CN112126704A - Molecular marker related to rice leaf inclination angle character and application thereof - Google Patents

Molecular marker related to rice leaf inclination angle character and application thereof Download PDF

Info

Publication number
CN112126704A
CN112126704A CN202011055016.4A CN202011055016A CN112126704A CN 112126704 A CN112126704 A CN 112126704A CN 202011055016 A CN202011055016 A CN 202011055016A CN 112126704 A CN112126704 A CN 112126704A
Authority
CN
China
Prior art keywords
snp
molecular marker
rice
base
gene
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
CN202011055016.4A
Other languages
Chinese (zh)
Inventor
薛红卫
韦如娟
渠莉
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Shanghai Jiaotong University
Original Assignee
Shanghai Jiaotong University
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Shanghai Jiaotong University filed Critical Shanghai Jiaotong University
Priority to CN202011055016.4A priority Critical patent/CN112126704A/en
Publication of CN112126704A publication Critical patent/CN112126704A/en
Pending legal-status Critical Current

Links

Classifications

    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/6895Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/13Plant traits
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/156Polymorphic or mutational markers

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Immunology (AREA)
  • Mycology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Botany (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The invention discloses an application of a molecular marker vg0140443758 in identifying rice leaf inclination angle traits, wherein the SNP locus of the molecular marker vg0140443758 is located at 40443758 th base of No.1 chromosome of rice, the SNP locus is located in an LC4 gene coding sequence, base mutation of the SNP locus enables corresponding coded amino acid to be changed from proline (P) into arginine (A), and base mutation of the SNP locus is changed from G into C.

