CN104561034A - Rapid identification method for powdery mildew resistant gene of foxtail millet - Google Patents
Rapid identification method for powdery mildew resistant gene of foxtail millet Download PDFInfo
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Abstract
The invention relates to a rapid identification method for a powdery mildew resistant gene of foxtail millet, relates to knowledges of plant comparative genomics, genetics, bioinformatics and the like and belongs to the field of plant biotechnology. The rapid identification method for the powdery mildew resistant gene of the foxtail millet comprises the following main steps: 1) downloading a whole genome sequence of the foxtail millet and collecting an MLO type gene; 2) identifying the MLO type gene; 3) determining phylogenetic relationship of the MLO type gene; and 4) comparing the MLO type powdery mildew gene. The rapid identification method for the powdery mildew resistant gene of the foxtail millet has the advantages that a foxtail millet powdery mildew gene mining period is effectively shortened, and rapid identification of the powdery mildew gene is facilitated; corresponding coseparation functional markers (SNP, SCAR and the like) are developed by virtue of the identified powdery mildew gene, the identified powdery mildew gene also can be used for powdery mildew resistant gene molecular marker-assisted selection rapidly with high accuracy; by combining with other disease-resistant gene molecular markers, a multi-resistance breeding material can be created, breeding cycle can be shortened, and breeding efficiency can be improved; and a foundation is laid for explaining a foxtail millet powdery mildew resistant gene molecular mechanism.
Description
Technical field
The present invention is by means of millet order-checking whole genome sequence, utilize the method Rapid identification millet powdery mildew genes such as plant comparative genomics, genetics, information biology and candidate gene strategy, this patent is mainly concerned with the download of millet whole genome sequence, the qualification of candidate gene, the comparison of gene, the means such as cluster, and then identify powdery mildew gene, belong to Plant Biotechnology scientific domain.
Background technology
Millet (Setaria italica) originates in China, is one of comparatively common farm crop of northern China.The nutritive ingredients such as millet rich in proteins, Lin Suanna Vitamin B2 Sodium Phosphate, nicotinic acid, calcium, iron.In production, millet is vulnerable to the infringement of the multiple diseases such as fungi, bacterium, virus, insect, and wherein millet Powdery Mildew is a kind of comparatively common fungal disease of millet.This type of disease all can be fallen ill to heading from seedling, the blade of main harm millet, also endangers cane and tassel.During infection process, blade starts to produce yellow point, then expand and develop into circle or oval scab, the mould layer of the raw adularescent powdery in surface.Generalized case bottom blade is more than upper blade, and vacuum side of blade is more than front, and mildew even can cover the full leaf of millet, and the photosynthesis of what this was serious had influence on millet plant, its eubolism is interfered, and cause early ageing, output incurs loss.
Millet Powdery Mildew is fallen ill, and to mainly contain two: one be establishing in large scale susceptible variety to popular condition; Two is have the envrionment conditions being beneficial to Powdery Mildew and being suitable for surviving.General millet planting density is bigger than normal, and field humidity is excessive or occur the plot that plant lodges, and falls ill often comparatively serious.Generally there is infection center in July at the beginning of early and middle ten days to 8 month in this disease, go up gradually with temperature after mid-August, diseased plant rate increases sharply, and causes under appropriate conditions being very popular.When there is illness, if control spreading of disease not in time, bring great loss often to the production of millet.Production there is the measure that this type of disease of many controls occurs, as rational close planting, the rational application of fertilizer, dressing seed, chemical agent spray, but these all can not tackle the problem at its root, and breeding resistant variety is considered to effect a radical cure this type of disease method most effectively all the time.Along with the development of biotechnology, the improvement of using transgenic technology to carry out plant variety has been applied in the production of farm crop, and therefore the acquisition of millet disease-resistant gene has great importance for the further investigation of the breeding of millet resistant heredity and disease resistance mechanisms.
MLO type disease-resistant gene is the special class disease-resistant gene of plant.Investigator find the earliest MLO (
mildewresistance
locus
o) gene pairs powder mildew resistance starts from 1937-1938, acquired the barley of a lot of kind in Ethiopia by fritz, two strains wherein all have efficient resistance to Powdery Mildew (Blumeria graminis f.sp.hordei) all physiological strains that oneself knows.Further research shows, in barley the recessive mutation mlo of MLO gene can make barley to nearly all oneself know that the physiological strain of barley powdery mildew bacteria produces resistance that is lasting, wide spectrum.Recently, investigator finds that the mildew-resistance gene of a lot of plant is all MLO type Gene Handling, as tomato, and pea, Arabidopis thaliana, rose, capsicum, Root or stem of Littleleaf Indianmulberry etc.Therefore the MLO type disease-resistant gene excavated in plant has important effect to Biology of Plant-Powdery Mildew Interaction breeding.
