CN104361262A - Populus diversifolia sexless breeding method based on gene regulatory network - Google Patents
Populus diversifolia sexless breeding method based on gene regulatory network Download PDFInfo
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Abstract
The invention discloses a populus diversifolia sexless breeding method based on a gene regulatory network. The method comprises the following steps: forming a populus diversifolia positioning group; conducting explant culture according to the populus diversifolia positioning group, and obtaining phenotype data, transcriptomics data, proteomics data and metabonomics data of the populus diversifolia rooting ability according to the populus diversifolia positioning group; positioning QTL, eQTL, pQTL and mQTL of the populus diversifolia rooting ability respectively according to the phenotype data, the transcriptomics data, the proteomics data and the metabonomics data of the populus diversifolia positioning group; forming the gene regulatory network of the populus diversifolia rooting process according to the QTL, the eQTL, the pQTL and the mQTL of the populus diversifolia rooting ability, and positioning network quantitative trait loci (nQTL) of the populus diversifolia rooting ability according to the gene regulatory network; conducting populus diversifolia sexless breeding according to the nQTL of the populus diversifolia rooting ability. According to the method of the embodiment, the populus diversifolia single plant with strong rooting ability can be effectively screened out, the reproductive rate of the populus diversifolia is improved, and the stress resistant sexless breeding of the populus diversifolia is greatly promoted.
Description
Technical field
The present invention relates to breeding technical field, particularly relate to the asexual selection of a kind of diversiform-leaved poplar based on gene regulatory network.
Background technology
Diversiform-leaved poplar is described as " hero tree ", is to be distributed in the salt tolerant of NORTHWEST CHINA desert area, unique arbor species of cold-resistant, drought-enduring, anti-blown sand.But, because the trait segregation of diversiform-leaved poplar seedling is very serious, be unfavorable for filtering out excellent diversiform-leaved poplar individual plant.Thus, in order to overcome the serious shortcoming of diversiform-leaved poplar trait segregation, front order diversiform-leaved poplar carries out seed selection mainly through vegetative method.But the rootability of diversiform-leaved poplar is poor, when cuttage, cause cottage propagation very difficult because rooting rate is lower.Therefore, the key link that diversiform-leaved poplar problem of taking root has become diversiform-leaved poplar Screening of Germplasm is solved.
Summary of the invention
The present invention is intended to solve one of technical matters in correlation technique at least to a certain extent.
For this reason, the object of the invention is to propose the asexual selection of a kind of diversiform-leaved poplar based on gene regulatory network, effectively can filter out the diversiform-leaved poplar individual plant that rootability is strong, improve the breeding potential of diversiform-leaved poplar, greatly facilitate the seed selection of diversiform-leaved poplar clones with resistance.
According to the asexual selection of the diversiform-leaved poplar based on gene regulatory network of the embodiment of the present invention, comprising: build diversiform-leaved poplar target group; Carry out explant cultivation according to described diversiform-leaved poplar target group, and in the process of described cultivation, obtain the phenotypic data of diversiform-leaved poplar rootability, transcription group data, proteomics data and metabolism group data; Respectively according to the QTL of the phenotypic data of described diversiform-leaved poplar target group, transcription group data, proteomics data and metabolism group data location diversiform-leaved poplar rootability, express quantitative trait locus eQTL, protein amounts character site pQTL and metabolin quantitative trait locus mQTL; The gene regulatory network of diversiform-leaved poplar rooting process is built according to QTL, eQTL, pQTL and mQTL of described diversiform-leaved poplar rootability, and according to described gene regulatory network location diversiform-leaved poplar rootability the number networks character site nQTL; The asexual seed selection of diversiform-leaved poplar is carried out according to the nQTL of described diversiform-leaved poplar rootability.