Description

Molecular marker related to rice leaf inclination angle character and application thereof
Technical Field
The invention relates to the field of plant breeding, in particular to a molecular marker related to rice leaf inclination angle characters and application thereof.
Background
Leaf dip is an important agronomic trait in monocotyledonous plants such as rice (Oryza sativa) and contributes to both plant architecture and grain yield. The erect leaf character in rice makes plants more suitable for dense planting by improving the sunlight capture efficiency of seedling populations. Therefore, the regulation and control of the leaf inclination angle have important significance for rice close planting. At present, research proves that LC4(LEAF INCLINCATION 4) gene for encoding F-BOX protein influences the development of LEAF joints, and the inclination of the LEAF can be reduced by knocking out or down-regulating F-BOX gene, thereby regulating the inclination degree of rice leaves.
SNP (Single Nucleotide polymorphism) refers to variation of a single Nucleotide at the genome level, and includes deletion, insertion, conversion, transversion and the like of a single base. SNPs may be present in non-coding sequences, both within and outside the coding sequence of a gene. From the viewpoint of influence on the genetic traits of organisms, SNPs are divided into 2 types: one is synonymous SNP (synnyms SNP), i.e., the change of the coding sequence caused by SNP does not affect the amino acid sequence of the protein translated by SNP, and the mutated base and the unmutated base have the same meaning; another non-synonymous SNP (non-synymousus SNP) means that a change in the base sequence can alter the sequence of a protein translated using it as a template, thereby affecting the function of the protein. Such changes are often the direct cause of changes in biological traits, and non-synonymous SNPs are of great significance in genetic research. In addition, the SNP has the characteristics of large quantity, wide distribution, high representativeness, genetic stability and easy realization of automation of analysis. SNPs, which are genetic markers, contribute to genetic variation of complex traits in higher plants, and are therefore widely used in plant genetic research.
Rice is one of the important grain crops in China, and the breeding of excellent varieties is the source for guaranteeing grain production. The molecular marker can reveal the difference of test materials on the DNA molecular level, and becomes a reliable and efficient tool for identifying and analyzing germplasm resources and varieties. If a molecular marker capable of rapidly distinguishing excellent leaf inclination angle characters of different varieties of rice can be found, molecular markers closely related to leaf inclination angles are screened to assist breeding, reasonable close planting is rapidly achieved, yield in unit area is increased, and greater economic benefits are obtained.
Disclosure of Invention
In order to achieve the purpose, the invention provides application of a molecular marker vg0140443758 in identifying rice leaf inclination angle traits, wherein the SNP site of the molecular marker vg0140443758 is located at 40443758 th base of rice chromosome 1.
In certain embodiments, the SNP sites are non-synonymous SNPs.
In certain embodiments, the SNP site is located in the LC4 gene coding sequence and the base mutation at the SNP site changes the corresponding encoded amino acid from proline (P) to arginine (a).
In certain embodiments, the base of the SNP site is mutated from G to C.
In certain embodiments, the molecular marker vg0140443758 comprises within the coding sequence of the LC4 gene: the SNP locus, 0-955 base pairs at the 3 'end and 0-376 base pairs at the 5' end of the SNP locus, and the LC4 gene coding sequence is shown as SEQ ID NO.1 or 3.
In certain embodiments, the molecular marker vg0140443758 comprises the sequence shown as SEQ ID No.1 or 3.
In another aspect, the application also provides primers capable of identifying or amplifying the SNP molecular marker vg0140443758 related to the rice leaf inclination angle trait, wherein the primers can be hybridized and paired with the LC4 gene sequence, and the SNP molecular marker vg0140443758 is obtained by amplification, and the molecular marker vg0140443758 comprises the following parts in the LC4 gene coding sequence: the SNP locus, 0-955 base pairs at the 3 'end and 0-376 base pairs at the 5' end of the SNP locus, the LC4 gene coding sequence is shown as SEQ ID NO.1 or 3, and the SNP locus is positioned at the 956 th base of the LC4 gene coding sequence.
In certain embodiments, the LC4 gene sequence is set forth in SEQ ID No. 2.
