Patent Application
20150033389
The invention relates to a method for producing a genetically modified plant with improved growth properties as compared to a corresponding non-genetically modified wild type plant, said method comprising reducing or deleting the amount or activity of an EBI1 or EBI2 polypeptide in a plant cell, a plant or a part thereof.
Plants use light-dark cues and an internal 24-h (circadian) clock to orient themselves in their local environment and to synchronize their metabolism accordingly. The circadian clock of the model plant Arabidopsis (Arabidopsis thaliana) is made up of a complex series of interacting feedback loops whereby proteins regulate their own expression across day and night. Early bird (ebi) is a circadian mutation that causes the clock to speed up: ebi plants have short circadian periods, early phase of clock gene expression, and are early flowering.
The gene responsible for the ebi-1 phenotype, AtNFXL-2, is a zinc finger transcription factor, a homolog of the human NF-X1 protein. In humans, NF-X1 binds to the X-box found in class II MHC genes. Arabidopsis has two NF-X1 homologs, AtNFXL-1 and AtNFXL-2, which are thought to act antagonistically to regulate genes involved in salt, osmotic and drought stress, with AtNFXL-1 activating and AtNFXL-2 repressing stress-inducing genes. AtNFXL-1 has also been suggested to be a negative regulator of defense-related genes and temperature stress. Thus, the clock phenotype of the AtNFXL-2 mutant provides an intriguing link between the clock and biotic and abiotic stress responses. This link has been alluded to in a recent review and in the identification of a possible role for the clock protein GI in cold stress tolerance.
The circadian phenotypes of the ebi-1 mutant have been characterized by Johansson, M. et al. (2011) Partners in Time: EARLY BIRD Associates with ZEITLUPE and Regulates the Speed of the Arabidopsis Clock. Plant Physiol. 155(4): 2108-2122.
Populus trees have two EBI1 genes: EBI1a (SEQ ID NO: 1) and EBI1b (SEQ ID NO: 3) as well as two EBI2 genes: EBI2a (SEQ ID NO: 6) and EBI2b (SEQ ID NO: 8). See also Johansson et al. (2011), Supplemental Table I and Supplemental
Increased plant production of biomass particularly in agriculture and forestry is of large importance for food and as a renewable resource for energy and materials fulfilling the demands of an increasing population and as a CO2 sink for increasing levels of green house gases. At present most forest production is based on the production of boreal forests where trees are exposed to large seasonal variation in day length and temperature resulting in rather short growing seasons. To increase productivity of these and other forests it is essential to obtain germplasm that thrive at extensive latitudinal clines and produce large quantities of biomass during the most productive time.
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It has surprisingly been found that trees with decreased levels of EARLY BIRD1 (EBI1) and EARLY BIRD2 (EBI2) transcript grow better than wild type trees. The growth phenotype is inversely proportional to the level of expressed transcript (more growth when there is less transcript) indicating that the effect is due to the down-regulation of the targeted transcripts. It is suggested that EBI genes are useful as targets for down-regulation to obtain increased growth and generating more biomass of forest trees.
Consequently, in one aspect the invention provides a method for producing a genetically modified plant with improved growth properties as compared to a corresponding non-genetically modified wild type plant, said method comprising:
The term “improved growth properties” should be understood as primary growth, including a lengthening of the stem and roots, as well as secondary growth of a plant, including production of secondary tissue, “wood”, from the cambium and an increase in the girth of stems and roots. One way of following the growth might be by measuring the height and the diameter of the stem and optionally calculating the volume of the stem and compare it with a wild type population or with parental control trees of the plant of interest.
In an additional aspect, the method according to the invention comprises the additional steps of:
Preferably, the said EBI1 polypeptide comprises a domain having at least about 161 amino acids, said domain being at least 75% identical, such as 80%, 85%, 90%, 95% or 100% identical, with the amino acid sequence shown as SEQ ID NO: 5. More preferably, the said EBI1 polypeptide has an amino acid sequence which is at least 75%, such as 80%, 85%, 90%, 95% or 100%, identical with the sequence shown as SEQ ID NO: 2 (EBI1a) or SEQ ID NO: 4 (EBI1b).
Preferably, the said EBI2 polypeptide comprises a domain having at least about 191 amino acids, said domain being at least 75% identical, such as 80%, 85%, 90%, 95% or 100% identical, with the amino acid sequence shown as SEQ ID NO: 10. More preferably, the said EBI2 polypeptide has an amino acid sequence which is at least 75%, such as 80%, 85%, 90%, 95% or 100%, identical with the sequence shown as SEQ ID NO: 7 (EBI2a) or SEQ ID NO: 9 (EBI2b).