According to the asexual selection of the diversiform-leaved poplar based on gene regulatory network of the embodiment of the present invention, by carrying out explant cultivation to the diversiform-leaved poplar target group built, and obtain the phenotypic data of diversiform-leaved poplar rootability and the QTL of location diversiform-leaved poplar rootability, eQTL, pQTL and mQTL, to build the gene regulatory network of diversiform-leaved poplar rooting process, and locate diversiform-leaved poplar rootability the number networks character site nQTL accordingly, thus can be able to disclose on the basis of the gene regulatory network forming this dynamic process from gene to protein again to phenotype structure one, the nQTL of this dynamic process of positioning effects, and guide the asexual seed selection of diversiform-leaved poplar, overcome diversiform-leaved poplar shape be separated seriously be unfavorable for screen problem while, effectively can filter out the diversiform-leaved poplar individual plant that rootability is strong, improve the breeding potential of diversiform-leaved poplar, greatly facilitate the seed selection of diversiform-leaved poplar clones with resistance.
In addition, the asexual selection of the diversiform-leaved poplar based on gene regulatory network according to the above embodiment of the present invention, can also have following additional technical characteristic:
Described QTL, eQTL, pQTL and mQTL according to described diversiform-leaved poplar rootability build the gene regulatory network of diversiform-leaved poplar rooting process, specifically comprise: the interactively between QTL, eQTL, pQTL and mQTL obtaining described diversiform-leaved poplar rootability; The differential equation group of the gene regulatory network representing diversiform-leaved poplar rooting process is set up according to described interactively.
Described according to described gene regulatory network location diversiform-leaved poplar rootability the number networks character site nQTL, specifically comprise: estimate the first kind differential equation coefficient that the genotype of described eQTL, described pQTL, described mQTL is corresponding respectively; Determine the Equations of The Second Kind differential equation coefficient of the genotypic difference determining described eQTL, described pQTL, described mQTL; After obtaining described first kind differential equation coefficient and described Equations of The Second Kind differential equation coefficient, the nQTL of the gene regulatory network structure that differential equation group described in positioning effects is corresponding.
Described diversiform-leaved poplar target group comprises multiple diversiform-leaved poplar maternal plant and multiple half-sib progeny colony, and described structure diversiform-leaved poplar target group specifically comprises: multiple diversiform-leaved poplar maternal plant described in random selecting in diversiform-leaved poplar distributing region; Gather the seed of each maternal plant respectively and cultivate into filial generation seedling, to build the multiple half-sib progeny colonies corresponding respectively with described multiple diversiform-leaved poplar maternal plant.
Describedly carry out explant according to described diversiform-leaved poplar target group and cultivate and specifically comprise: the stem section of getting predetermined number respectively from each filial generation each maternal plant and each half-sib progeny colony, and the stem section obtained is cultivated respectively.
Described phenotypic data, transcription group data, proteomics data and the metabolism group data obtaining diversiform-leaved poplar rootability in the process of described cultivation specifically comprise: in the process of described cultivation, record the rootability phenotypic data of described diversiform-leaved poplar target group, and in the process of described cultivation, set multiple time point; From described diversiform-leaved poplar target group, filter out rootability according to described rootability phenotypic data and be greater than the first predetermined threshold value or rootability is less than the maternal plant of the second predetermined threshold value and sub-strain; Each time point in rooting process obtains described rootability and is greater than the first predetermined threshold value or rootability is less than the maternal plant of the second predetermined threshold value and the incision tissue of sub-strain, and transcription analysis, proteomic assays and metabonomic analysis are carried out to the incision tissue got, to obtain described diversiform-leaved poplar rootability transcription group data, proteomics data and metabolism group data.
Described respectively according to the QTL of the phenotypic data of described diversiform-leaved poplar target group, transcription group data, proteomics data and metabolism group data location diversiform-leaved poplar rootability, express quantitative trait locus eQTL, protein amounts character site pQTL and metabolin quantitative trait locus mQTL, specifically comprise: the phenotypic data of described diversiform-leaved poplar target group and diversiform-leaved poplar molecular marker data are carried out association analysis with the QTL of positioning effects diversiform-leaved poplar rootability; The transcription group data of described diversiform-leaved poplar target group and diversiform-leaved poplar molecular marker data are carried out association analysis with the eQTL of gene content in positioning effects diversiform-leaved poplar rooting process; The proteomics data of described diversiform-leaved poplar target group and diversiform-leaved poplar molecular marker data are carried out association analysis with the pQTL of protein content in positioning effects diversiform-leaved poplar rooting process; The metabolism group data of described diversiform-leaved poplar target group and diversiform-leaved poplar molecular marker data are carried out association analysis with the mQTL of metabolite content in positioning effects diversiform-leaved poplar rooting process.