In certain embodiments, the primer is capable of hybridization pairing with LC4 gene coding sequence.
In certain embodiments, the base of the SNP site is mutated from G to C.
In another aspect, the application also provides application of the primers capable of recognizing or amplifying the SNP molecular marker vg0140443758 related to the rice leaf inclination angle trait in identifying the rice leaf inclination angle trait.
In another aspect, the present application further provides a kit comprising the primers of any one of claims 5 to 6, which can recognize or amplify the SNP molecular marker vg0140443758 related to the inclination trait of rice leaves.
On the other hand, the application also provides the molecular marker vg0140443758, the primers capable of identifying or amplifying the SNP molecular marker vg0140443758 related to the rice leaf inclination angle trait and the application of the kit in rice close planting breeding, wherein the SNP site of the molecular marker vg0140443758 is located at 40443758 th base of No.1 chromosome of rice, and the base of the SNP site is mutated from G to C.
In certain embodiments, the use comprises identifying the rice leaf inclination trait using the molecular marker vg 0140443758.
In another aspect, the present application also provides a method for analyzing SNPs associated with inclination of rice leaves, comprising:
(1) searching the expression site of the LC4 gene in rice in an ePlant database;
(2) analyzing all genotypes of the LC4 gene in the rice population and corresponding leaf inclination angle phenotype data in an MBKBASE database;
(3) searching non-synonymous SNP on LC4 gene on Rice Var Map v2.0 website;
(4) and (3) analyzing according to the SNP result predicted by the website: 1) analyzing the conservation of SNP gene loci; 2) looking up the detailed information of the SNP: mutation sites, alternative bases, allele mutation frequency, and the effect of allelic variation; 3) comparing the SNP with the original nucleotide sequence at NCBI to determine the mutation site occurring in the coding region or the mutation site of the promoter region 4) comparing the SNP with the nucleotide sequence of a reference system at NCBI to construct an evolutionary tree and analyze the influence of the SNP on species genetic relationship 5) comparing the amino acid sequence of the SNP with the amino acid sequences of F-box proteins in different gramineous plants at NCBI. 6) Among the above SNPs, SNPs that are not synonymous mutations and have an influence on species relativity, i.e., SNPs that have an influence on the function of the gene, are found.
The invention provides a method for analyzing and controlling SNP of rice leaf inclination angle gene LC4, and non-synonymous mutation SNP with application value is screened. By utilizing the method, the SNP molecular markers of other functional genes in the rice can be analyzed, and the SNP molecular markers with potential application values are determined.
The invention also provides a non-synonymous mutation SNP molecular marker with application value. The SNP is related to inclination angle characters of rice leaves and has great significance for differentiation of japonica indica rice. The SNP mutation site is positioned at the C end of the LC4 protein, and can influence the specific recognition function of the LC4 protein and the substrate protein and influence the regulation and control of the inclination angle of rice leaves. Through further experimental verification, the SNP locus can be used as a molecular marker for rapidly distinguishing the inclination angle of the rice leaf, and the inclination angle of the rice leaf can be rapidly screened by utilizing the SNP molecular marker, so that the breeding period is shortened, the breeding process is accelerated, the cost is saved, reasonable close planting is carried out, and the production benefit is improved.
Detailed Description
The present invention will now be further described with reference to examples, which are intended to be illustrative only, and the present invention may be embodied in many different forms of embodiments, and the scope of the present invention is not limited to the embodiments set forth herein.
Example 1 SNP screening relating to inclination of Rice leaves
It is known that F-BOX gene LEAF INCLINCATION 4(LC4) can adjust the inclination angle of rice leaves, thereby optimizing the plant type of rice, reasonably planting closely and improving the yield of the rice in unit area. Therefore, if the SNP molecular marker for rapidly identifying the rice variety with the suitable leaf inclination angle can be screened out, molecular assisted breeding can be utilized, the breeding process is accelerated, and the plant yield is improved.
