WO2024052866A1 - Powdery mildew-resistant grapevine - Google Patents
Powdery mildew-resistant grapevine Download PDFInfo
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- WO2024052866A1 WO2024052866A1 PCT/IB2023/058895 IB2023058895W WO2024052866A1 WO 2024052866 A1 WO2024052866 A1 WO 2024052866A1 IB 2023058895 W IB2023058895 W IB 2023058895W WO 2024052866 A1 WO2024052866 A1 WO 2024052866A1
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Classifications
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- C—CHEMISTRY; METALLURGY
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- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/415—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from plants
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
- C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
- C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
- C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
- C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
- C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
- C12N15/8279—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance
- C12N15/8282—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance for fungal resistance
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
- C12N9/14—Hydrolases (3)
- C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
- C12N9/22—Ribonucleases RNAses, DNAses
Definitions
- Vitis vinifera belongs to the group of European-Asian Vitis species and can be divided into two subspecies: Vitis vinifera sativa (i.e., the domestic vine) and Vitis vinifera sylvestris (i.e., the wild vine), the latter showing leaves with generally a very open petiolar sinus (Fregoni, 2013).
- the mutation which is obtained by genome editing is in fact carried out by the CRISPR/Cas9 complex inside the cell, in which it can be inserted, in particular by eliminating its wall, if it is not to be inserted by means of stable genetic modification or bombardment methods.
- 200.2023 2 The wall removal starting from plant embryogenetic cells produces a protoplast, which must maintain the ability to regenerate the plant. Such an ability has been demonstrated in a limited number of scientific works and in particular for protoplasts derived from embryogenic material obtained from different tissues (Reustle et al., 1995; Zhu et al., 1997; Bertini et al., 2019).
- the biological cycle of Erysiphe necator starts with overwintering, a phase that can be passed in two ways: as a latent mycelium in the buds or as a cleistothecium.
- the pathogen mainly localises in the hibernating buds, which will then give rise to the so-called “flagellar shoots” at budding. Symptoms can be observed on all green organs of the plant.
- infections on leaves it will be possible to observe small, circular, translucent chlorotic spots that later become covered with mycelium giving a whitish/powdery appearance to the affected tissues.
- MLO genes are thought to negatively regulate other genes associated with the trafficking of vesicles that transport the materials necessary for the attachment of callose papillae to the pathogen's point of penetration, thus favouring its infection (Pessina, et al., 2016).
- VviMLO3 genes of the VviMLO family in Vitis vinifera following infection by Erysiphe necator
- VviMLO4 genes of the VviMLO family in Vitis vinifera following infection by Erysiphe necator
- VviMLO17 three of them (VviMLO3; VviMLO4; VviMLO17) are overexpressed following infection, hypothesising their involvement in the process (Feechan, et al., 2008).
- VviMLO6 VviMLO7; VviMLO11; VviMLO13 according to the nomenclature proposed by Winterhagen et al., 2008 and corresponding to VviMLO13; VviMLO17; VviMLO3; VviMLO4 in Feechan et al., 2008
- VviMLO6 VviMLO7; VviMLO11; VviMLO13
- a transgenic approach was used for gene silencing.
- Another object of the invention is to individuate suitable gRNAs that target specific MLO gene sites wherein their application to plant cells or protoplasts creates powdery mildew resistant mutants.
- Another object of the invention is not only to create and select a resistant mutation but to obtain a mutated plant that contemporarily has an ampelographic appearance that clearly distinguishes it from the non-resistant variant.
- the object is achieved by an Erysiphe necator susceptibility gene comprising a resistance conferring mutation wherein the mutation causes a shift in the codon reading window by insertion of one or two nucleotides or by deletion of one or two nucleotides into a DNA sequence that has more than 70% identity, preferably more than 80% identity, more preferably more than 90% identity, and most preferably more than 95% identity with SEQ ID No.10 and wherein, preferably the insertion or deletion, in particular the insertion of one nucleotide, preferably adenine is present in the fourth exon.
- Resistance herein is intended as powdery mildew resistance.
- the Erysiphe necator susceptibility gene comprising a resistance conferring mutation, comprises the DNA sequence according to SEQ ID No. 9.
- the susceptibility to Erysiphe necator is decreased in this 200.2023 5 mutated gene with respect to the corresponding Erysiphe necator susceptibility gene comprising the DNA sequence according to SEQ ID No.8.
- the Erysiphe necator susceptibility gene comprising a resistance conferring mutation is designated VviMLO17 (according to the nomenclature of Feechan, et al., 2008).
- VviMLO17 refers to the nomenclature proposed by Feechan et al. (2008).
- the Erysiphe necator susceptibility gene comprising a resistance conferring mutation, comprises a DNA sequence that has more than 70% identity, preferably more than 80% identity, more preferably more than 90% identity, and most preferably more than 95% identity with SEQ ID No.11 and - comprises inside said DNA sequence an insertion, in particular an adenine, at position 202 bp with respect to a DNA sequence that has more than 70% identity, preferably more than 80% identity, more preferably more than 90% identity, and most preferably more than 95% identity with SEQ ID No.10, or - comprises the sequence according to SEQ ID No.9.
