CN111235170A - Application of qMYR2 gene in adjusting or screening content of oil and fat components in rice - Google Patents

Application of qMYR2 gene in adjusting or screening content of oil and fat components in rice Download PDF

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CN111235170A
CN111235170A CN202010051190.5A CN202010051190A CN111235170A CN 111235170 A CN111235170 A CN 111235170A CN 202010051190 A CN202010051190 A CN 202010051190A CN 111235170 A CN111235170 A CN 111235170A
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qmyr2
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rice
myristoyl
acp thioesterase
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何予卿
周浩
夏朵
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Hubei Shuangshui Shuanglu Biological Technology Co ltd
Huazhong Agricultural University
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Abstract

The invention relates to an application of a qMYR2 gene in regulating the content of oil and fat components in rice and an application of the qMYR2 gene as a screening marker of the content of the oil and fat components in rice breeding, and also relates to a method for regulating the content of the oil and fat components in rice by carrying out genetic operation on the qMYR2 gene, and a rice cross breeding method by taking the qMYR2 gene or a mutant thereof as the screening marker.

Description

Application of qMYR2 gene in adjusting or screening content of oil and fat components in rice
Technical Field
The invention relates to the field of rice molecular breeding, in particular to application of a qMYR2 gene in adjusting and screening the content of oil and fat components in rice.
Background
Lipids are stored in plant seeds mainly in the form of triglycerides. The oil in the rice is very important for the storage, the eating quality and the health of consumers, and the oil content of the rice is generally 2 to 4 percent. The eating quality and palatability of rice are affected by the fatty acid composition and content of rice. Currently, little is known in the art about the lipid synthesis pathway of rice, Liu et al demonstrate that OsFAD3 converts linoleic acid (C18:2) to linolenic acid (C18: 2). Zaplin et al demonstrated that OsFAD2-1 converts oleic acid to linoleic acid. Several researchers have also preliminarily identified several Quantitative Trait Loci (QTLs).
However, the genes and QTLs identified at present are too few, and the heredity and molecular basis of rice oil synthesis still cannot be known, so that main genes influencing oil components and contents in rice need to be found and used as screening marks or targets of genetic operation.
Disclosure of Invention
The inventor of the invention finds out through research that 23 sites which are significantly related to oil content and oil composition are identified, and 11 candidate genes which are possibly involved in a pathway related to rice oil metabolism in rice are obtained through verification of linkage analysis. After further investigation, we found that 4 of these sites contributed greatly to the natural variation in lipid composition and were differentiated in subpopulations. One of the genes is qMYR2 gene, and our research shows that qMYR2 is a main effective gene for positively regulating C14:0 content. If the mutation of the gene leads to the reduction or disappearance of the function of the protein, the content of C14:0 in rice is reduced.
Based on the research, the invention provides application of the qMYR2 gene in regulating the content of oil and fat components in rice, wherein the sequence of the qMYR2 gene is shown as SEQ ID NO. 1.
In a preferred embodiment, the oil component is C14: 0.
The invention also provides a method for regulating the content of oil and fat components in rice, which comprises the steps of introducing qMYR2 gene, improving the expression level of qMYR2 gene, reducing the expression level of qMYR2 gene or mutating qMYR2 gene to improve, reduce or eliminate the function of protein expressed by the qMYR2 gene, wherein the sequence of the qMYR2 gene is shown as SEQ ID NO. 1.
For example, if the rice variety of interest is otherwise excellent in traits but has a too high content of C14:0 and contains a normally functioning gene qMYR2, the C14:0 content of the rice can be reduced by knocking out or mutating the qMYR2 gene in the rice variety of interest, so that the qMYR2 gene is not expressed, or the expressed protein has reduced or no myristoyl-ACP thioesterase function.