Firstly, the accession number of an LC4(LEAF expression 4) gene is searched on a Rice Genome Annotation Project website, the basic information of the gene is obtained, the expression site of the LC4 gene in Rice is searched in an ePlant database, and all genotypes of the LC4 in a Rice population and corresponding LEAF inclination angle phenotype data are analyzed in an MBKBASE database. Inputting the Locus Name (LOC _ Os01g69940.1) of the gene on the Rice Var Map v2.0 website, searching all SNPs on the gene, and finding out 63 SNPs in total, wherein 2 non-synonymous SNPs exist.
The analysis of the SNP results affecting the LC4 gene function obtained from the website and database was as follows:
(1) the distribution of each genotype (allele) in the rice population was analyzed for LC 4. Most of genotype (allele) T1 is present in indica (904/1138); the reference genotype T2 is present in temperate japonica rice (972/1020). The difference of SNP of LC4 is mainly focused on indica rice.
(2) The relationship between each genotype (allele) of LC4 and leaf inclination phenotype was analyzed by searching rice leaf inclination phenotype data. The appearance probability of the rice leaf angle erect phenotype in different genotypes is different, which indicates that the gene locus OsG00017820 is related to the Leaf Angle (LA) character, and indicates that the SNP of LC4 can influence the leaf inclination phenotype of rice.
(3) From the detailed information obtained for all the SNPs of LC4, non-synonymous SNPs whose mutation positions occur in the coding region and which may have an effect on the LC4 gene function were screened. A total of 63 SNPs were found in the genomic region of LC4, where vg0140443758 was a non-synonymous mutation, which occurred at 40443758 in chr01, with the major allele being G, mutated to C (G- > C). This SNP causes downstream genetic variation, which is a nonsynonymous mutation. Details of vg0140443758 were further analyzed. The data show that this SNP accounts for 0.40% of all samples (19/4726), with japonica and oryza sativa containing this SNP by a greater proportion, 1.10%. The intermediate types of the temperate japonica rice, the tropical japonica rice and the japonica rice contain the SNP, wherein the SNP is respectively 0.90%, 0.20% and 3.70%, and the mutation ratio of the SNP in the intermediate type of the japonica rice is the highest. This SNP is absent in indica and Aus rice. The SNP is proved to have great significance for the differentiation of japonica indica rice.
(4) Further analysis of the protein structure of LC4 revealed a conserved F-box domain between amino acids 93 and 133. This domain is about 50 amino acids long, and is typically found in the N-terminal half of many proteins. Further analysis of LC4 gene conservation and the conservation analysis of the locus of vg 0140443758. The sequence of the coding region of LC4 is highly conserved, and the SNP site is positioned in the coding region of LC4, which shows that the SNP site has potential functions or may play an important role in cell development and regulation. The amino acid change at vg0140443758 occurred at 319 to the C-terminus, not within the conserved F-box domain. This SNP may affect the specific recognition of LC4 protein as part of the E3 ubiquitin ligase complex with substrate proteins.
(5) Non-synonymous SNP molecular markers are screened from 63 SNPs of LC4 through the steps, and the Variation ID is vg 0140443758. The result of analyzing and predicting the influence of snpEff on the allelic variation of vg0140443758 at LC4 shows that the SNP is nonsynonymous mutation, and the 319 th amino acid proline (Pro, P) is mutated into arginine (Arg, A), so that the downstream gene variation is caused. And the average score of the accessibility of the SNP chromatin is 78.497, which indicates that the chromatin area around the variation has high accessibility, and indicates that the variation degree of vg0140443758 is high and the LC4 gene function is possibly influenced.
(6) The nucleotide sequence of LC4 was aligned with the nucleotide sequence of vg0140443758 at NCBI and a phylogenetic tree was constructed. The SNP is found to change the evolution relation of the LC4 gene in the japonica rice group DNA (chromosome 1, variety: Japanese rice, complete and rice genome DNA, chromosome 1, PAC clone: P0592G05), and shows that the SNP may influence the evolution relation of LC4 among species. Then, vg0140443758 was aligned with the amino acid sequence of the F-box protein in different gramineae plants at NCBI. The alignment result shows that the amino acid similarity of the F-box protein of vg0140443758 and the F-box protein of other gramineae plants is higher, which indicates that the structure and the function of LC4 in gramineae plants are very similar, but the SNP changes the amino acid property, and the expression of LC4 gene can be influenced after mutation.