- Sequence identity as used herein is defined as the number of identical consecutive aligned nucleotides, or amino acids, over the full length of the present sequences divided by the number of nucleotides, or amino acids, of the full length of the present sequences and multiplied by 100%.
- said DNA sequence encodes an amino acid sequence with more than 70% identity, preferably more than 80% identity, more preferably more than 90% identity, and most preferably more than 95% identity with SEQ ID No.13.
- said DNA sequence encodes the amino acid sequence according to SEQ ID No.13.
- the Erysiphe necator susceptibility gene comprising a resistance conferring mutation according to the invention advantageously comprises an insertion of the nucleotide adenine with respect to the wild-type variant.
- a second aspect of the invention refers to a protoplast or plant cell that comprises the Erysiphe necator susceptibility gene comprising a resistance conferring mutation according to the invention. Such a protoplast or plant cell can be used for regenerating a respective plant.
- a third aspect of the invention relates to a powdery mildew resistant plant comprising in its genome the Erysiphe necator susceptibility gene comprising a resistance conferring mutation according to the invention.
- a plant having said modification (insertion) exhibits a reduction in powdery mildew disease severity compared to a plant lacking this modification in the respective gene.
- the powdery mildew resistant plant according to the invention is a Vitis vinifera, in a preferred embodiment of the Chardonnay type, for example its clone 76.
- the adult leaves of the powdery mildew resistant plant show the following ampelographic characteristics: - OIV 067 is 5; - OIV 079 is 1; - OIV 094 is 1; and - preferably OIV 080 is 2, wherein OIV and the scores used are defined by the guidelines of the International Organization of Vine and Wine of 2021.
- OIV 080 2 indicates a brace-shaped base of the petiolar sinus.
- a fourth aspect of the invention refers to a method for providing an Erysiphe necator susceptibility gene comprising a resistance conferring mutation, a powdery mildew resistant protoplast, plant cell, tissue or grapevine plant, comprising the following step: - mutating a gene designated VviMLO17 by insertion of a nucleotide, in particular an adenine, in a gene sequence according to SEQ ID 8 in the position between the sixth and seventh nucleotide.
- an Erysiphe necator susceptibility gene comprising a resistance conferring mutation, a powdery mildew resistant protoplast, plant cell, tissue or grapevine plant is obtained by inserting a nucleotide, in particular an adenine, between the positions 201 bp and 202 bp in a DNA sequence with more than 70% identity, preferably more than 80% identity, more preferably more than 90% identity, and most preferably more than 95% identity with SEQ ID No.10.
- the insertion is obtained by CRISPR/Cas9 genome editing using as gRNA a gRNA with the sequence according to SEQ ID No.7. This permits a precise cut and mutation.
- the mutation is obtained in protoplasts.
- the protoplasts than can be regenerated to form the relative plant.
- the method can comprise further steps as described herein.
- DNA-free genomic editing by transfecting protoplasts with CRISPR/Cas9 ribonucleoparticles was used for the functional inactivation of the VviMLO17 gene, which the inventors showed to be a susceptibility gene for the powdery mildew disease. It’s the first time that it was demonstrated that VviMLO17 works alone, and therefore the inventors are demonstrating for the first time that VviMLO17 it is indeed a true susceptibility gene.
- Yet another aspect of the invention refers to a seed, fruit, or plant part of a grapevine plant comprising the gene according to the invention.
- Another aspect of the inventions refers to a method for the selection of mildew-resistant grapevine plants comprising the following steps: - selecting one or more powdery mildew-resistant mutants; - selecting among the powdery mildew-resistant mutants those that show ampelographic differences with respect to the wild-type plant. In particular, these ampelographic differences refer to the leave characteristics of the plant. This selection permits to have plants that can be easily identified.
- a further aspect of the invention refers to a method for identifying a powdery mildew resistant plant, in particular a grapevine plant, comprising the step of detecting the Erysiphe necator susceptibility gene comprising a resistance conferring mutation according to the invention and/or determining the ampelographic characteristics as defined in the invention.
- a last aspect of the invention concerns a kit for the preparation of a genome edited plant comprising: - a gRNA with the sequence according to SEQ ID No: 7.
- the kit further comprises Cas9.
- the genome editing according to the invention permitted to obtain a mutation that heavily influenced morphological characteristics of the plant itself, to such an extent that it might even be possible to define a new cultivar while maintaining the other characteristics, primarily the organoleptic ones, of the wine by satisfying the traditionalist wine consumer. 200.2023 8
- This particular modification surprisingly showed in an ampelographic analyses of certain morphological characters of the green organs the presence of significant differences between the leaf issued by the plant in which the genome editing was correctly carried out and other plants regenerated from embryogenic calli or from non-transfected protoplasts. These phenotype differences can easily be individuated by the person skilled in the art and help to individuate without genetic analysis for example counterfeited plants.
- the method for producing edited grapevine plants from protoplasts developed by the authors and described in EP 4151084 that significantly reduced the stress for the plant elements during production helped to obtain the targeted insertion point mutation avoiding further the formation of undesired other point mutations and subsequent soma clonal variations.