At present, the conventional method excavating disease-resistant gene conventional has map based cloning, the methods such as transposon tagging.But because the fundamental research of millet is not deep enough, not only the time is grown but also is difficult to clone these genes exactly therefore to utilize these methods.Therefore, the MLO type disease-resistant gene how in Rapid identification millet will become the important prerequisite of millet mildew-resistance breeding.
Plant comparative genomics (Comparative Genomics) is based on gene order-checking basis, compares, understand the subject of the function of gene, expression mechanisms and spore to known gene and genome structure.Between Land use models Plant Genome and other Plant Genome on coded sequence and structural homology, clone's other plant gene, discloses gene function and molecular mechanism, illustrates spore relation and genomic immanent structure.The method that this patent adopts and thinking: the research of model plant arabidopsis gene group has disclosed the function of MLO type gene, utilize the homology clone millet MLO type disease-resistant gene in its order of gene, according to the feature of the superiority in model plant Arabidopis thaliana experimental system and known MLO type disease-resistant gene, " seizure " millet mildew-resistance gene fast.This patent describes premised on millet whole genome sequence, in conjunction with knowledge such as comparative genomics, genetics, genomics, information biology and candidate gene strategy, excavates powdery mildew gene fast.
Summary of the invention
Technical problem
The object of this invention is to provide a kind of by conjunction with knowledge such as plant comparative genomics, plant genetics, genomics and information biology, excavate millet mildew-resistance gene fast.Its result can be used for the exploitation of millet powdery mildew gene compact linkage molecule mark on the one hand, carries out molecular marker assisted selection breeding, on the other hand also for other crop powdery mildew gene identification provide reference frame.
Technical scheme
Cardinal principle: first Biology of Plant-Powdery Mildew Interaction gene (MLO) is cloned from barley, research finds that this gene is the special disease-resistant gene of a class, is different from most of NBS (nucleotide-binding site) the type disease-resistant gene of previously clone; Subsequently, investigator has cloned powdery mildew gene in succession from the plants such as tomato, Arabidopis thaliana, pea, capsicum, Root or stem of Littleleaf Indianmulberry, and what research found these genes encodings is all MLO type disease-resistant gene.Subsequently, by test of many times, numerous investigator confirms that MLO type disease-resistant gene has become the distinctive class mildew-resistance gene of plant.Further discovery, plant MLO type gene is a gene family; And Phylogenetic Relationships analysis discovery is carried out to the MLO gene family deriving from different plant species, in different plant species mildew-resistance gene always cluster together, become a class, this class MLO gene all has the characteristic feature of mildew-resistance gene sequence.Completing of millet gene order-checking provides a convenient approach for excavating powdery mildew gene.Therefore, can by means of the Phylogenetic Relationships of MLO gene family in the millet full-length genome checked order and the MLO powdery mildew gene of having cloned and for maintaining the conservation of amino acids of powdery mildew gene MLO critical function to identify millet powdery mildew gene.
Key step is as follows:
1) download of millet whole genome sequence and the collection of MLO type gene thereof
First millet whole genome sequence is downloaded from millet sequenced genes group database (http://www.phytozome.net/search.php); Use " DNATOOLS " software to the millet full-length genome amino acid sequence data building database obtained, then pram database (protein family database is used, http://pfamjanelia.org/search/sequence) in hidden Markov model (HMM) Blastp (E-value=0.001) sequence alignment is carried out to the aminoacid sequence of MLO structural domain and the millet full-length genome amino acid sequence database to have set up, preliminary screening goes out candidate gene sequence.Secondly, utilize the MLO type gene order announced, BLAST comparison is carried out to millet genome database, obtain candidate gene sequence.
2) qualification of millet MLO type gene family
By the candidate gene of homologous nucleotide sequence obtained in the above results, analyzed by Pram (E-value=1.0), remove the gene order (Fig. 1) without ' MLO ' structural domain.The ClustalW instrument (Multiple Sequence Alignment program) disease-resistant gene sequence provided by MEGA3.1 software again carries out Multiple Sequence Alignment, removes tumor-necrosis factor glycoproteins.
3) by the Phylogenetic Relationships qualification millet MLO type powdery mildew gene of plant MLO type gene
Because previous research is verified, dicotyledons MLO type powdery mildew gene is positioned at plant MLO Phylogenetic Tree same district group, therefore in Phylogenetic Relationships research, we are MLO type mildew-resistance gene with millet MLO type gene together with the cluster analysis of the MLO type gene family of Arabidopis thaliana with some other crops, to obtain millet mildew-resistance gene (Fig. 2).