Example 2 analysis of the Association of the SNP molecular marker vg0140443758 with the shape of the leaf inclination
Preparing rice plant groups with different leaf inclination shapes, extracting different plant genome DNAs, designing primers by using the genome DNAs as templates according to an LC4 gene sequence (SEQ ID NO.2), analyzing the type vg0140443758(G/C) of the SNP molecular marker by using a KASP method or a conventional PCR method, and determining the association between the SNP type and the leaf inclination character through fluorescence coloration or sequencing, so that the SNP molecular marker vg0140443758 can be used for rapidly and massively identifying the inclination shapes.
The foregoing detailed description of the preferred embodiments of the invention has been presented. It should be understood that numerous modifications and variations could be devised by those skilled in the art in light of the present teachings without departing from the inventive concepts. Therefore, the technical solutions available to those skilled in the art through logic analysis, reasoning and limited experiments based on the prior art according to the concept of the present invention should be within the scope of protection defined by the claims.
Sequence listing
<110> Shanghai university of transportation
<120> molecular marker related to rice leaf inclination angle character and application thereof
<130> CN084-20003PICN
<160> 3
<170> PatentIn version 3.5
<210> 1
<211> 1332
<212> DNA
<213> Artificial Sequence (Artificial Sequence)
<220>
<223> LC4 Gene coding sequence 1
<400> 1
atgggggagg tggcggcgct gcggcagctg gtcggcgagg tgcaggagct ctgggacctc 60
tacggcgcca actcccaccc cctcccaagg tggtatttac tggactttga gcatggttca 120
atcaaagatg atcattgtag agcaaggact ggatacaact cagaattact aaagatcatg 180
gaagctaacc aatctcctcc tcgcaagcgc tcacggaggg acaaaaaccg tgagaaagca 240
cccaactcaa actcaactga agaaatgcaa caggagattt ggagtgagtt ccctggagac 300
ctttttgaaa ccgttgttgc aagacttcca gttgctgcaa ttttccgatt tcgcactgtt 360
tgccggaatt ggtattctat gttgggctca gaaagtttct ctcagcagta ctcagaagtt 420
ccacagaggc tgccatggtt ctatacaatc acccatgaga atgccagcaa caatgtagcg 480
atgtatgacc cttcgctgaa aaaatggcac cacccatcag ttcccctggc tcctgcaaag 540
atagtaattc cagtggcatc tgcaggtggc cttgtctgtt tattggatct tagccacagg 600
aacttctaca tatgcaatcc gctaacacaa tcactcaagg aaattccgcg caggtcagtc 660
caggcatggt caagagtggc agtagggatg gtgatgaacg gaggaacctc taatgaaggt 720
tacaaagtaa tgtggttagg aaatgatggg aattatgaag tctatgattc tatgaagaat 780
atgtggtctt gtccaggcac ttttcctcca agcatcaaac ttccgcttgc tctaaatttt 840
aggtcacagc ctgtggcggt tggcagcatg ctatacttca tgtgtgcaga accagagggt 900
gttttgtcgt atgatgtaag cactgggata tggagacaat tcgtcatccc actgccactt 960
catctgactg accacacact tgccgagttc cagggaaggg ttatgctggt gggtctgctc 1020
tgcaaaaatg cagcgacatg tgtctgcatt tgggagttgc agaagatgac tctcctctgg 1080
aaggaggtgg acagaatgcc aaatatctgg tgcttagaat tctacggtaa gcacatgaag 1140
atgacatgcc tgggcaacag tggtttgctc atgctctcct tgaaggcgaa gcggatgaac 1200
cgcctcgtga catacaacct tttgaacaag gagtggcaga aggttcctga ttgcatgctc 1260
ccatgcagcc gcaaaaagca gtggatagca tgtggcacag catttggtcc atgcccctct 1320
gccttggcct ga 1332
<210> 2
<211> 3596
<212> DNA
<213> Artificial Sequence (Artificial Sequence)
<220>
<223> LC4 Gene sequence
<400> 2
aaatgatatc tggtagtttc agtatcaggc aacctggcac atgccatcat ttcatggttg 60
ctagcaacag gaattaacat atctgccgag aacaattgaa gcaactagtg attgataaag 120
aagtatcatc aagacccagg agcatcagtt cagccccagt tattactata gagagtacat 180
actcagtttt tgggcagatg actgcagatt cagaaataag taatacacac tgaagacgag 240
acgatatcat gataatgaaa acaagcaaaa aaccaagact aaacagatgt cttctgtcca 300
gccttctggc aaggacctta atatctctaa gaagacttaa accagttggt gtagtgccga 360
ccccaaattc ctctagatga tagaccaaac gatatcgatt gcttcagcga gatacaaaaa 420
caaccacagg ttacatgatt ttgtacatga cagataacct tctcacggta agacggaaat 480
atctaaggat aggccaatga tccggaatgt gtgaaatctc aaccaccttt ggtgaagaaa 540
gtgaaaaaaa actgtcaggc caaggcagag gggcatggac caaatgctgt gccacatgct 600
atccactgct ttttgcggct gcatgggagc atgcaatcag gaaccttctg ccactccttg 660
ttcaaaaggt tgtatgtcac gaggcggttc atccgcttcg ccttcaagga gagcatgagc 720
aaaccactgt tgcccaggca tgtcatcttc atgtgcttac cgtagaattc taagcaccag 780
atatttggca ttctgtccac ctccttccag aggagagtca tcttctgcaa ctcccaaatg 840
cagacacatg tcgctgcatt tttgcagagc agacccacca gcataaccct tccctggaac 900
tcggcaagtg tgtggtcagt cagatgaagt ggcagtggga tgacgaattg tctccatatc 960
ccagtgctta catcatacga caaaacaccc tctggttctg cacacatgaa gtatagcatg 1020