Accompanying drawing explanation
Fig. 1 is according to an embodiment of the invention based on the process flow diagram of the asexual selection of diversiform-leaved poplar of gene regulatory network;
Fig. 2 is the schematic diagram of the relation of gene interaction according to an embodiment of the invention.
Embodiment
Be described below in detail embodiments of the invention, the example of described embodiment is shown in the drawings, and wherein same or similar label represents same or similar element or has element that is identical or similar functions from start to finish.Be exemplary below by the embodiment be described with reference to the drawings, be intended to for explaining the present invention, and can not limitation of the present invention be interpreted as.
Below with reference to the accompanying drawings describe according to the asexual selection of the diversiform-leaved poplar based on gene regulatory network of the embodiment of the present invention.
Fig. 1 is according to an embodiment of the invention based on the process flow diagram of the asexual selection of diversiform-leaved poplar of gene regulatory network.
As shown in Figure 1, based on the asexual selection of diversiform-leaved poplar of gene regulatory network, should comprise:
S101, builds diversiform-leaved poplar target group.
Wherein, diversiform-leaved poplar target group comprises multiple diversiform-leaved poplar maternal plant and multiple half-sib progeny colony.Particularly, can first from the multiple diversiform-leaved poplar maternal plant of random selecting in diversiform-leaved poplar distributing region, for example, in one embodiment of the invention, can from 500 the diversiform-leaved poplar maternal plants of random selecting in diversiform-leaved poplar distributing region, wherein, in order to prevent, between the maternal plant chosen, there is sibship, 500 maternal plants that strain spacing is greater than predetermined threshold value (as 50 meters) can be chosen.Then, gather the seed of each maternal plant respectively and cultivate into filial generation seedling, to build multiple half-sib progeny colonies corresponding respectively with multiple diversiform-leaved poplar maternal plant.
S102, carries out explant cultivation according to diversiform-leaved poplar target group, and obtains the phenotypic data of diversiform-leaved poplar rootability, transcription group data, proteomics data and metabolism group data in the process of cultivating.
Wherein, rootability phenotypic data refers to the mean value of the quantity of taking root of the stem section to the preset data amount that each plant (maternal plant or filial generation) obtains.
Particularly, the stem section of predetermined number (such as, can be 20) can be got respectively from each maternal plant, and the stem section obtained is cultivated as explant, observe in the process of cultivating and record the rootability phenotypic data of the stem section of each maternal plant.For each half sibs colony, get the stem section of predetermined number respectively from each progeny plant, and the stem section obtained is cultivated as explant, observe in the process of cultivating and record the rootability phenotypic data of the stem section of each filial generation.
Further, rootability can be filtered out according to rootability phenotypic data from diversiform-leaved poplar target group and be greater than the first predetermined threshold value or rootability is less than the maternal plant of the second predetermined threshold value and sub-strain.The plant that rootability is greater than the first predetermined threshold value is the plant that rootability is stronger, and the plant that rootability is less than the second predetermined threshold value is the more weak plant of rootability.Wherein, first predetermined threshold value and the second predetermined threshold value can set according to historical test data, for example, the 130%, second predetermined threshold value that first predetermined threshold value can be set to the quantity population mean of taking root of the stem section that whole plant is chosen can be set to 70% of the quantity population mean of taking root of the stem section that whole plant is chosen.
