lines, the expression of related genes of a jasmonic acid synthesis pathway or a signal pathway is obviously up-regulated, and the resistance of the three OXALEX1 transgenic rice lines to the bacterial blight of the white leaf blight is also obviously improved.
Therefore, the invention also provides a recombinant overexpression vector, which contains the ALEX1 gene.
preferably, the recombinant overexpression vector contains a UBI promoter sequence.
the invention also protects a host bacterium containing the in-situ activation expression vector or the recombinant overexpression vector.
therefore, the following applications based on the above research results are all within the scope of the present invention:
The long-chain non-coding RNA ALEX1 gene, the in-situ activation expression vector, the recombinant overexpression vector or the host bacterium are applied to improving the content of jasmonic acid and/or jasmonic acid-isoleucine complex in rice.
The long-chain non-coding RNA ALEX1 gene, the in-situ activation expression vector, the recombinant overexpression vector or the host bacterium are applied to improving the bacterial leaf blight resistance of rice.
Specifically, the application is to activate the expression of a long-chain non-coding RNA ALEX1 gene in rice in situ or to transform the long-chain non-coding RNA ALEX1 gene into rice by constructing a super-expression vector; namely a method for improving the bacterial leaf blight resistance of rice: the expression of long-chain non-coding RNA ALEX1 gene in rice is activated in situ or the long-chain non-coding RNA ALEX1 gene is transformed into rice by constructing a super-expression vector of the long-chain non-coding RNA RNAALLEX 1 gene.
The long-chain non-coding RNA ALEX1 gene, the in-situ activation expression vector, the recombinant overexpression vector or the host bacterium are applied to culturing the rice variety resisting bacterial blight.
2, the promoter sequence based on the rice long-chain non-coding RNA gene ALEX1 is applied to improving the content of jasmonic acid and a jasmonic acid-isoleucine complex in rice or enhancing the resistance of rice to bacterial blight.
Compared with the prior art, the invention has the following beneficial effects:
The invention provides a long-chain non-coding RNA gene ALEX1 and application thereof in improving bacterial leaf blight resistance of rice, the invention clones a long-chain non-coding RNA ALEX1 gene from rice, and the nucleotide sequence of the gene is shown as SEQ ID NO:1, the transcription product of the gene is induced by the bacterial blight of the leaf blight to be up-regulated and expressed. Biological function research on ALEX1 proves that activation of the expression of the gene can improve the content of the jasmonic acid in rice and obviously enhance the resistance of the rice to the bacterial blight of the rice, and the long-chain non-coding RNA ALEX1 can positively regulate the resistance of the rice to the bacterial blight of the rice. The invention firstly discloses a report about influence of long-chain non-coding RNA on a jasmonic acid signal of rice or regulation and control of bacterial blight disease resistance, provides a new strategy and genetic resources for cultivating new rice disease resistance varieties, particularly new rice bacterial blight resistance varieties, and has very important theoretical significance and application value.
drawings
FIG. 1 shows the cluster analysis and expression level verification of the response lncRNA of the bacterial blight. (a) PXO99A was inoculated with a heat map of lncRNA differentially expressed in rice leaves, and we used p <0.05, absolute value of expression change >2 as the threshold for significant differential expression analysis. (b) The lncRNA expression profile in RNA-seq was verified by quantitative real-time PCR. The rice gene ACTIN2 was used as an internal control. The expression level of Xoo — 0h was set to 1 and the data represent the mean ± standard deviation of triplicates.
FIG. 2 is GO enrichment and KEGG pathway analysis of Cis targets differentially expressing lncRNA. (a) GO entries for 512 annotated genes in the GO database were analyzed, enriched in "cellular components" and "biological process" ontologies. The enrichment factor was calculated by the number of genes mapped to GO terms, and the log10(FDR) value represents the significance of GO terms. (b) KEGG pathway enrichment analysis of 704 genes, the first 20 enrichment pathways are shown in the figure, with the x-axis being-log 10 (p-value), i.e. the significance of KEGG pathway enrichment.
FIG. 3 shows the insertion site of ALEX 1-activated expression plant and its expression analysis. (a) Model gene distribution within the 10kb region upstream or downstream of the enhancer trap insertion site. (b) Expression level of lncRNA near the insertion site. RT-PCR was used to detect the expression of XLOC _418473, XLOC _437332 and ALEX 1. Rice ACTIN2 was used as an internal control.
FIG. 4 shows the expression and full-length detection of ALEX 1. (a) ALEX1 was induced to express at 6h and 12h after P.albugineus infection, RT-PCR was used to detect the expression of ALEX1, and rice ACTIN2 was used as an internal reference. (b) 5' -RACE peak detection. (c) 3' -RACE peak detection. (d) The 294nt sequence of ALEX1 is full length.