On the contrary, if the target rice species has excellent other properties but the content of C14:0 in the rice is too low and the rice species does not contain the qMYR2 gene with normal function, the content of C14:0 in the rice can be increased by introducing the qMYR2 gene or mutating the abnormal qMYR2 gene in the target rice species to restore the mutation to the qMYR2 gene with normal myristoyl-ACP thioesterase function.
The invention also provides application of the qMYR2 gene as a screening marker of rice oil component content in rice breeding, wherein the sequence of the qMYR2 gene is shown as SEQ ID NO. 1.
The invention also provides a rice cross breeding method, which comprises the step of selecting a target genotype by using the qMYR2 gene or a mutant thereof as a screening marker.
In a preferred embodiment, the rice cross-breeding method comprises the steps of:
s1: identifying the qMYR2 gene and its mutation status in the parent;
s2: selecting qMYR2 gene or mutant thereof as a screening marker;
s3: aggregating the screening markers with other dominant traits.
For example, rice has excellent other properties, but the content of C14:0 in rice is too high, and the rice contains a qMYR2 gene with normal function, and in order to reduce the content of C14:0 in the rice by a cross breeding method, the qMYR2 gene is selected to generate a gene which causes phosphatidylcholine: the mutant parent with reduced or eliminated function of the glycero-diphospho-cholinesterase 2 is hybridized with the rice, and the qMYR2 gene mutant is used as a molecular marker to enable the mutant gene to be aggregated with other advantageous traits.
On the contrary, the existing rice has excellent other properties, but the content of C14:0 in the rice is too low, and the rice does not contain a qMYR2 gene with normal function, and in order to improve the content of C14:0 in the rice by a cross breeding method, a qMYR2 gene parent with normal myristoyl-ACP thioesterase function is firstly selected to be hybridized with the rice, and the normal qMYR2 gene is used as a molecular marker to enable the mutant gene to be aggregated with other advantageous properties.
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FIG. 1 shows the percentage contents of 10 oil components in 533 rice varieties detected by GC-MS;
FIG. 2 shows the phenotypic distribution of lipid-related traits of Australian rice (Aus), indica rice (Ind) and japonica rice (Jap) among 533 rice varieties;
FIG. 3 is a Manhattan plot (Manhattan plot) of C14:0 content correlation analysis in indica subpopulations, with dashed lines representing significance threshold (-log)10(P)=7.06)
FIG. 4 is a Manhattan plot and Linkage Disequilibrium (LD) heatmap of the region around a significant peak on chromosome 2, with arrows indicating nucleotide variation sites of the candidate gene and vertical dashed lines indicating the candidate region around the peak;
FIG. 5 is the gene structure of qMYR2 and polymorphisms of the gene;
FIG. 6 is a representation of the C14 in a Recombinant Inbred (RIL) population identified by linkage analysis as 88B2/HD9802S for qMYR 2: a statistical map of QTL scan results for 0-content major loci;
FIG. 7 is a C18:2 content statistics of different qMYR2 haplotypes, where test subjects in a are 305 indica rice varieties in the acquisition population and test subjects in B are RIL populations derived from 88B2/HD 9802S;
figure 8 is a statistical plot of 10 fatty acid content in wild-type and knockout mutant families, P <0.05, P < 0.01; p < 0.001.
Detailed Description
The principles and features of this invention are described below in conjunction with the following drawings, which are set forth by way of illustration only and are not intended to limit the scope of the invention.
1. Sample source
The rice material used in the present invention includes natural population of 533 cultivars of cultivated rice and three self-bred recombinant populations. The natural population is used for whole genome association analysis, and the three recombinant inbred populations are used for linkage analysis.
Among them, 533 cultivars of rice included 50 aus (aus), 305 indica (indica) and 178 japonica (japonica).
Three recombinant near-breeding varieties were derived from the following hybrid lines, respectively: 97 Zhenshan/Minghui 63(ZS97/MH63), 88B-2/HD9802S and B805D/H6S.