4) comparison of millet powdery mildew gene and known plant MLO powdery mildew gene
BioXM2.6 software is utilized to convert the aminoacid sequence of the MLO powdery mildew gene of millet MLO type powdery mildew gene and Arabidopis thaliana, tomato, pea, barley the file of Fasta form to, these files are imported BioEdit7.0 software, use Clustal software in this software to carry out Multiple Sequence Alignment, disclose the conservative property in powdery mildew gene important amino acid residue and region.Thus identify the powdery mildew gene (Fig. 3) of millet further.
Positively effect of the present invention:
1) shorten millet powdery mildew gene and excavate the cycle, be conducive to the Rapid identification of powdery mildew gene.Mildew-resistance gene not only takes time and effort, efficiency is low to adopt ordinary method (map based cloning, transposon tagging etc.) to excavate, and is difficult to successfully.The present invention is based on plant comparative genomics, genetics, bioinformatics method and excavate millet powdery mildew gene fast, not only can shorten the time, powdery mildew gene determination rates can also be improved.
2) millet (Setaria italica) is one of important crops.Because millet hereditary basis is narrow, Germplasm Resources Diversity is low, therefore more difficult by conventional molecule marker (RAPD, ISSR, SSR, AFLP etc.) qualification millet powdery mildew gene.The powdery mildew gene exploitation be tested and appraised is divided into from functional indicia (SNP, SCAR etc.) accordingly, can fast for the molecular marker assisted selection of disease-resistant gene, carry out the initiative of multiresistance breeding material, can shortening the breeding cycle, improve breeding efficiency.
3) lay a good foundation for setting forth millet mildew-resistance molecular mechanism.The qualification of millet mildew-resistance gene, by transgenic technology, RNAi, virus induced gene silencing (virus induced gene silencing, VIGS) molecular mechanism of the Effect of Anti Powdery Mildew such as technology provides genetic resources, is conducive to the mechanism of action setting forth millet mildew-resistance fast.
Accompanying drawing explanation
The qualification of Fig. 1 millet MLO gene;
What this figure showed is 12 MLO type gene identification results, each gene containing one ' MLO' conserved domain.
The Phylogenetic Relationships analysis of Fig. 2 plant MLO gene family and the qualification of millet MLO type powdery mildew gene thereof;
Arabidopis thaliana is the model plant of plant science research, in phylogenetic tree construction, the powdery mildew gene (PsMLO) of 15 MLO type genes (wherein 3 genes are powdery mildew genes: AtMLO02, AtMLO06 and AtMLO12) of Arabidopis thaliana, Gene against Powdery Mildew in Tomato (SIMLO), barley powdery mildew gene (HvMLO and HvMLO02) and pea is selected to and the analysis of millet MLO type gene clusters.Identify 1 millet MLO type powdery mildew gene altogether.In figure, the gene of italic mark is exactly millet powdery mildew gene.
The compare of analysis of Fig. 3 millet MLO type powdery mildew gene;
1 millet powdery mildew gene and barley (HvMLO), tomato (S1MLO), pea (PsMLO), Arabidopis thaliana powdery mildew gene (AtMLO02, AtMLO06 and AtMLO12) to compare, qualification powdery mildew infects the conservative type in amino-acid residue and the region played an important role.In figure, TM1-TM7 represents 7 revolving die regions of millet MLO type powdery mildew gene; Black round dot represents that powdery mildew infects important amino-acid residue; CaMBD represents calmodulin CaM binding region; I and II represents and infects important amino acid region to powdery mildew.
Embodiment
The qualification of disease-resistant gene has important effect in the research of crop disease-resistant theory of heredity and disease-resistant variety seed selection.Present method Rapid identification can go out millet powdery mildew gene.Specific implementation process is as follows:
1) collection of millet MLO type gene
In order to obtain the whole MLO type gene family member of millet, we are first with the MLO type gene of Arabidopis thaliana, the mildew-resistance MLO gene order of tomato, pea, capsicum, rose, capsicum, Root or stem of Littleleaf Indianmulberry builds HMM model, retrieves MLO type gene from millet genome sequence, secondly the MLO gene order delivered in Different Crop as target sequence (from DFCI database: TC171015, TC267529, DFCI:TC327983, TC289653, TC312087, TC132500, TC133436, TC317623, TC317025, TC315947, TC325903, TC315944, TC315912, TC322759, TC322059, TC330654, TC282713, TC293173, TC281861, TC283253, TC283383, TC285032, TC290021, TC302716, TC283487, TC282866, TC283441, TC281428, TC285118, TC285090, from GenBank database: AY967408, AF384145, AF384144, AY029312-AY029315, AY029317-AY029319, Z95352, AF369563-AF369565, AF369567, AF369569-AF369576, Z83834, Z95496, AY581255), BLAST comparison is carried out to millet database (http://www.phytozome.net/search.php), select the highest sequence of similarity to download, obtain the MLO type gene (Si017007m.g of 12 candidates altogether, Si032792m.g, Si021516m.g, Si021895m.g, Si006288rm.g, Si001141m.g, Si009989m.g, Si012504m.g, Si026238m.g, Si034907m.g, Si034998m.g, Si021865m.g, ).