In addition, multiple time point can be set in advance in the process of cultivating, each time point acquisition rootability in rooting process is greater than the first predetermined threshold value or rootability is less than the maternal plant of the second predetermined threshold value and the incision tissue of sub-strain, and transcription analysis, proteomic assays and metabonomic analysis are carried out to the incision tissue got, to obtain diversiform-leaved poplar rootability transcription group data, proteomics data and metabolism group data.
S103, respectively according to the QTL of the phenotypic data of diversiform-leaved poplar target group, transcription group data, proteomics data and metabolism group data location diversiform-leaved poplar rootability, express quantitative trait locus eQTL, protein amounts character site pQTL and metabolin quantitative trait locus mQTL.
In an embodiment of the present invention, due to gene expression, between protein expression and metabolite content, there is complicated mutual and cause-effect relationship, therefore, mathematical model can be built and build gene expression, quantitative relation between protein expression and metabolite content, and carry out association analysis with molecular labeling further, to find the QTL affecting gene, albumen and metabolite content, i.e. eQTL, pQTL and mQTL.Wherein, for building gene expression, the mathematical model of quantitative relation between protein expression and metabolite content can with reference to correlation technique, and the particular type of the present invention to mathematical model does not limit.
Particularly, the phenotypic data of diversiform-leaved poplar target group and diversiform-leaved poplar molecular marker data can be carried out association analysis with the QTL of positioning effects diversiform-leaved poplar rootability; The transcription group data of diversiform-leaved poplar target group and diversiform-leaved poplar molecular marker data are carried out association analysis with the eQTL of gene content in positioning effects diversiform-leaved poplar rooting process; The proteomics data of diversiform-leaved poplar target group and diversiform-leaved poplar molecular marker data are carried out association analysis with the pQTL of protein content in positioning effects diversiform-leaved poplar rooting process; The metabolism group data of diversiform-leaved poplar target group and diversiform-leaved poplar molecular marker data are carried out association analysis with the mQTL of metabolite content in positioning effects diversiform-leaved poplar rooting process.
Wherein, molecular labeling can be any attainable mark, and the type of the present invention to molecular labeling is not specifically limited.For example, molecular labeling can be SSR marker, SNP marker etc.
Because the location of eQTL, pQTL and mQTL can be analyzed multiple characters simultaneously, thus the problem of traditional proterties analytical approach quantity of information deficiency can be overcome.
S104, builds the gene regulatory network of diversiform-leaved poplar rooting process according to QTL, eQTL, pQTL and mQTL of diversiform-leaved poplar rootability, and according to gene regulatory network location diversiform-leaved poplar rootability the number networks character site nQTL.
Particularly, first can obtain the interactively between QTL, eQTL, pQTL and mQTL of diversiform-leaved poplar rootability, then set up the differential equation group of the gene regulatory network representing diversiform-leaved poplar rooting process according to interactively.Thus, the gene regulatory network of diversiform-leaved poplar rooting process is constructed.
Further, the first kind differential equation coefficient that in differential equation group, the genotype of eQTL, pQTL, mQTL is corresponding can be estimated respectively, then the Equations of The Second Kind differential equation coefficient of the genotypic difference determining eQTL, pQTL, mQTL is determined, and after obtaining first kind differential equation coefficient and Equations of The Second Kind differential equation coefficient, the nQTL of the gene regulatory network structure that positioning effects differential equation group is corresponding.Wherein, the molecular labeling of the differential equation group of gene regulatory network and diversiform-leaved poplar association analysis be can be carried out, thus high-res, original text precision, high systematic diversiform-leaved poplar gene regulatory network obtained.
For example, if for three genes Gen1, Gen2 and Gen3, the interactively of three as shown in Figure 2, the expression of Gen1 is subject to the suppression of Gen3, Gen1 promotes transcribing of Gen2, and jointly promote transcribing of Gen3 at Gen1 and Gen2, so, the interactively according to Gen1, Gen2 and Gen3 can set up following differential equation group:
And the parameter k in estimate equation group
1s, k
2s, k
3s, k
1d, k
2d, k
3d, k
21, k
31, k
32, k
13, wherein, k
1sfor the speed of Gen1 synthesis, k
2sfor the speed of Gen2 synthesis, k
3sfor the speed of Gen3 synthesis, k
1dfor the speed of Gen1 degraded, k
2dfor the speed of Gen2 degraded, k
3dfor the speed of Gen3 degraded, k
21for Gen2 is to the activation degree of base Gen1, k
31for Gen3 is to the activation degree of Gen1, k
32for Gen3 is to the activation degree of Gen2, k
13for Gen1 is to the activation degree of Gen3, M
1for the amount of gene 1mRNA, M
2for the amount of Gen2mRNA, M
3for the amount of Gen3mRNA.