- the gRNA according to the invention was indeed no promising starting point, but led to the introduction of a point mutation in both alleles as a result of the gRNA/Cas9 cut and not point mutations as casual products of the in-vitro cultivation process.
- the transfected plants are obtained by the following steps: (I) preparation of a Cas9:gRNA complex with a molar ratio of 1:3 - 3: 1, in particular with a weight ratio between 1: 1 and 3:1, and incubating the ribonucleoprotein complex in the dark; (II) addition of the Cas9:gRNA complex prepared in the previous step to the protoplasts; (III) addition of a PEG 3000 - PEG 5000 solution, preferably PEG 4000, to the mixture obtained in step (II) and incubation, preferably at room temperature, in the dark; (IV) addition of a saline solution containing MES, in particular a W5 solution, stirring and incubation, preferably at room temperature, and preferably in the dark; (V) at least once repetition of step (IV), in particular with the doubled volume of saline solution; (VI) centrifugation of the transfected protoplasts washed in the previous steps preferably for 2
- gRNA is intended as any kind of guide RNA which functions as a guide for the Cas9 enzyme which targets RNA or DNA, with which it forms complexes.
- gRNAs such as the cr/tracrRNA system.
- incubations are to be performed in step (VII)
- these 200.2023 9 preferably occur without the addition of further washing solutions.
- no further incubation occurs in step (VII), greatly reducing the stress for the protoplasts.
- the various steps performed in the dark further reduce the stress for the protoplasts, an effect which makes them more "available" to plant cultivation.
- the final volume of the mixture of step (I) is 15-25 ⁇ L and/or the incubation time in step (I) is 10 min. Higher volumes should preferably be avoided.
- the protoplasts for the addition of the Cas9-gRNA complex were re-suspended in a concentration of 2 ⁇ 10 5 protoplasts in 200 ⁇ L of a MMG solution and in step (III) 200 - 225 ⁇ L, preferably 200 ⁇ L of PEG 3000 - PEG 5000 solution, preferably PEG 4000, preferably at 40% by weight by volume, are added.
- step (IV) a volume of saline solution containing MES is added, in particular a W5 solution, which is twice the volume of the MMG solution and for which the incubation time is about 8-12 min, in particular 10 min.
- step (VII) a concentration of 1 ⁇ 10 5 ppt/mL on petri is used.
- Obtaining the protoplasts themselves allows the application of different methods also known in the state of the art. Different sources of cells are conceivable, such as for example also floral stamens.
- the flower organ that gives the best results for inducing the proliferation of embryogenic calli that can then give crops that can be maintained and propagated over time are the stamens.
- MSII medium (Dhekney, et al., 2009): MS macronutrients, MS micronutrients, MS vitamins, 5,0 ⁇ M 6-BAP, 2,5 ⁇ M 2,4 D; 2,5 ⁇ M NOA; 0,1 g/L inositol; 2% sucrose; 7 g/L Agar-TC at a pH of 6,0.
- said protoplasts can be obtained from the following steps: 200.2023 10 (0-1) obtaining embryogenic calli from apical leaves of plants grown in vitro; (0-2) proliferation of embryogenic calli and regeneration of somatic embryos; (0-3) from embryos, possibly transgenic embryos, induction of embryogenic callus and isolation of protoplasts.
- a modified procedure for obtaining protoplasts is advantageous: (0-1) obtaining embryogenic calli from flower organs; (0-2) proliferation of embryogenic calli; (0-3) isolation of protoplasts from embryogenic calli.
- the possibility of obtaining plants from transfected protoplasts can be further improved by intervening on the steps of the method which relate to the preparation of protoplasts for the cultivation of seedlings.
- the following preparatory steps are added for regenerating grapevine plants from the transfected protoplasts: (VIII) a culture medium, preferably of the Nitsch type, is added to the transfected protoplasts, wherein the liquefied medium is preferably added at a temperature above 35°C and below 48°C; (IX) the same volume of culture medium, preferably of the Nitsch type, in the liquid state is added to the culture medium after solidification; (X) incubation of the protoplasts, preferably at 27-28°C, in the dark until regeneration of embryos at the cotyledonary stage; (XI) germination of the embryos and subsequent development of the seedlings.
- step (VIII) 2 mL of culture medium is added to 800- ⁇ L of the protoplast solution and the medium is separated into two halves, after solidification the same amount of culture medium is added as a reserve, and in step (VIII) and (IX) the culture medium is preferably of the Nitsch type supplemented with 2 mg/L 1-naphthaleneacetic acid (NAA), 0.5 mg/L 6-benzylaminopurine (6-BAP), 0.3 M glucose, 0.09 M sucrose and 2 g/L gellan gum (pH 5,7) wherein in step (IX) the medium was supplemented with 0.3% activated carbon or similar, e.g., glutathione; where during step (X) the liquid medium was replaced every 10-20 days, preferably every 12-18 days with fresh medium as defined above but without glucose, after 3-4 months of culture, the somatic embryos at the cotyledonary stage derived from protoplasts, were transferred to a solid preferably of
- the 200.2023 11 indication of the amount of medium and of the protoplast solution is not to be only understood as an absolute value, but more a ratio that is maintained: 2 mL medium/800- ⁇ L protoplast solution is equivalent for example to 1 mL medium/400 ⁇ L protoplast solution.