2. Sample processing
Husking rice to obtain brown rice, grinding, sieving with 80 mesh sieve, drying at 80 deg.C for 24 hr, and extracting lipid. 0.2g of rice flour was put into a10 ml glass tube, and 4.5ml of a sulfuric acid-methanol solution (1:19) and 100. mu.l of a heptadecanoic acid standard solution in chloroform were added and mixed well. The preparation of the heptadecanoic acid standard solution was 1.07g of a heptadecanoic acid standard in 10ml of chromatographically pure chloroform. The mixture was incubated in a water bath at 85 ℃ for 2 h. After cooling to room temperature, fatty acid methyl esters were extracted using n-hexane and analyzed by gas chromatography-mass spectrometer (GC-MS). The sum of all identified fatty acid contents was taken as the oil content. Two tests were performed for each sample and the average was used for subsequent analysis.
3. GC-MS analysis results
The results of GC-MS analysis are shown in FIG. 1, and of the 10 fatty acids identified, palmitic acid (C16:0), oleic acid (C18:1) and linoleic acid (C18:2) accounted for more than 90% of the total fatty acid content. We found that there are wide variations in a large number of oil-and-fat related traits, from 1.5-fold difference in C18:2 content to 7.4-fold difference in myristic acid (C14:0) content. The total fatty acid content is in the range of 22.99-40.96 mg/g.
Of these, Australian rice (aus) has the highest C16:0 content, followed by indica (Ind) and japonica (Jap), and the opposite C18:1 and C18:2 contents (FIG. 2).
4. Association analysis and linkage analysis
Genome Wide Association Study (GWAS): GWAS was performed on indica, japonica and all samples, respectively. In each analysis group, only SNPs with a minor site frequency (MA) F > 5% and a deletion rate < 15% were selected for association analysis.
Linkage analysis: linkage analysis was performed on three RIL populations-ZS 97/MH63(96 strains), 88B-2/HD9802S (108 strains) and B805D/H6S (135 strains). These lines were all sequenced by second generation and then aligned to the rice reference genome with 50bp double-ended reads. Wherein, the sequences with the aligned mass more than or equal to 40 and the bases with the average mass more than or equal to 10 are used for identifying SNP. Genetic Bin maps were constructed for identifying QTLs by using MPR algorithm genotyping to infer the genotype of the parental lines.
Based on the above work, we finally obtained 520 ten thousand high quality SNPs for assessing population structure and affinity, and identified 23 significant association sites therein. In 23 loci, we found qMYR2 to be the major QTL associated with C14:02 content (fig. 3).
As shown in FIG. 4, qMYR2 is located on the long arm of chromosome 2, and we are based on the point-to-point Linkage Disequilibrium (LD) correlation coefficient (r)2< 0.6) analyzed the sequence in the 25.86-26.02Mb (162kb) region, and finally determined that the candidate gene corresponding to this QTL was LOC _ Os02g43090 (sequence SEQ ID NO:1) and the homologous gene encoding myristoyl-ACP thioesterase in Arabidopsis was FATB (acyl-ACP thioesterase B) gene.
The G-A mutation at position 169 (Ex1-G/A) on exon 1 of the LOC _ Os02G43090 gene has a large minor allele frequency, and this mutation results in an amino acid change (FIG. 5).
The genotype of the Ex1-G/A locus of qMYR2 differs between indica variety 88B-2 and HD 9802S. Also, QTL analysis using the RIL population derived from the 88B-2/HD9802S hybrid demonstrated that the comparative effect of the qMYR2 haplotype on C14:0 content was qMYR2 (FIG. 6, Table 1).
TABLE 1 phenotypic analysis of lipid-related traits
Figure BDA0002371244460000061
Figure BDA0002371244460000071
Based on the A and T bases of the mutation sites, we divided qMYR2 into haplotype A (SEQ ID NO:1) and haplotype B (SEQ ID NO: 2). The C14:0 content of haplotype A lines was higher than haplotype B lines in both 305 indica variety populations and RIL populations (FIG. 7).