In a further aspect, the invention provides a the method as describe above, comprising reducing or deleting the expression of at least one nucleic acid molecule, wherein said molecule is selected from: (a) a nucleic acid molecule encoding a EBI1 polypeptide or EBI2 polypeptide; and (b) a nucleic acid molecule having a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 (EBI1a), SEQ ID NO: 3 (EBI1b), SEQ ID NO: 6 (EBI2a); and SEQ ID NO: 8 (EBI2b).
In accordance with the present invention, the method comprise the further step of transforming regenerable cells of a plant with said nucleic acid construct or recombinant DNA construct and regenerating a transgenic plant from said transformed cell. When introducing the above DNA construct or vector into a plant cell, certain considerations must be taken into account, well known to those skilled in the art. The nucleic acid to be inserted should be assembled within a construct that contains effective regulatory elements that will drive transcription, as described above. There must be available a method of transporting the construct into the cell. Once the construct is within the cell, integration into the endogenous chromosomal material either will or will not occur.
Transformation techniques, well known to those skilled in the art, may be used to introduce the DNA constructs and vectors into plant cells to produce transgenic plants, in particular transgenic trees, with improved growth properties.
A person of skill in the art will realise that a wide variety of host cells may be employed as recipients for the DNA constructs and vectors according to the invention. Non-limiting examples of host cells include cells in embryonic tissue, callus tissue type I, II, and III, hypocotyls, meristem, root tissue, tissues for expression in phloem, leaf discs, petioles and stem internodes.
As listed above, Agrobacterium transformation is one method widely used by those skilled in the art to transform tree species, in particular hardwood species such as poplar. Production of stable, fertile transgenic plants is now a routine in the art. Other methods, such as microprojectile or particle bombardment, electroporation, microinjection, direct DNA uptake, liposome mediated DNA uptake, or the vortexing method may be used where Agrobacterium transformation is inefficient or ineffective, for example in some gymnosperm species.
Alternatively, a combination of different techniques may be employed to enhance the efficiency of the transformation process, e.g. bombardment with Agrobacterium coated microparticles or microprojectile bombardment to induce wounding followed by co-cultivation with Agrobacterium.
It will be understood, that the particular choice of a transformation technology will be determined by its efficiency to transform certain plant species as well as the experience and preference of the person practising the invention with a particular methodology of choice. It will be apparent to the skilled person that the particular choice of a transformation system to introduce nucleic acid into plant cells is not essential to or a limitation of the invention, nor is the choice of technique for plant regeneration.
Following transformation, transgenic plants are preferably selected using a dominant selectable marker incorporated into the transformation vector. Typically, such a marker will confer antibiotic or herbicide resistance on the transformed plants and selection of transformants can be accomplished by exposing the plants to appropriate concentrations of the antibiotic or herbicide. A novel selection marker using the D-form of amino acids and based on the fact that plants can only tolerate the L-form offers a fast, efficient and environmentally friendly selection system. An interesting feature of this selection system is that it enables both selection and counter-selection.
Subsequently, a plant may be regenerated, e.g. from single cells, callus tissue or leaf discs, as is standard in the art. Almost any plant can be entirely regenerated from cells, tissues and organs of the plant. After transformed plants are selected and grown to maturity, those plants showing altered growth properties phenotype are identified. Additionally, to confirm that the phenotype is due to changes in expression levels or activity of the polypeptide or polynucleotide disclosed herein can be determined by analyzing mRNA expression using Northern blots, RT-PCR or microarrays, or protein expression using immunoblots or Western blots or gel shift assays.
Consequently, in a further aspect the method according to the invention comprises at least one step selected from:
In another aspect the invention provides a method wherein reducing or deleting of the amount or activity of an EBI1 polypeptide or EBI2 polypeptide is caused by any one of:
In a preferred aspect, the method according to the invention comprises:
In a further aspect, the invention provides a genetically modified, especially a transgenic, plant produced by the methods as described above. In accordance with the present invention, the transgenic plant may be a perennial plant which preferable is a woody plant or a woody species. In a useful embodiment, the woody plant is a hardwood plant which may be selected from the group consisting of acacia, eucalyptus, hornbeam, beech, mahogany, walnut, oak, ash, willow, hickory, birch, chestnut, poplar, alder, maple, sycamore, ginkgo, a palm tree and sweet gum. Hardwood plants from the Salicaceae family, such as willow, poplar and aspen including variants thereof, are of particular interest, as these two groups include fast-growing species of tree or woody shrub which are grown specifically to provide timber and bio-fuel.