- Embryogenic calli for certain varieties can be obtained from young apical leaves of plants grown in vitro, following for example the protocol reported in the work of Dhekney et al. (2009). After proliferation of the embryogenic callus, somatic embryos can be regenerated. Those skilled in the art know other manners for producing somatic embryos. In the case of Chardonnay, for example, embryogenic calli can be obtained from flower organs, as mentioned above.
- One of the best sprouting medium proved to be medium C2D5B:C2D macro; C2D micro; C2D vitamins; 5 mL/L 6-BAP; 30 g/L sucrose; 7 g/L Agar-TC at a pH of 5.8.
- the sprouting phase is the most critical as it shows a much lower yield than the germination phase.
- the features described for one aspect of the invention can be transferred mutatis mutandis to any other aspect of the invention. Summing up, it can be seen that the invention achieves the intended objects, and in particular provides a gene and corresponding edited plant with powdery-mildew resistance, provides the gRNA necessary for its production and further gives the possibility to recognize the edited plant without genetic analysis simply controlling some ampelographic characteristics.
- the gene according to the invention can also be obtained independently of the steps concerning the application of the CRISPR/Cas9 system by replacing it with other systems such as ZNF (zinc finger proteins) and TALEN (transcription activator-like effector nucleases) to obtain the specified mutation or by selecting it among naturally occurring mutations or mutations obtained by biological processes.
- ZNF zinc finger proteins
- TALEN transcription activator-like effector nucleases
- Figure 1 shows above the target site of a Chardonnay VviMLO17 gene (wild-type) and below the Cas9/gRNA induced mutation in edited protoplasts.
- Figure 2A shows the sequencing results of a portion of the VviMLO17 gene within which the gRNA target site is located.
- Figure 2B shows the sequencing results of a portion of the VviMLO17 gene with the insertion mutation with respect to Fig.2A.
- Figure 3 shows the alignment of the sequences of Figures 2A and 2B.
- Figure 4 shows the photos of a non-edited control plant regenerated from protoplasts (left) and of an edited plant (right) with the mutation according to the invention followed by the respective analysis of four OIV characteristics.
- Figure 5 shows for the same plants as illustrated in Figure 4 the results of powdery mildew infections.
- Figure 6 shows microscope images (10X) of leaves of non-edited control plant regenerated from protoplasts (left) and of an edited plant (right) 8 days after artificial powdery mildew infection.
- Figure 7 shows in a columnar diagram the difference in the number of fungal conidia per cm 2 of leaf of control plants and the edited plant after natural infection.
- Figure 8A shows the amino acid sequence (SEQ ID No.12) coded from the DNA sequence represented in Figure 2A (SEQ ID No.10).
- Figure 8B shows the amino acid sequence (SEQ ID No.13) coded from the DNA sequence represented in Figure 2B (SEQ ID No.11).
- Figure 9 shows the alignment between the amino acid sequences of Figures 8A and 8B.
- the modified protocol is applicable to any type of protoplast, whether modified with the CRISPR/Cas9 system or with other systems known in the state of the art, such as ZFN (Zinc Finger Nucleases), TALEN (Transcription activator-like effector nucleases) systems, etc.
- ZFN Zinc Finger Nucleases
- TALEN Transcription activator-like effector nucleases
- the sequence of the exon to be targeted it is preferable to consider the sequence of the exon to be targeted, the genome of the organism to which the gene to be targeted belongs and the type of nuclease to be used to apply the cut, for example the Cas9 enzyme derived from Streptococcus pyogenes.
- the market offers a large variety of software packages to design gRNA proposals, but the difficulty remains in selecting the right gRNA among those proposed.
- the GeneArtTM Precision gRNA Synthesis Kit (Invitrogen, catalogue A29377) is used for the synthesis of guide RNA. First a pair of partially overlapping oligonucleotides (target F1 primer target R1 primer) were designed to contain the sequence of the target DNA fragment.
- the oligonucleotides useful for the synthesis of the gRNA targeting the VviMLO17 gene are represented in table 3.
- Table 3 200.2023 14 The gRNA then designed corresponds to GGAGTTGATGGATCCCAT (SEQ ID No: 7), and the corresponding PAM sequence is AGG.
- the oligonucleotides are purified from gRNA/DNA.
- an in vitro cut of the VviMLO17 gene is done, directly mixing the RNP (ribonucleoprotein) with the amplicon of the sequence of the target gene.
- the primers used only delimit the first 1959 base pairs (bp) and not the entire gene.
- the patent application EP 3320098 describes the importance of the VviMLO17 gene in the context of powdery mildew resistance and provides mutants that seem to silence this gene to some extent, but almost casually targeting other genes, since they did not obtain a silenced gene by directly targeting the VviMLO17 gene.