2) qualification of millet MLO type gene conserved domain
In order to verify these MLO gene accuracys further, we have carried out the qualification of conserved domain " MLO " to these 12 MLO genes.With the aminoacid sequence of each MLO type gene for benchmark, PFAM (http://pfam.sanger.ac.uk/) website is carried out the qualification of ' MLO ' conserved domain, result shows, each MLO type gene has one or more ' MLO ' structural domain (Fig. 1).
3) the Phylogenetic Relationships analysis of millet MLO type gene
In previous research, find that dicotyledons powdery mildew gene aggregates into district's group; Therefore, in phylogenetic tree construction, we have selected 15 MLO type genes (wherein 3 genes are powdery mildew genes: AtMLO02, AtMLO06 and AtMLO12) of model plant Arabidopis thaliana, the powdery mildew gene of Gene against Powdery Mildew in Tomato, barley powdery mildew gene and pea analyze with millet MLO type gene clusters together with cluster analysis.Millet MLO type gene and other crop powdery mildew gene protein sequences are carried out multisequencing connection to join (adopting C1usta1X1.83 software to carry out), and utilize Genedoc software (http://www.nrbsc.org/gfx/genedoc/index.html) to show multisequencing to join the result of joining.C1ustal multisequencing is joined the result of joining output in MEGA4.0 software, and utilize this software to construct adjacent tree (neighbor-joining, NJ) respectively, utilize Bootstrapping method to assess these evolutionary trees.Found that in dicotyledons mildew-resistance gene district group, there is 1 millet MLO type powdery mildew gene (see Fig. 2).
4) comparison of millet MLO type disease-resistant gene
In the research of barley MLO type powdery mildew gene, in succession found some important areas and single amino acids in research, they infect large wheat powdery mildew irreplaceable effect.In order to identify in 1 millet powdery mildew gene, these important areas and amino acid whether high conservative, we have carried out amino acid alignment analysis to from 3 mildew-resistance genes (AtMLO02, AtMLO6 and AtMLO12) of Arabidopis thaliana, tomato powdery mildew gene (S1MLO), powdery mildew of pea gene (PsMLO).Find millet 1 powdery mildew gene and known MLO type powdery mildew gene 7 cross-film districts, 30 important amino-acid residue, 1 calmodulin CaM binding region (CaMBD) and two regions played an important role with powdery mildew identification (I and II) high conservative (Fig. 3).Show that this gene is exactly millet MLO type mildew-resistance gene.