In further embodiments, the woody plant is a conifer which may be selected from the group consisting of cypress, Douglas fir, fir, sequoia, hemlock, cedar, juniper, larch, pine, redwood, spruce and yew. In useful embodiments, the woody plant is a fruit bearing plant which may be selected from the group consisting of apple, plum, pear, banana, orange, kiwi, lemon, cherry, grapevine and fig. Other woody plants which may be useful in the present method may also be selected from the group consisting of cotton, bamboo and rubber plants. Other plants, which may be useful is grasses grown for biomass production, for example Miscanthus and Switchgrass.
The present invention extends to any plant cell of the above transgenic plants obtained by the methods described herein, and to all plant parts, including harvestable parts of a plant, seeds and propagules thereof, and plant explant or plant tissue. The present invention also encompasses a plant, a part thereof, a plant cell or a plant progeny comprising a DNA construct according to the invention. The present invention extends further to encompass the progeny of a primary transformed or transfected cell, tissue, organ or whole plant that has been produced by any of the aforementioned methods, the only requirement being that progeny exhibit the same genotypic and/or phenotypic characteristic(s) as those produced in the parent by the methods according to the invention.
Consequently, the invention provides a genetically modified plant having improved growth properties as compared to a corresponding non-genetically modified wild type plant, wherein said plant has a reduced amount or activity of a EBI1 or EBI2 polypeptide, and wherein the genome of said plant comprises a genetic modification selected from any one of:
EBI2 polypeptide, induced by introducing into at least one plant cell a nucleic acid construct able to recombine with and silence, inactivate, or reduce the activity of the endogenous gene,
wherein said EBI1 polypeptide has an amino acid sequence having at least 80% amino acid sequence identity to a sequence selected from among SEQ ID NOS: 2, 4 and 5, or wherein said EBI2 polypeptide has an amino acid sequence having at least 80% amino acid sequence identity to a sequence selected from among SEQ ID NOS: 7, 9 and 10.
In another embodiment, the invention provides the use of EBI1 and EBI2 genes for the identification of plants having increased growth as compared to the wild-type.
In a further embodiment, the invention provides the use of EBI1 and EBI2 genes and polypeptides in the identification of agents useful for inhibiting EBI1 or EBI2 activity, thereby being useful for improving plant growth.
In yet a further embodiment, the invention provides the use of EBI1 and EBI2 genes as candidate genes in marker assisted breeding.
EBI1 and EBI2 appear to have a light induced and diurnal expression with a circadian pattern e.g. EBI2, less clear so EBI1, when assayed every four hours under 48 h in an 18 h light/6 h dark day length regime (18° C./18° C.) starting 3 h before dawn (
As shown in
RNAi trigger regions were amplified from Populus tremula×tremuloides cDNA by PCR using Platinum pfx DNA polymerase (Invitrogen, Carlsbad, Calif., USA) according to the product manual with following primer sets:
The EBI1constructs were used to down-regulate EPI1a and EPI1b, and the EBI2 constructs were used down-regulate EBI2a and EBI2b.
The PCR products were cloned in pENTR™/SD/D-TOPO® vector (Invitrogen, Carlsbad, Calif., USA). In order to remove the ineffective trigger region descended from pENTR™/SD/D-TOPO® vector, these vectors were digested with Notl and self-ligated. These entry vectors were subjected to dideoxy-nucleotide sequencing and used in the LR-Gateway reaction (Invitrogen, Carlsbad, Calif., USA) with the destination vector, pANDA35HK. Agrobacterium mediated transformation was subsequently used in order to transform hybrid aspen, Populus tremula L. ×P. tremuloides Mich. Clone T89 was transformed and regenerated according to methods known in the art.
The transgenic poplar lines were grown together with their wildtype control (wt) trees, in a growth chamber under a photoperiod of 18 h and a temperature of 18° C./18° C. (day/night). The plants were fertilized weekly Weibulls Rika S NPK 7-1-5 diluted 1 to 100 (final concentrations NO3, 55 g/1; NH4, 29 g/1; P, 12 g/1; K, 56 g/1; Mg 7,2 g/1; S, 7,2 g/1; B, 0,18 g/1; Cu, 0,02 g/1; Fe, 0,84 g/1; Mn, 0,42 g/1; Mo, 0,03 g/1; Zn, 0,13 g/L). Height and diameter was measured and used for analysis of growth.
Knock-out of EBI1 and EBI2 resulted in transgenic trees with an increase in both elongation as well as radial growth compared to the wildtype T89 (
As shown in Table I, some of the EBI1 transgenic trees show 25-28% increased volume growth index and 5-13% increased height. Some of the EBI2 transgenic trees show 15-36% volume growth index and 6-14% increased height.
The level of gene expression was in good agreement with the observed phenotype (
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/SE2013/050191 | 3/5/2013 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 61607404 | Mar 2012 | US |