FIG. 5 shows the detection of the resistance of ALEX1 in-situ expression activated plants to bacterial blight of rice. (a) Comparing the resistance of the wild type and ALEX1 activated expression plants to Xoo, inoculating the flag leaves of the rice with PXO99A, and taking pictures after 14 days; (b) leaf lesion length (n ═ 30) of wild type and ALEX1 activated expressing plants 4 weeks after PXO99A infection, asterisks indicate statistical differences from wild type after t-test (x × P < 0.001); (c) real-time fluorescent quantitative PCR analysis of relative DNA content between HrpC of Xoo and rice EF-1 alpha in wild type and ALEX1ox-1 activation expression plants, and data are mean value of three replicates +/-standard deviation.
FIG. 6 shows the detection of the regulation of jasmonic acid signals of ALEX1 in-situ expression activated plants. (a) Relative expression levels of export genes in the JA signaling of ALEX1ox-1 and WT plants, ACTIN2 was used as an internal control, data represent mean ± standard deviation of triplicates, asterisks indicate statistically significant differences from wild type by t-test (P < 0.01;. P < 0.001); (b) MeJA treatment with different concentration gradients is carried out on rice seedlings 3 days after germination, the change of ALEX1ox-1 and WT plant root system development after 3 days of treatment is shown in a graph, and the scale bar is 2 cm; (c) ALEX1ox-1 and WT plants were tested for their endogenous jasmonic acid content using LC-MS/MS for the determination of JA, JA-Ile and OPDA concentrations, and the data are presented as mean. + -. standard deviation of triplicates, and asterisks indicate statistical differences from wild type by t-test (P < 0.05;. P < 0.001).
FIG. 7 is a phenotypic analysis of ALEX1 overexpressing plants. (a) Detecting the expression effect of ALEX1 in 10 ALEX1 overexpression plants by RT-PCR; (b) lesion phenotype after 10 days of infection by the bacterial blight; (c) statistical lesion length, n 15, asterisks indicate statistically significant differences by t-test compared to wild type (× P < 0.001).
FIG. 8 shows the expression level of JA-associated genes in ALEX1 overexpressed plants. ACTIN2 was used as an internal control, and data represent the mean. + -. standard deviation of triplicates, and asterisks indicate statistically significant differences by t-test compared to wild type (. about.P < 0.01;. about.P < 0.001).
Detailed Description
The invention is further described with reference to the drawings and the following detailed description, which are not intended to limit the invention in any way. Reagents, methods and apparatus used in the present invention are conventional in the art unless otherwise indicated.
unless otherwise indicated, reagents and materials used in the following examples are commercially available. The primer sequences used were synthesized by Beijing Rui Boxing Ke Biotechnology GmbH.
Example 1 screening of IncRNA differentially expressed in Rice after infection with Ralstonia solanacearum
In order to research the effect of lncRNA in rice disease resistance reaction, the inventor conducts strand-specific lncRNA sequencing on rice leaf samples infected by 0h, 2h, 6h, 12h and 24h of bacterial blight pathogenic bacteria PXO99A to obtain 5.7 × 10 8 reads, wherein 4.9 × 10 8 reads are matched with a reference genome of rice and account for 85.26% of the obtained total data, 70 transcripts are obtained after splicing and assembling, 5 basic screening processes and coding potential screening are conducted to finally obtain 48727 rice lncRNA transcripts with high reliability, the screened lncRNA is subjected to quantitative analysis by using cuffdiffeff software to obtain FPKM information of the lncRNA of each sample, the expression level of 567 lncRNA shows significant Linolenic acid change due to infection of bacterial blight of the sample (figure 1), in order to confirm the reliability of deep sequencing data of lncRNA expression spectrum, 8 RNA with different expression modes are selected, and the results of the research result show that the early-resistant RNA synthesis of the lincRNA has obvious Linolenic acid expression effect on rice and the early-resistant rice diseases, the early-late-early-late rice disease resistance gene (JACqcRNA) shows that the relevant mRNA is obtained by the research and the research results of the early-late rice disease resistance gene and the early-late-early-late rice disease resistance gene (early-late-early-late-early-late-early-late-early-late-.
Example 2 obtaining and functional identification of ALEX1 in situ expression activated plants
567 of the bacterial blight responsive lncRNA identified above are candidate genetic resources for regulating resistance of rice to bacterial blight. To investigate whether the abnormal expression of lncRNA influences the pathogenesis of bacterial blight of rice, a main rice mutant database in the world is searched, and a plant with lncRNA activated and expressed shows obvious bacterial blight resistance is identified (figure 5). Since this lncRNA is only Expressed specifically and highly in leaves after the infection with the bacterial blight and hardly Expressed under normal physiological conditions (FIG. 4), we named it as ALEX1(An LncRNA Expressed in Xoo-induced leaves), and two activated expression lines of ALEX1 were named ALEX1ox-1 and ALEX1 ox-2.