ctgccaaccg ccacaggctg tgacctaaaa tttagagcaa gcggaagttt gatgcttgga 1080
ggaaaagtgc ctggacaaga ccacatattc ttcatagaat catagacttc ataattccca 1140
tcatttccta accacattac tttgtaacct tcattagagg ttcctccgtt catcaccatc 1200
cctactgcca ctcttgacca tgcctggact gacctgcgcg gaatttcctt gagtgattgt 1260
gttagcggat tgcatatgta gaagttcctg tggctaagat ccaataaaca gacaaggcca 1320
cctgcagatg ccactggaat tactatcttt gcaggagcca ggggaactga tgggtggtgc 1380
cattttttca gcgaagggtc atacatcgct acattgttgc tggcattctc atgggtgatt 1440
gtatagaacc atggcagcct ctgtggaact tctgagtact gctgagagaa actttctgag 1500
cccaacatag aataccaatt ccggcaaaca gtgcgaaatc ggaaaattgc agcaactgga 1560
agtcttgcaa caacggtttc aaaaaggtct ccagggaact cactccaaat ctcctgttgc 1620
atttcttcag ttgagtttga gttgggtgct ttctcacggt ttttgtccct ccgtgagcgc 1680
ttgcgaggag gagattggtt agcttccatg atctttagta attctgagtt gtatccagtc 1740
cttgctctac aatgatcatc tttgattgaa ccatgctcaa agtccagtaa ataccacctg 1800
caagatatca ctaaaaccaa ttagtccatc ttatttacta gcaaagaagt tctggagagt 1860
aggcacaact gcacaagaac ttttaaagtg aagagagata agatgatcca cagctttgta 1920
cagcaggaaa tgcatgattc tatctacaga cgctggaatg atcaatatga tgaactagtc 1980
tactcaaagt ctccaaaagt gttgatgaac tagagcacct gacttatggg gggagggggg 2040
gtatcagtca cgcaaatgac cttttcacgc aatagtagcg tcaaatggag tctagggact 2100
atcactccat gtgtggatgg aaagtttgat gacaaagatg gaaaacacgt gcgctgcagg 2160
ttttcacatt tcgaaactag attactcata cataaccctt gagtgcaagt gtatccacca 2220
taaacacatg ctctatctct ctgaccgata taactgaaca ggagagcact gcactaataa 2280
catcatgctg tttgaggtat gtagttatgc ccctcagctt ccaatggcgc gcaaattcct 2340
aatatgccca aaacggattg caagcagatt aagcgatccg atactgctga gattatgaga 2400
ccaactgtag ccaatagaat tgcattattt tatcacagaa gatatgcgca aatcaacaga 2460
aaactgtata ctttgttttc taaaatgtcc aactaaaaat atagcatcaa tattataatc 2520
atcgtgtgcg gagtgcctga taatgcaccg aaacaagcac cactctgtcg ttcatataca 2580
taagatagat tgcagttgct caacaaatta cattagtttt gtatggcaac cacactttag 2640
ccttggtaat cgagtaatcg tgtatttcct ttggatttcg agttaaaaaa acgttgcaac 2700
tggtatattt cttttcatcg aaaccggcgt caaaataatc ggtgttttca tttttgtctt 2760
gatcccttgc ttacatagca gtagaaacag tgcaacaccc gaagtcaact taattaggat 2820
atcttaagat gagcagagag cctcgcatgg tgcaaaaaca acccccaagt ggtggacttt 2880
gttgcgctta ataccatgga tatacgtaaa gaatcttgtc ctatcgcttc gggcaatgtc 2940
aaggcttgaa acttggagac gggtaattat aatcaattta attaacaaac aacaacaagc 3000
atatgcacga aattctccca tttctgtcac gcacgccacc gtttcctcga attgatcctt 3060
cctaccctac caaatccacc agcacaagga agccaaaaaa ataaaagatt ttttgcaacg 3120
gaaatacagt aataataata accaatcaag aaggggagcc aaaatcgcat gagcgtgtta 3180
gtgaaagatc taaaaaaaat ttctttacac ataggggacg ccagatgatg aagaagaacc 3240
ccagagagag gcgaatcgaa tcgaatcggg gggagaatcg caggcacaga tccgggcgga 3300
ggaatcgatt ggaggagcaa gaagtgatag agggagaaga gttgcttgcc ttgggagggg 3360
gtgggagttg gcgccgtaga ggtcccagag ctcctgcacc tcgccgacca gctgccgcag 3420
cgccgccacc tcccccatcc tccctcctcc cgccgccgcc gcagcggcgc ccctctcctc 3480
ctcctcctct tcccccagaa caacaacaaa aaatattttc ttttcttttc ttttcttttc 3540
tcttcttctt ctgctgctgc tgctgctgct gctgctgcga gaagtggtgg gtttgc 3596
<210> 3
<211> 1332
<212> DNA
<213> Artificial Sequence (Artificial Sequence)
<220>
<223> LC4 Gene coding sequence 2
<400> 3
atgggggagg tggcggcgct gcggcagctg gtcggcgagg tgcaggagct ctgggacctc 60
tacggcgcca actcccaccc cctcccaagg tggtatttac tggactttga gcatggttca 120
atcaaagatg atcattgtag agcaaggact ggatacaact cagaattact aaagatcatg 180
gaagctaacc aatctcctcc tcgcaagcgc tcacggaggg acaaaaaccg tgagaaagca 240
cccaactcaa actcaactga agaaatgcaa caggagattt ggagtgagtt ccctggagac 300
ctttttgaaa ccgttgttgc aagacttcca gttgctgcaa ttttccgatt tcgcactgtt 360
tgccggaatt ggtattctat gttgggctca gaaagtttct ctcagcagta ctcagaagtt 420
ccacagaggc tgccatggtt ctatacaatc acccatgaga atgccagcaa caatgtagcg 480
atgtatgacc cttcgctgaa aaaatggcac cacccatcag ttcccctggc tcctgcaaag 540
atagtaattc cagtggcatc tgcaggtggc cttgtctgtt tattggatct tagccacagg 600
aacttctaca tatgcaatcc gctaacacaa tcactcaagg aaattccgcg caggtcagtc 660
caggcatggt caagagtggc agtagggatg gtgatgaacg gaggaacctc taatgaaggt 720
tacaaagtaa tgtggttagg aaatgatggg aattatgaag tctatgattc tatgaagaat 780
atgtggtctt gtccaggcac ttttcctcca agcatcaaac ttccgcttgc tctaaatttt 840
aggtcacagc ctgtggcggt tggcagcatg ctatacttca tgtgtgcaga accagagggt 900
gttttgtcgt atgatgtaag cactgggata tggagacaat tcgtcatccc actgcgactt 960
catctgactg accacacact tgccgagttc cagggaaggg ttatgctggt gggtctgctc 1020
tgcaaaaatg cagcgacatg tgtctgcatt tgggagttgc agaagatgac tctcctctgg 1080
aaggaggtgg acagaatgcc aaatatctgg tgcttagaat tctacggtaa gcacatgaag 1140
atgacatgcc tgggcaacag tggtttgctc atgctctcct tgaaggcgaa gcggatgaac 1200
cgcctcgtga catacaacct tttgaacaag gagtggcaga aggttcctga ttgcatgctc 1260
ccatgcagcc gcaaaaagca gtggatagca tgtggcacag catttggtcc atgcccctct 1320
gccttggcct ga 1332