5. Transgene analysis
In order to further determine the function of qMYR2, qMYR2 in ZS97 is knocked out by using a CRISPR-Cas9 system, a 23bp target point with C-terminal NGG is designed in the preparation of a CRISPR/Cas9 knock-out construct, after the target point is determined, a 20bp target point is inserted into an intermediate vector pER8-Cas9-U6 or pER8-Cas9-U3 and cloned to pCXUN-Cas9 to obtain a knock-out vector, the knock-out construct is named KO-MYR2, introduced into escherichia coli strainns 5 α for sequencing, after the correctness is verified, the Agrobacterium tumefaciens Traumefaciens strain sequencing strain EHA105 is introduced, and then the plant is transferred to ZS97 to verify the genotype of a knock-out system by means of transgenic verification.
Compared with the wild type ZS97 (haplotype a), the ZS97 knockout line KO-qMYR2 had a significantly increased C18:1 content and a significantly decreased C14:0 content (fig. 8). The site was demonstrated to be useful for modulating fatty acid composition in rice.
Combining the above experiments, qMYR2 is the major gene that positively regulates the C14:0 content. If the mutation of the gene leads to the reduction or disappearance of the function of the protein, the content of C14:0 in rice is reduced.
Although the above examples only show that the CRISPR-cas9 system is used to obtain the knockout mutant and the Ex1-G/A mutant, it will be understood by those skilled in the art after reading the disclosure of the present application that the gene is introduced, knocked out, knocked down or mutated into related functions with reduced or no related functions, so as to achieve the purpose of regulating the content of C14:0 in rice.
The above description is only for the purpose of illustrating the preferred embodiments of the present invention and is not to be construed as limiting the invention, and any modifications, equivalents, improvements and the like that fall within the spirit and principle of the present invention are intended to be included therein.
Sequence listing
<110> university of agriculture in Huazhong
HUBEI SHUANGSHUI SHUANGLU BIOLOGICAL TECHNOLOGY Co.,Ltd.
Application of <120> qMYR2 gene in regulating or screening content of oil and fat components in rice
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<213> Rice (Oryza sativa)
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tgtggcattg tcgcaaagcc taacccacct cctgcagcca tgcaagtaaa ggcacaggct 180
caaacccttc ccaaggttaa tggtacgaag gttaacctca agacggtgaa gcctgacatg 240
gaggaaacgg tgcctcacag tgctccaaag acgttctata accaactgcc ggattggagc 300
atgcttcttg cggctattac aaccatcttc ctcgccgcag agaagcagtg gacactgctt 360
gattggaagc cgaagaaacc tgacatgctt gttgacacat ttggctttgg taggatcatc 420
caggacggta tggtgtttag gcagaacttc atgattcggt cctacgagat tggcgctgat 480
cgtacagctt ctatagagac attgatgaat catttacagg aaacggctct taaccatgta 540
aggactgctg gtcttcttgg agatggtttt ggggctacac cggagatgag caaacggaac 600
ttgatatggg ttgtcagcaa aatccagctt cttgttgagc aataccccgc atggggagat 660
atggttcaag ttgacacatg ggtcgctgct gctggcaaaa atggcatgcg tcgagactgg 720
catgttcgtg actacaactc tggccgaaca atcttgagag ctacaagtgt ttgggtgatg 780
atgcacaaga aaactagaag actttcaaaa atgccagatg aagttagagc tgaaataggc 840
ccatatttca atgaccgttc agctataaca gaggagcaga gtgaaaagtt agcctag 897
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caaacccttc ccaaggttaa tggtacgaag gttaacctca agacggtgaa gcctgacatg 240
gaggaaacgg tgcctcacag tgctccaaag acgttctata accaactgcc ggattggagc 300
atgcttcttg cggctattac aaccatcttc ctcgccgcag agaagcagtg gacactgctt 360
gattggaagc cgaagaaacc tgacatgctt gttgacacat ttggctttgg taggattatc 420
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ttgatatggg ttgtcagcaa aatccagctt cttgttgagc aataccccgc atggggagat 660
atggttcaag ttgacacatg ggtcgctgct gctggcaaaa atggcatgcg tcgagactgg 720
catgttcgtg actacaactc tggccgaaca atcttgagag ctacaagtgt ttgggtgatg 780
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ccatatttca atgaccgttc agctataaca gaggagcaga gtgaaaagtt agccaagaca 900
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cttgaatcag gagctgacat tgtgaaggca cacacagagt ggcgaccaaa gcgatcgcat 1260
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Claims (9)

  1. The application of qMYR2 gene in regulating the content of oil and fat components in rice, wherein the sequence of qMYR2 gene is shown as SEQ ID NO. 1.