Further, association analysis can be carried out to orient the nQTL affecting the gene regulatory network comprising Gen1, Gen2 and Gen3 according to the differential equation group after differential equation group determination parameter and molecular labeling.
S105, carries out the asexual seed selection of diversiform-leaved poplar according to the nQTL of diversiform-leaved poplar rootability.
The asexual selection of diversiform-leaved poplar based on gene regulatory network of the embodiment of the present invention, by carrying out explant cultivation to the diversiform-leaved poplar target group built, and obtain the phenotypic data of diversiform-leaved poplar rootability and the QTL of location diversiform-leaved poplar rootability, eQTL, pQTL and mQTL, to build the gene regulatory network of diversiform-leaved poplar rooting process, and locate diversiform-leaved poplar rootability the number networks character site nQTL accordingly, thus can be able to disclose on the basis of the gene regulatory network forming this dynamic process from gene to protein again to phenotype structure one, the nQTL of this dynamic process of positioning effects, and guide the asexual seed selection of diversiform-leaved poplar, overcome diversiform-leaved poplar shape be separated seriously be unfavorable for screen problem while, effectively can filter out the diversiform-leaved poplar individual plant that rootability is strong, improve the breeding potential of diversiform-leaved poplar, greatly facilitate the seed selection of diversiform-leaved poplar clones with resistance.
In addition, term " first ", " second " only for describing object, and can not be interpreted as instruction or hint relative importance or imply the quantity indicating indicated technical characteristic.Thus, be limited with " first ", the feature of " second " can express or impliedly comprise at least one this feature.In describing the invention, the implication of " multiple " refers to two or more, such as two, three etc., unless otherwise expressly limited specifically.
In the description of this instructions, the description of reference term " embodiment ", " some embodiments ", " example ", " concrete example " or " some examples " etc. means the specific features that describes in conjunction with this embodiment or example or feature is contained at least one embodiment of the present invention or example.In this manual, to the schematic representation of above-mentioned term not must for be identical embodiment or example.And the specific features of description or feature can combine in one or more embodiment in office or example in an appropriate manner.In addition, when not conflicting, the feature of the different embodiment described in this instructions or example and different embodiment or example can carry out combining and combining by those skilled in the art.
Although illustrate and describe embodiments of the invention above, be understandable that, above-described embodiment is exemplary, can not be interpreted as limitation of the present invention, and those of ordinary skill in the art can change above-described embodiment within the scope of the invention, revises, replace and modification.
Claims (7)
1., based on the asexual selection of diversiform-leaved poplar of gene regulatory network, it is characterized in that, comprising:
Build diversiform-leaved poplar target group;
Carry out explant cultivation according to described diversiform-leaved poplar target group, and in the process of described cultivation, obtain the phenotypic data of diversiform-leaved poplar rootability, transcription group data, proteomics data and metabolism group data;
Respectively according to the QTL of the phenotypic data of described diversiform-leaved poplar target group, transcription group data, proteomics data and metabolism group data location diversiform-leaved poplar rootability, express quantitative trait locus eQTL, protein amounts character site pQTL and metabolin quantitative trait locus mQTL;
The gene regulatory network of diversiform-leaved poplar rooting process is built according to QTL, eQTL, pQTL and mQTL of described diversiform-leaved poplar rootability, and according to described gene regulatory network location diversiform-leaved poplar rootability the number networks character site nQTL;
The asexual seed selection of diversiform-leaved poplar is carried out according to the nQTL of described diversiform-leaved poplar rootability.