We have confirmed by 5 '-RACE and 3' -RACE that ALEX1 is located on the antisense DNA strand of chromosome 8 of rice, and ALEX1 gene covers the range from 22381757bp to 22382050bp, which can transcribe lncRNA of 294nt in length (FIG. 4). The insertion sites of ALEX1ox-1 and ALEXox-2 constructed by using an enhancer capture system are 60bp upstream of ALEX1 and belong to the promoter region of the gene, and the experimental result shows that the insertion of the enhancer trap at the sites has the effect of enhancing the expression of ALEX1 (FIG. 3). To further clarify the correspondence between the resistance of the transgenic plant to the bacterial blight and the activation expression of ALEX1, we searched genes near the insertion site of the ALEX1 enhancer trap in detail and found that there were only 3 lncRNA sites within a 10kb region of the insertion site and no protein coding gene (fig. 3). We then investigated the expression levels of these three lncRNAs by RT-PCR. Neither XLOC _418473 nor XLOC _437332 was detected as expressed in ALEX1ox-1 or wild type, whereas ALEX1 was not expressed in WT, but was significantly upregulated in ALEX1ox-1 (FIG. 3). The above results indicate that the insertion of the enhancer capture system into this site only enhanced the expression of ALEX1, and that the resistance of ALEX1ox-1 to bacterial blight was due to the cumulative expression of ALEX1, rather than to changes in the expression of any other regulatory factor near the insertion site.
Then, we detect the expression of the genes related to jasmonic acid signal pathways in wild-type and ALEX1 activated expression strains, and find that the mRNA expression levels of important regulatory factors such as JAZ8, MYC2, PR1a, PR1b, PR10a and RSOsPR10 are obviously changed, the elongation of the roots of the ALEX1ox-1 plants is also obviously inhibited, and the measurement result of the content of endogenous hormones also shows that the content of jasmonic acid and the active form jasmonic acid-isoleucine in the ALEX1 activated expression strains is obviously increased (FIG. 6). Wherein, the sequences of the primers are shown in the table 1:
TABLE 1 expression primers for jasmonic acid signal pathway-related genes
Example 3 ALEX1 in situ expression activates treatment of exogenous methyl jasmonate and determination of endogenous jasmonic acid content in plants
In-situ expression of No. 11 flowers and ALEX1 in wild type activated rice seeds to germinate in water at 32 ℃ for 3 days. Methyl jasmonate (Sigma Aldrich #392707) was diluted to the indicated concentration in deionized water and used to treat the above 3-d-old seedlings. The condition of the roots was photographed after 6 days of culture in a climate chamber at 27 ℃ and 70% humidity. Methyl jasmonate treatment experiments showed that the JA signal was enhanced in rice ALEX1 in situ expression activated plants (fig. 6).
JA. JA-Ile and OPDA were analyzed by liquid chromatography coupled to mass spectrometry (LC-MS/MS). briefly, the top leaf of 3 weeks old rice was homogenized in liquid nitrogen.A sample of 200mg of a powder sample of fresh tissue was added to 1,000. mu.L 500:1 extraction buffer containing isopropanol: water: HCl, with an internal standard of 10ng H2JA (Cerilliant). the mixture was stirred at 4 ℃ for 30 minutes, then 1ml CH 2 Cl 2 was added, gently stirred for 30 minutes, after centrifugation at 13,000 Xg for 10 minutes, the lower layer of about 900. mu.L of solvent was collected at 4 ℃, 100. mu.L of 60% methanol was added to the sample, 10. mu.L of each was injected into a C18 column to further measure the content of the plants by LC-MS/MS (AB ex Q-5600 + system). assay of endogenous hormones shows that the expression of ALEX1 and the content of JA-Ile were significantly increased in the plants mediated by the ALEX1 expression signal (FIG. 6. these combined defense signals in the ALTOF 1, indicating that the rice plant was likely to be involved in the rice leaf blight reaction.
Example 4 construction, transformation and disease-resistant phenotypic analysis of ALEX1 overexpression plants
The total RNA of the rice of middle flower No. 11 which is infected by wild type or the bacterial blight is adopted to amplify an ALEX1 full-length DNA sequence 294bp,
The primer F sequence used was:
5’-GGACTAGTCCGGCGACAAGATTTGCAGAG-3’,
The sequences of the primers R used were:
5’-ATAAGAATGCGGCCGCCGTGACATCACCTGGCAATGG-3’,
SpeI and NotI were used as cleavage sites.
Constructing an ALEX1 overexpression vector guided by a UBI promoter by adopting pRHV plasmid presented by a Wangguan beam researcher of Chinese academy of agricultural sciences; carrying out transgenic treatment by using an agrobacterium-mediated callus genetic transformation method, and transferring the corresponding vector into rice; the transformants were screened with hygromycin (Hyg) to obtain transgenic rice plants with ALEX1 overexpression.