Claims (2)
1. millet mildew-resistance gene, is characterized in that being selected from following 1 gene:
Si034998m.g
Aminoacid sequence:
MAGAPGDRELPETPTWAVALVCAVIVLLSVAMEHGLHKLGHWFHTRQKKAMREALEKIKAELMLMGFISLLLAVGQTPISKICIPTKAGSVMLPCKPKDDGESGGDRRRRLLWYPGEEVNHRRFLAGAVGEDYCKEKGKVSLISTTGVHQLHIFIFVLAVFHVVYSVATMALARLKMRRWKRWESETSSLEYQFANDPSRFRFTNQTSFVKRHLGVSSTPGVRWMVAFFRQFFASVTKVDYLTMRQGFINAHLSPNAKFDFQKYIKRSLEDDFKVVVGISLPLWFVAIFILFMDVQGFGTLIWISFVPLVILLLVGTKLEIVIMEMAKEIQDKATVIKGAPIVEPSDRFFWFNRPKWVLFLIHLTLFQNAFQMAHFIWTLLTPGLKTCYHENLGLGIMKVSVGLGLQVLCSYITFPLYALVTQMGSHMKKTIFEEQTAKAVMKWRKAAKDKVKQREAGFEGLMSTDTTPSHSRPTSPGGGSSPVHLLQKYRGRSEDPESAPTSPGRGQELGDMYPVTDQHRMHRLDPERRRAASSTAVDIDIADADFSFSIQR
Nucleotide sequence:
ATGGCGGGGGCCCCGGGCGATAGGGAGCTGCCGGAGACGCCGACGTGGGCGGTGGCCCTCGTGTGCGCCGTCATCGTGCTCCTCTCCGTCGCCATGGAGCACGGCCTCCACAAGCTCGGACACTGGTTCCACACGCGGCAGAAGAAGGCTATGCGGGAGGCGCTCGAGAAGATCAAAGCAGAGCTGATGCTGATGGGGTTCATCTCCCTGCTCCTCGCCGTGGGGCAAACGCCCATCTCCAAGATATGCATCCCTACCAAGGCAGGCAGCGTCATGCTACCGTGCAAACCCAAGGACGACGGCGAAAGCGGCGGTGACCGCCGCCGGAGGCTCCTGTGGTACCCTGGAGAAGAGGTCAACCATCGTAGGTTCTTGGCCGGCGCGGTTGGGGAAGACTACTGCAAGGAAAAAGGCAAGGTGTCCCTGATCTCCACGACCGGCGTCCACCAGCTGCATATTTTCATCTTTGTGCTAGCGGTGTTCCATGTCGTTTACAGCGTAGCTACCATGGCTTTAGCGCGTCTGAAAATGAGGAGATGGAAGAGATGGGAATCAGAGACCAGCTCACTGGAGTACCAGTTCGCAAACGATCCTTCAAGATTCCGATTCACAAACCAGACATCGTTCGTGAAGCGGCACCTGGGCGTCTCCAGCACACCTGGAGTCAGATGGATGGTGGCATTCTTCAGGCAGTTCTTTGCTTCGGTGACCAAGGTGGATTACCTGACCATGCGCCAAGGCTTCATTAATGCTCATCTGTCGCCCAATGCTAAGTTCGAT7TCCAAAAGTACATCAAGCGGTCGTTGGAGGACGACTTCAAAGTCGTCGTTGGCATCAGCCTCCCGCTGTGGTTTGTCGCCATCTTCATACTCTTCATGGATGTCCAAGGATTCGGCACGCTTATTTGGATCTCTTTCGTCCCACTCGTTATCCTCTTGTTAGTTGGAACCAAACTAGAGATTGTCATCATGGAGATGGCCAAGGAGATACAGGACAAGGCGACCGTGATCAAGGGGGCGCCTATTGTGGAGCCAAGCGACAGGTTCTTCTGGTTCAACCGGCCTAAATGGGTCCTGTTCCTCATACACCTGACGCTCTTCCAGAATGCATTCCAGATGGCACATTTCATCTGGACACTGCTCACCCCAGGCTTGAAAACTTGCTACCACGAAAATTTGGGACTGGGCATCATGAAAGTTTCAGTGGGGTTGGGTCTCCAGGTCCTCTGCAGCTACATCACCTTCCCTCTCTACGCACTTGTCACACAGATGGGCTCGCACATGAAAAAGACAATCTTCGAGGAGCAGACGGCGAAGGCGGTGATGAAATGGCGCAAGGCGGCCAAGGACAAGGTGAAGCAACGGGAGGCTGGGTTCGAGGGGTTGATGAGCACCGACACGACGCCGAGCCATAGCAGGCCGACGTCGCCGGGCGGGGGCAGCTCGCCGGTGCACCTGCTCCAAAAGTACAGGGGAAGGTCGGAGGATCCCGAGAGCGCCCCGACCTCGCCGGGGAGGGGGCAGGAGCTCGGGGACATGTACCCGGTGACCGACCAGCACCGGATGCACAGGCTAGACCCTGAGAGGAGGCGGGCGGCCTCGTCCACCGCCGTGGACATCGATATCGCCGATGCTGATTTTTCGTTCAGCATCCAGCGGTGA。
2. the application of Rapid identification millet powdery mildew gene described in claim 1, comprising:
1) initiative or the new variety initiative of the breeding material of mildew-resistance ML0 gene is carried: utilize the MLO GENE SOURCES given by right 1 to be parent material, in hybridization, backcross progeny, the breeding material that transformation has MLO resistant gene can be obtained.
2) mildew-resistance fundamental research: molecular marker analysis is carried out to the MLO type mildew-resistance gene of right 1; Molecular Mapping or the assignment of genes gene mapping are carried out to this gene; This gene is cloned and Interaction among genes analysis.
3) mildew-resistance transgenic research: utilize the MLO type powdery mildew gene given by claim 1 to carry out transgenic research.
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