- Targeted silencing of other MLO genes was not specific and also silenced the MLO07 gene (corresponding to VviMLO17).
- the inventors of the present invention were able to design a gRNA directly targeting VviMLO17, and have chosen it despite expected technical difficulties.
- the authors of EP 3320 098 used the name VvMLO07 according to Winterhagen, that corresponds to VviMLO17 according to Feechan used herein.
- the VviMLO17 gene (corresponding to VvMLO07 in EP 3 320 098), contrarily to the gene of the present invention, was not mutated (non- functioning protein), but simply silenced, with the RNA interference system. Moreover, the 200.2023 15 silencing does not appear to be complete, as the expression is about half that of non-transgenic plants.
- the transfection of the protoplasts is performed with Cas9-gRNA ribonucleotides (RNPs).
- RNPs Cas9-gRNA ribonucleotides
- the Cas9:gRNA complex was prepared with a ratio of 1:1 - 3:1 (w/v) in a final volume of 20-25 ⁇ L and the ribonucleoprotein complex was incubated at room temperature for 10 minutes in the dark.2 ⁇ 10 5 protoplasts were used for the transfection, resuspended in 200 ⁇ L MMG solution.
- the MMG solution preferably comprises 0,5 M mannitol, 4 mM MES (2- N-morpholino ethanesulfonic acid) and 15 mM MgCl2 in distilled H2O.
- the gRNA, prepared in the previous step, are added to the protoplasts.
- the most favourable ratio of Cas9 : gRNA in terms of yield was 1:1, in particular using a ratio of 60 ⁇ g : 60 ⁇ g. 200 ⁇ L 40% (w/v) PEG 4000 solution was then added to the protoplast-RNP mixture. The mixing occurred by pipetting gently, for example with tips with the top cut to avoid breaking the cells, followed by incubation at room temperature for 20 minutes in the dark.
- a W5 solution comprises 5 mM glucose, 2 mM MES (pH 5.7), 154 mM NaCl, 125 mM CaCl 2 , and 5 mM KCl in distilled H 2 O.
- the solution is prepared fresh before use.
- 800 ⁇ L W5 solution was added, mixed and then incubated again for 10 minutes at room temperature in the dark. At the end of the washings, the transfected protoplasts were centrifuged for 3 minutes at 100 ⁇ g and the supernatant was removed.
- culture medium Particular attention is paid to the amount of culture medium.2 mL of culture medium are added to the transfected protoplasts, cultivated by the disc-culture method. To achieve the maximum homogeneity of the protoplasts in the solid culture medium, the liquefied medium is added at a temperature above 35°C and below 48°C. The 2 mL are divided into two petri dishes, placing a 1 mL culture drop in each, adding the same volume of culture medium in the liquid state in each petri after solidification. By putting a single drop, the cells have greater contact with the liquid nutrient medium. The plates are then incubated at 28°C in the dark until the regeneration of cotyledonary stage embryos.
- the entire method, applied here to Chardonnay, and the application of the gRNA according to the invention, in particular the transfection of protoplasts, is transferable to other types of grapevines or plants.
- the biological material of plant origin used is a table grapevine of the species Vitis vinifera subsp. vinifera with the name Chardonnay widely present and available on the markets, since it is one of the most important vine grapes, number 2455 in the Vitis International Variety Catalogue.
- Figure 1 illustrates above the result of the sequencing of the target site of a Chardonnay VviMLO17 gene (wild-type) and below the Cas9/gRNA induced mutation in edited protoplasts.
- the sequencing of the gene at the gRNA target site revealed the insertion of a 3-base-pair adenine, confirming the occurrence of genome editing.
- the adenine insertion in the edited sequence represented corresponds to SEQ ID No. 9
- the represented control sequence corresponds to SEQ ID No.8.
- the 200.2023 17 mutation is present in both alleles.
- Figures 2A and 2B show a greater portion of the VviMLO17 gene within which the gRNA target site is located. The portion of the gene contains a part of the third exon, the entire sequence of the fourth and fifth exons and the two introns between them.
- Figure 2A refers to the non-edited gene portion which corresponds to SEQ ID No: 10, while Figure 2B illustrates the gene portion of the edited plant corresponding to SEQ ID No: 11.
- the arrow indicates the mutation.
- FIG. 10 and 11 represent part of the third exon, the fourth and fifth complete exons with the two introns between the third and fourth exon and the other between the fourth and fifth exon; in the fourth exon is the mutation.
- Figure 3 shows the alignment of the two gene portions represented in Figures 2A and 2B.
- the consensus sequence corresponds exactly to the sequence of the wild-type plant (SEQ ID No: 10).
- the mutation is an adenine insertion in position 202 bp.
- Figure 4 shows the photos of a non-edited control plant regenerated from protoplasts (left) and of an edited plant (right) followed by the respective analysis of four OIV characteristics.
- OIV “Descriptive character code for vine varieties and Vitis species”
- a guide produced by the International Organisation of Vine and Vine that provides a large number of morphological descriptors that can be used to describe varieties of the genus Vitis and proceed with their recognition on the basis of the observable phenotype (OIV, 2021).