2. the method for claim 1, is characterized in that, described QTL, eQTL, pQTL and mQTL according to described diversiform-leaved poplar rootability build the gene regulatory network of diversiform-leaved poplar rooting process, specifically comprise:
Obtain the interactively between QTL, eQTL, pQTL and mQTL of described diversiform-leaved poplar rootability;
The differential equation group of the gene regulatory network representing diversiform-leaved poplar rooting process is set up according to described interactively.
3. method as claimed in claim 2, is characterized in that, described according to described gene regulatory network location diversiform-leaved poplar rootability the number networks character site nQTL, specifically comprises:
Estimate the first kind differential equation coefficient that the genotype of described eQTL, described pQTL, described mQTL is corresponding respectively;
Determine the Equations of The Second Kind differential equation coefficient of the genotypic difference determining described eQTL, described pQTL, described mQTL;
After obtaining described first kind differential equation coefficient and described Equations of The Second Kind differential equation coefficient, the nQTL of the gene regulatory network structure that differential equation group described in positioning effects is corresponding.
4. the method as described in any one of claim 1-3, is characterized in that, described diversiform-leaved poplar target group comprises multiple diversiform-leaved poplar maternal plant and multiple half-sib progeny colony, and described structure diversiform-leaved poplar target group specifically comprises:
Multiple diversiform-leaved poplar maternal plant described in random selecting in diversiform-leaved poplar distributing region;
Gather the seed of each maternal plant respectively and cultivate into filial generation seedling, to build the multiple half-sib progeny colonies corresponding respectively with described multiple diversiform-leaved poplar maternal plant.
5. method as claimed in claim 4, it is characterized in that, describedly carry out explant according to described diversiform-leaved poplar target group and cultivate and specifically comprise: the stem section of getting predetermined number respectively from each filial generation each maternal plant and each half-sib progeny colony, and the stem section obtained is cultivated respectively.
6. method as claimed in claim 5, is characterized in that, described phenotypic data, transcription group data, proteomics data and the metabolism group data obtaining diversiform-leaved poplar rootability in the process of described cultivation specifically comprise:
In the process of described cultivation, record the rootability phenotypic data of described diversiform-leaved poplar target group, and in the process of described cultivation, set multiple time point;
From described diversiform-leaved poplar target group, filter out rootability according to described rootability phenotypic data and be greater than the first predetermined threshold value or rootability is less than the maternal plant of the second predetermined threshold value and sub-strain;
Each time point in rooting process obtains described rootability and is greater than the first predetermined threshold value or rootability is less than the maternal plant of the second predetermined threshold value and the incision tissue of sub-strain, and transcription analysis, proteomic assays and metabonomic analysis are carried out to the incision tissue got, to obtain described diversiform-leaved poplar rootability transcription group data, proteomics data and metabolism group data.
7. the method for claim 1, it is characterized in that, described respectively according to the QTL of the phenotypic data of described diversiform-leaved poplar target group, transcription group data, proteomics data and metabolism group data location diversiform-leaved poplar rootability, express quantitative trait locus eQTL, protein amounts character site pQTL and metabolin quantitative trait locus mQTL, specifically comprise:
The phenotypic data of described diversiform-leaved poplar target group and diversiform-leaved poplar molecular marker data are carried out association analysis with the QTL of positioning effects diversiform-leaved poplar rootability;
The transcription group data of described diversiform-leaved poplar target group and diversiform-leaved poplar molecular marker data are carried out association analysis with the eQTL of gene content in positioning effects diversiform-leaved poplar rooting process;
The proteomics data of described diversiform-leaved poplar target group and diversiform-leaved poplar molecular marker data are carried out association analysis with the pQTL of protein content in positioning effects diversiform-leaved poplar rooting process;
The metabolism group data of described diversiform-leaved poplar target group and diversiform-leaved poplar molecular marker data are carried out association analysis with the mQTL of metabolite content in positioning effects diversiform-leaved poplar rooting process.
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