Claims (10)

1. The application of the molecular marker vg0140443758 in identifying the rice leaf inclination angle trait is disclosed, wherein the SNP locus of the molecular marker vg0140443758 is located at 40443758 th base of No.1 chromosome of rice.
2. The use according to claim 1, wherein the SNP site is located in the LC4 gene coding sequence, and the base mutation of the SNP site changes the corresponding coding amino acid from proline (P) to arginine (A).
3. The use of claim 2, wherein the base of the SNP site is mutated from G to C.
4. Use according to claim 3, wherein the molecular marker vg0140443758 comprises in the coding sequence of the LC4 gene: the SNP locus, 0-955 base pairs at the 3 'end and 0-376 base pairs at the 5' end of the SNP locus, and the LC4 gene coding sequence is shown as SEQ ID NO.1 or 3.
5. The primers capable of identifying or amplifying the SNP molecular marker vg0140443758 related to the rice leaf inclination angle trait can be hybridized and paired with an LC4 gene sequence, and the SNP molecular marker vg0140443758 is obtained by amplification, and the molecular marker vg0140443758 comprises the following parts in the LC4 gene coding sequence: the SNP locus, 0-955 base pairs at the 3 'end and 0-376 base pairs at the 5' end of the SNP locus, the LC4 gene coding sequence is shown as SEQ ID NO.1 or 3, and the SNP locus is positioned at the 956 th base of the LC4 gene coding sequence.
6. The primer according to claim 5, wherein the base of the SNP site is mutated from G to C.
7. Use of the primers capable of recognizing or amplifying SNP molecular marker vg0140443758 related to rice leaf inclination trait according to any one of claims 5-6 for identifying rice leaf inclination trait.
8. Kit, wherein the kit comprises the primer which can identify or amplify the SNP molecular marker vg0140443758 related to the rice leaf inclination angle trait according to any one of claims 5 to 6.
9. The molecular marker vg0140443758, the primers capable of identifying or amplifying the SNP molecular marker vg0140443758 related to the rice leaf inclination trait according to any one of claims 5 to 6 and the use of the kit according to claim 8 in rice close planting breeding, wherein the SNP locus of the molecular marker vg0140443758 is located at 40443758 th base of No.1 chromosome of rice, and the base of the SNP locus is mutated from G to C.
10. The use according to claim 9, comprising identifying the inclination trait of rice leaves using the molecular marker vg 0140443758.
CN202011055016.4A 2020-09-30 2020-09-30 Molecular marker related to rice leaf inclination angle character and application thereof Pending CN112126704A (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
CN202011055016.4A CN112126704A (en) 2020-09-30 2020-09-30 Molecular marker related to rice leaf inclination angle character and application thereof