- the guide provides numerical scores corresponding to the level of character expression and each of these is accompanied by a picture describing it and reference cultivars, i.e. cultivars that clearly express a certain level of expression for that character.
- the plants here described are plants grown in a controlled environment and have one or at most two shoots of small size and growth.
- - OIV 080 Shape of the base of the petiolar sinus of the adult leaf The shape of the petiolar sinus base also changes, as in callus- and protoplast- regenerated plants, a U-shaped opening can be seen, whereas in the edited plant it is more like a brace.
- - OIV 094 Depth of the upper lateral sinuses of the adult leaf Again with regard to the upper lateral sinuses, their degree of depth is clearly more important in plants regenerated from callus and protoplast than in plants edited on the VviMLO17 gene, where sometimes very shallow sinuses are found generating even indecision as to the level of expression to be attributed to the OIV 067 character.
- Table 4 indicates the scores for these four OIV characters: Table 4 Figure 4 relating to the ampelographic characters uses an “a” to designate elements belonging to the wild-type plant, while “b” designates the edited plant. Same numerals refer to the same elements in the compared plants.10a and 10b, respectively, denominate the leaf itself.12a and 12b, respectively, denominate the shape that best corresponds to the outline of the leaf.
- the plants grew in close contact in an environment with controlled light and temperature conditions in which powdery mildew developed.
- the figure shows the seventh leaf from the apex of a plant regenerated from protoplast (left) and the plant edited in the S gene in homozygosis (right).
- the image highlights that the leaf of the plant on the left shows widespread growth and development of the fungus, while the plant on the right is characterised by rare and circumscribed areas of infection.
- Figure 6 shows the development of the hyphae of the fungus on leaves of a non-edited control plant regenerated from protoplasts (left) and of an edited plant (right) 8 days after artificial powdery mildew infection.
- Figure 7 shows in a column chart the difference in the number of fungal conidia per cm 2 of leaf of control plants and the edited plant about 20 days after the onset of natural infection. There is a significant decrease between the conidia counted on the control leaves and that on the leaves of the edited plant (asterisk). Statistics were done with t-test (Student's t-test; p ⁇ 0.01). The microscopic images illustrate the initial infectious process, while the photos of the leaves show the infectious state after about one month.
- Figure 8A and 8B show, respectively, the amino acid sequence (SEQ ID No.12) coded from the DNA sequence represented in Figure 2A (SEQ ID No. 10) and the amino acid sequence (SEQ ID No.13) coded from the DNA sequence represented in Figure 2B (SEQ ID No.11), while Figure 9 shows the alignment between the amino acid sequences of Figures 8A and 8B.
- the adenine insertion resulted in two stop codons (TAA and TGA, positions 413-415 bp and 422-424 bp) that were premature with the consequent change in the reading frame resulting in a very different amino acid sequence.
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Abstract
The invention describes a powdery-mildew resistant grapevine plant and a respective gene, in particular a VviMLO17 gene that can be obtained by genome editing using a gRNA/Cas9 complex inducing a point mutation. Described is a respective gRNA useful to create resistant mutations in grapevine cells or protoplasts, in particular the above mutation. The DNA sequence comprising the mutation reads TCCTATGAGGAT, while the gRNA has the following sequence: GGAGTTGATGGATCCCAT..
Description
200.2023 1 TITLE: POWDERY MILDEW-RESISTANT GRAPEVINE Applicant: EdiVite S.r.l., Quartiere San Mauro 30, 35020 San Pietro Viminario (PD), ITALY Inventors: Bertini, Edoardo; Zenoni, Sara; Tornielli, Giovanni Battista; D’Inca, Erica; Fasoli, Marianna; Polverari, Annalisa * * * * * TECHNICAL FIELD The invention relates to powdery mildew-resistant grapevines (Vitis vinifera), preferably produced by the transfection of protoplasts from grapevine plants and the subsequent regeneration of the relative edited grapevine plants from the transfected protoplasts. The described protocols particularly relate to the field of genomic editing to combat diseases, in particular powdery mildew, in plants while maintaining the identity and organoleptic profile of grapevine fruits. Vitis vinifera belongs to the group of European-Asian Vitis species and can be divided into two subspecies: Vitis vinifera sativa (i.e., the domestic vine) and Vitis vinifera sylvestris (i.e., the wild vine), the latter showing leaves with generally a very open petiolar sinus (Fregoni, 2013). BACKGROUND ART Maintaining the qualitative characteristics and the great variety of the ampelographic heritage typical of each area dedicated to viticulture, also giving the most valuable grape varieties resistance characteristics, is a demand that emerges from every part of the vine-growing sector and can be addressed by the most modern and rapid genetic improvement methods. The genome editing mediated by the CRISPR/Cas9 system has opened new perspectives and its application to the grapevine would make possible what is impossible for traditional breeding: obtaining a resistant clone of a traditional grapevine without changing its identity and the organoleptic profile of its fruits. From a biotechnological point of view, the application of genome editing for the production of a modified grapevine clone is not immediate and requires overcoming some technical obstacles. The mutation which is obtained by genome editing is in fact carried out by the CRISPR/Cas9 complex inside the cell, in which it can be inserted, in particular by eliminating its wall, if it is not to be inserted by means of stable genetic modification or bombardment methods.