  2. 2. The use according to claim 1, wherein the oil component is C14: 0.
  3. 3. A method for regulating the content of oil and fat components in rice is characterized by comprising the steps of introducing qMYR2 gene into rice seeds for producing the rice, improving the expression level of qMYR2 gene, reducing the expression level of qMYR2 gene or mutating qMYR2 gene to improve, reduce or eliminate the protein function expressed by the qMYR2 gene, wherein the sequence of the qMYR2 gene is shown as SEQ ID NO: 1.
  4. 4. The method according to claim 3, wherein rice seed from which the rice is produced contains a qMYR2 gene having normal myristoyl-ACP thioesterase function, the qMYR2 gene is knocked out or down-regulated, or the qMYR2 gene is mutated such that myristoyl-ACP thioesterase function of a protein expressed by the qMYR2 gene is reduced or absent.
  5. 5. The method according to claim 3, wherein the rice seed from which the rice is produced is free of qMYR2 gene having normal myristoyl-ACP thioesterase function, is transformed with qMYR2 gene having normal myristoyl-ACP thioesterase function, or is back-mutated to qMYR2 gene having normal myristoyl-ACP thioesterase function from qMYR2 gene having no normal myristoyl-ACP thioesterase function.
  6. The application of the qMYR2 gene as a screening marker of rice oil component content in rice breeding is disclosed, wherein the sequence of the qMYR2 gene is shown as SEQ ID NO. 1.
  7. 7. A rice cross breeding method is characterized by comprising the step of selecting a target genotype by using a qMYR2 gene or a qMYR2 gene mutant as a screening marker.
  8. 8. The rice cross-breeding method according to claim 7, wherein the existing rice seed contains qMYR2 gene having a function of n-myristoyl-ACP thioesterase,
    s1: identifying as a parent a rice species containing a mutation in the qMYR2 gene with reduced or abolished myristoyl-ACP thioesterase function;
    s2: crossing said existing rice seed with a parent comprising a mutation in the qMYR2 gene that reduces or eliminates myristoyl-ACP thioesterase function;
    s3: and the qMYR2 gene mutant is used as a screening marker, and the qMYR2 gene mutant and the superior traits of the existing rice seeds are aggregated together.
  9. 9. The rice cross-breeding method of claim 7, wherein the existing rice seed does not contain qMYR2 gene with normal myristoyl-ACP thioesterase function,
    s1: identifying rice seed containing a normal myristoyl-ACP thioesterase function qMYR2 gene as a parent;
    s2: crossing said existing rice seed with said parent comprising the qMYR2 gene for normal myristoyl-ACP thioesterase function;
    s3: and (3) taking the qMYR2 gene with the normal myristoyl-ACP thioesterase function as a screening marker, and aggregating the qMYR2 gene with the normal myristoyl-ACP thioesterase function and the advantageous traits of the existing rice seeds.
CN202010051190.5A 2020-01-17 2020-01-17 Application of qMYR2 gene in adjusting or screening content of oil and fat components in rice Pending CN111235170A (en)

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Citations (4)

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Application publication date: 20200605