In order to determine the disease resistance of different rice lines to the bacterial blight, a leaf-cutting inoculation method is adopted for infection. The disease resistance of the rice is determined by measuring the degree of the lesion. In the process, the bacterial blight and different rice strains are prepared at the same time, and the disease resistance of the rice at the booting stage is measured by adopting the rice at the booting stage.
Preparation of rice: and (3) planting the rice outdoors, wherein the distance between each row is 25cm, the plant distance is 20cm, and inoculating the bacterial blight when the rice grows to the booting stage. Activating the bacterial strain of the.
Infection experiment: the head of the scissors which is cleaned and sterilized is immersed into the bacterial liquid, the bacterial liquid is adhered to the head, and then the blades are transversely cut at the position 2-3 cm below the tips of the completely unfolded blades. The leaves were then allowed to develop disease for two weeks.
And (3) measuring the lesion spots: measuring the length from the blade tip to the bottom end of the scab, and measuring the length of the blade. And (3) photographing: and (4) sticking the infected leaves to white paper by using a double-sided adhesive tape, and then photographing.
Detection indexes of bacterial growth rate: infected leaves approximately 20cm long were collected at 0, 3 and 6 days post-infection. DNA samples were extracted and the gene copy number of bacterial hrpC and rice EF-1 alpha was quantified using qRT-PCR using the primer sequences shown in Table 2 below:
TABLE 2 expression primers for bacterial hrpC and rice EF-1 alpha genes
Primer name | Sequence (5 '→ 3') |
EF1a-F | CTGGACTGCCACACCTCACACAT |
EF1a-R | CCAACAGCCACCGTTTGCCTC |
HrpC-F | GGGGTGTCGTTGCGGGTATT |
HrpC-R | ATCGGTCTCGTCGGCATCGTA |
The above experimental detection of ALEX1 overexpression plants further proves the important role of the long-chain non-coding RNA ALEX1 in regulation and control of rice resistance to blight disease (FIG. 7 and FIG. 8).
Sequence listing
<110> Zhongshan university
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Claims (10)
1. A long-chain non-coding RNA ALEX1 gene is characterized in that the nucleotide sequence of the ALEX1 gene is shown as SEQ ID NO. 1.
2. A primer pair for amplifying the ALEX1 gene as claimed in claim 1, which is characterized by comprising an upstream primer and a downstream primer, wherein the nucleotide sequences of the upstream primer and the downstream primer are sequentially shown as SEQ ID NO. 3-4.
3. A recombinant overexpression vector comprising the ALEX1 gene of claim 1.
4. An in situ activating expression vector comprising an element that targets the promoter region of the ALEX1 gene and recruits a transcriptional activator.
5. A host bacterium comprising the overexpression vector of claim 3 or the in situ overexpression vector of claim 4.
6. Use of the long non-coding RNA ALEX1 gene of claim 1, the recombinant overexpression vector of claim 3, the in situ-activated expression vector of claim 4, or the host bacterium of claim 5 for increasing the content of jasmonic acid and/or a jasmonic acid-isoleucine complex in rice.
7. use of the long non-coding RNA ALEX1 gene of claim 1, the recombinant overexpression vector of claim 3, the in situ activation expression vector of claim 4 or the host bacterium of claim 5 for improving bacterial blight resistance of rice.
8. The use of claim 6 or 7, wherein the use is in-situ activation of expression of long-chain non-coding RNA ALEX1 gene in rice or construction of a overexpression vector of long-chain non-coding RNA ALEX1 gene for transformation into rice.
9. Use of the long non-coding RNA ALEX1 gene of claim 1, the recombinant overexpression vector of claim 3, the in situ activating expression vector of claim 4 or the host bacterium of claim 5 in breeding rice varieties resistant to bacterial blight.
10. An application of a promoter sequence based on a rice long-chain non-coding RNA gene ALEX1 in enhancing the resistance of rice to bacterial blight is characterized in that the nucleotide sequence of the promoter region of the ALEX1 gene is shown as SEQ ID NO. 2.
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CN114350842A (en) * | 2022-01-14 | 2022-04-15 | 华南农业大学 | High-throughput accurate screening method for rice jasmonic acid related miRNAs |
CN117551667A (en) * | 2024-01-03 | 2024-02-13 | 中国农业科学院农业基因组研究所 | Application of RBB1 gene in preparing rice disease spot material and regulating and controlling rice bacterial infection resistance |
CN117551667B (en) * | 2024-01-03 | 2024-03-12 | 中国农业科学院农业基因组研究所 | Application of RBB1 gene in preparing rice disease spot material and regulating and controlling rice bacterial infection resistance |
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