200.2023 2 The wall removal starting from plant embryogenetic cells produces a protoplast, which must maintain the ability to regenerate the plant. Such an ability has been demonstrated in a limited number of scientific works and in particular for protoplasts derived from embryogenic material obtained from different tissues (Reustle et al., 1995; Zhu et al., 1997; Bertini et al., 2019). The possibility of introducing the CRISPR/Cas9 complex inside protoplast cells and the subsequent generation of the mutation at the site of interest have also been demonstrated in grapevines (Malnoy et al., 2016; Osakabe et al., 2018). However, to date only two regenerations of edited grapevine plants obtained from protoplasts to which the CRISPR/Cas9 system has been applied have been demonstrated (Scintilla et al.2021 and EP 4151084). Due to its economic importance, the vine has always been the subject of genetic improvement: over the years, numerous aspects of modern varieties have been improved, such as productivity, quality characteristics and resistance to biotic and abiotic adversities. The latter aspect has proved to be of great interest in recent years, as adversities such as pathogenic organisms, phytophagous insects and climatic changes are now creating production and quality losses that are extremely important from an economic point of view. In particular, two fungal-type diseases that originated in North America and were imported to Europe in the mid-1800s, namely powdery mildew (Erysiphe necator) and downy mildew (Plasmopara viticola), still today if left uncontrolled can cause huge production losses, thus encouraging wine-growers to use large quantities of phytosanitary products with consequent repercussions on the environment and human health. The biological cycle of Erysiphe necator starts with overwintering, a phase that can be passed in two ways: as a latent mycelium in the buds or as a cleistothecium. In the first case, the pathogen mainly localises in the hibernating buds, which will then give rise to the so-called “flagellar shoots” at budding. Symptoms can be observed on all green organs of the plant. In the case of infections on leaves it will be possible to observe small, circular, translucent chlorotic spots that later become covered with mycelium giving a whitish/powdery appearance to the affected tissues. The use of sulphur is described as a chemical treatment, while biological treatment also allows the use of antagonistic microorganisms such as Ampelomyces quisqualis. There is a continuous co-evolution between plant and pathogen both on a selective pressure to modify resistance genes, on the part of the plant, or effectors, on the part of the pathogen, and thus overcome the mechanisms evolved by either organism to defend themselves (Buchanan, et al., 2015). Considering this, it is possible to act in two ways to try to implement pathogen
200.2023 3 resistance with methods of genetic improvement: by introducing resistance genes (R genes) or by silencing susceptibility genes (S genes). The most suitable methodology for blocking the functionality of S genes and at the same time avoiding major changes in the genome structure of cultivated plants is undoubtedly genome editing, which, if carried out according to the DNA-free approach, makes it possible to obtain a mutation at a specific point in the target gene, inactivating it or modifying its function, without altering other sites in the host genome. However, it is necessary to consider that most of these genes have not yet been clearly studied and even their functionality within the plant genome is often not fully understood. (van Schie, et al.2014). The susceptibility genes that would seem to be most interesting belong to the MLO gene family (mildew resistance locus). A closer look at the structure and localisation of the proteins produced by the MLO genes suggests that they are localised on the cell membrane of plant cells and consist of seven transmembrane domains with associated intra- and extracellular loops. The terminal nitrogen of the protein is located in an extracellular position while the terminal carbon is located in an intracellular position (Devoto, et al., 1999). At the level of involvement in powdery mildew infection, MLO genes are thought to negatively regulate other genes associated with the trafficking of vesicles that transport the materials necessary for the attachment of callose papillae to the pathogen's point of penetration, thus favouring its infection (Pessina, et al., 2016). A gene expression analysis of the various genes of the VviMLO family in Vitis vinifera following infection by Erysiphe necator showed that three of them (VviMLO3; VviMLO4; VviMLO17) are overexpressed following infection, hypothesising their involvement in the process (Feechan, et al., 2008). In more recent work, performed by Pessina et al. in 2016 on the Brachetto cultivar, it was indeed proved that the silencing of several genes of the VviMLO family (VviMLO6; VviMLO7; VviMLO11; VviMLO13 according to the nomenclature proposed by Winterhagen et al., 2008 and corresponding to VviMLO13; VviMLO17; VviMLO3; VviMLO4 in Feechan et al., 2008) causes an increased resistance to Erysiphe necator attack, by regenerating plants in which the expression of these genes has been diminished and on which the phenotypical analyses showed reduced susceptibility to attack by the pathogen. In this case, however, a transgenic approach was used for gene silencing.