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
CN202011055016.4A CN112126704A (en) 2020-09-30 2020-09-30 Molecular marker related to rice leaf inclination angle character and application thereof

Publications (1)

Publication Number Publication Date
CN112126704A true CN112126704A (en) 2020-12-25

Family

ID=73843225

Family Applications (1)

Application Number Title Priority Date Filing Date
CN202011055016.4A Pending CN112126704A (en) 2020-09-30 2020-09-30 Molecular marker related to rice leaf inclination angle character and application thereof

Country Status (1)

Country Link
CN (1) CN112126704A (en)

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20080301839A1 (en) * 2005-08-30 2008-12-04 Ravanello Monica P Transgenic plants with enhanced agronomic traits
CN102732551A (en) * 2011-04-07 2012-10-17 中国科学院上海生命科学研究院 Plant leaf inclination angle-controlling gene and purposes thereof
CN108727479A (en) * 2017-04-18 2018-11-02 中国科学院上海生命科学研究院 Regulate and control F-BOX albumen and its application of Leaf inclination
CN109777886A (en) * 2019-04-01 2019-05-21 浙江师范大学 The molecular labeling of the main effect QTL site qTLA-9 of adjusting and controlling rice Leaf inclination and its application

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20080301839A1 (en) * 2005-08-30 2008-12-04 Ravanello Monica P Transgenic plants with enhanced agronomic traits
CN102732551A (en) * 2011-04-07 2012-10-17 中国科学院上海生命科学研究院 Plant leaf inclination angle-controlling gene and purposes thereof
CN108727479A (en) * 2017-04-18 2018-11-02 中国科学院上海生命科学研究院 Regulate and control F-BOX albumen and its application of Leaf inclination
CN109777886A (en) * 2019-04-01 2019-05-21 浙江师范大学 The molecular labeling of the main effect QTL site qTLA-9 of adjusting and controlling rice Leaf inclination and its application

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
LI QU等: "Rice miR394 suppresses leaf inclination through targeting an F-box gene, LEAF INCLINATION 4", 《JOURNAL OF INTEGRATIVE PLANT BIOLOGY》 *
胡娟等: "水稻叶倾角分子机制及育种应用的研究进展", 《中国水稻科学》 *

Similar Documents

Publication Publication Date Title
CN107227373B (en) SNP functional molecular marker of japonica rice lodging-resistant gene and application
CN116064904A (en) Molecular marker closely linked with wheat stem rot resistance QTL Qfcr.sicau.2A and application
CN111575400A (en) Wheat stripe rust resistant QTL molecular marker IWB12253 and application thereof
CN116875736A (en) SNP molecular marker of rice blast resistance gene pizz, primer set and application
CN107541551A (en) The primer and the application that are used to detect spinach RPF1 genotype based on KASP technological development
CN106755465B (en) Molecular marker closely linked with wheat flag leaf length QTL QFLL
CN116103433B (en) CAPS molecular marker for identifying rice spike length character and application thereof
CN110698550B (en) Molecular detection method for rapidly identifying real plum/apricot plum strain
CN108642209B (en) Wheat plant thousand grain weight judgment marker and application thereof
CN106701751A (en) Molecular marker closely linked with wheat flag leaf length QTL QFll.sicau-4D and application thereof
CN110628930A (en) dCAPS molecular marker for identifying panicle length character of rice and application thereof
CN112126704A (en) Molecular marker related to rice leaf inclination angle character and application thereof
CN115786564A (en) Rice Pi-ta and Ptr dominant functional molecular marker and application thereof
CN114921581A (en) Dominant functional molecular marker of rice blast resistance gene Pi-d2 and application thereof
CN108642203B (en) SNP (Single nucleotide polymorphism) marker related to millet stem thickness character as well as detection primer and application thereof
CN106636386B (en) Molecular marker DNdCAPS8.03-1 linked with maize head smut resistant minor major site and application thereof
CN116732230B (en) Rice nitrogen efficient InDel molecular marker GRF4M1 and application thereof
Wang et al. Genome-wide identification of R genes and exploitation of candidate RGA markers in rice
CN112111593A (en) Molecular marker related to rice leaf inclination angle character and application thereof
CN113308566B (en) Primer and application of InDel molecular marker related to soybean main stem node number
CN114381544B (en) Watermelon leaf yellowing lethal major gene, dCAPS molecular marker for identifying major gene and application
CN116218887B (en) Application of amidase protein gene OsAMID in improving rice yield
CN110484651B (en) Molecular marker in wheat yield related gene TaNRT2-6D and application thereof
CN116769961B (en) Wheat spike number per spike QTL linkage molecular marker developed by multi-sieve-mixing-determining four-step method and application
CN113005215B (en) Haplotype molecular marker related to poplar wood yield and application thereof

Legal Events

Date Code Title Description
PB01 Publication
PB01 Publication
SE01 Entry into force of request for substantive examination
SE01 Entry into force of request for substantive examination
RJ01 Rejection of invention patent application after publication
RJ01 Rejection of invention patent application after publication

Application publication date: 20201225