200.2023 4 However, there are still some aspects that make this system difficult to apply, especially in a plant such as the vine, which shows a strong recalcitrance to the process of in-vitro regeneration, a necessary step to reconstitute a complete edited organism, problems that have been overcome by the method described in the following and in EP 4151084. DISCLOSURE OF THE INVENTION In this general framework, research and development of new plant protection strategies as alternatives to the use of chemical plant protection products is therefore necessary to make the wine-growing system more sustainable and adapted to the demands of the market and legislators. The invention thus aims to individuate a mutation in the Erysiphe necator susceptibility genes of Vitis Vinifera that causes an enhanced plant resistance. Another object of the invention is to individuate suitable gRNAs that target specific MLO gene sites wherein their application to plant cells or protoplasts creates powdery mildew resistant mutants. Another object of the invention is not only to create and select a resistant mutation but to obtain a mutated plant that contemporarily has an ampelographic appearance that clearly distinguishes it from the non-resistant variant. In a first aspect of the invention, the object is achieved by an Erysiphe necator susceptibility gene comprising a resistance conferring mutation wherein the mutation causes a shift in the codon reading window by insertion of one or two nucleotides or by deletion of one or two nucleotides into a DNA sequence that has more than 70% identity, preferably more than 80% identity, more preferably more than 90% identity, and most preferably more than 95% identity with SEQ ID No.10 and wherein, preferably the insertion or deletion, in particular the insertion of one nucleotide, preferably adenine is present in the fourth exon. Resistance herein is intended as powdery mildew resistance. An insertion of a new nucleotide at the beginning of the nucleotide sequence causes severe consequences. An extra nucleotide changes the reading frame of the gene and this causes a profound change in the amino acid sequence. As a consequence, in the invention, the protein breaks off in the new frame due to the presence of a STOP codon. In a particularly preferred embodiment of the invention, the Erysiphe necator susceptibility gene comprising a resistance conferring mutation, comprises the DNA sequence according to SEQ ID No. 9. Advantageously, the susceptibility to Erysiphe necator is decreased in this
200.2023 5 mutated gene with respect to the corresponding Erysiphe necator susceptibility gene comprising the DNA sequence according to SEQ ID No.8. In a preferred embodiment of the invention, the Erysiphe necator susceptibility gene comprising a resistance conferring mutation is designated VviMLO17 (according to the nomenclature of Feechan, et al., 2008). In the whole description of the invention, the designation VviMLO17 refers to the nomenclature proposed by Feechan et al. (2008). In a further embodiment of the invention, the Erysiphe necator susceptibility gene comprising a resistance conferring mutation, comprises a DNA sequence that has more than 70% identity, preferably more than 80% identity, more preferably more than 90% identity, and most preferably more than 95% identity with SEQ ID No.11 and - comprises inside said DNA sequence an insertion, in particular an adenine, at position 202 bp with respect to a DNA sequence that has more than 70% identity, preferably more than 80% identity, more preferably more than 90% identity, and most preferably more than 95% identity with SEQ ID No.10, or - comprises the sequence according to SEQ ID No.9. Sequence identity as used herein is defined as the number of identical consecutive aligned nucleotides, or amino acids, over the full length of the present sequences divided by the number of nucleotides, or amino acids, of the full length of the present sequences and multiplied by 100%. For example, a sequence with 80% identity to a sequence with 539 nucleotides comprises over the total length of these 539 nucleotides, 431 or 432 identical aligned nucleotides, i.e., 430 or 431/539 x 100% = 80%. Advantageously, said DNA sequence encodes an amino acid sequence with more than 70% identity, preferably more than 80% identity, more preferably more than 90% identity, and most preferably more than 95% identity with SEQ ID No.13. In a preferred embodiment, said DNA sequence encodes the amino acid sequence according to SEQ ID No.13. The Erysiphe necator susceptibility gene comprising a resistance conferring mutation according to the invention advantageously comprises an insertion of the nucleotide adenine with respect to the wild-type variant. A second aspect of the invention refers to a protoplast or plant cell that comprises the Erysiphe necator susceptibility gene comprising a resistance conferring mutation according to the invention. Such a protoplast or plant cell can be used for regenerating a respective plant.
200.2023 6 A third aspect of the invention relates to a powdery mildew resistant plant comprising in its genome the Erysiphe necator susceptibility gene comprising a resistance conferring mutation according to the invention. A plant having said modification (insertion) exhibits a reduction in powdery mildew disease severity compared to a plant lacking this modification in the respective gene. Preferably, the powdery mildew resistant plant according to the invention is a Vitis vinifera, in a preferred embodiment of the Chardonnay type, for example its clone 76. In a particularly preferred embodiment of the invention, the adult leaves of the powdery mildew resistant plant show the following ampelographic characteristics: - OIV 067 is 5; - OIV 079 is 1; - OIV 094 is 1; and - preferably OIV 080 is 2, wherein OIV and the scores used are defined by the guidelines of the International Organization of Vine and Wine of 2021. In alternative, OIV = 5 can be described as kidney-shaped, OIV 079 = 1 can be described as very open, OIV 94 = 1 indicates the absence of lateral sinuses and OIV 080 = 2 indicates a brace-shaped base of the petiolar sinus. A fourth aspect of the invention refers to a method for providing an Erysiphe necator susceptibility gene comprising a resistance conferring mutation, a powdery mildew resistant protoplast, plant cell, tissue or grapevine plant, comprising the following step: - mutating a gene designated VviMLO17 by insertion of a nucleotide, in particular an adenine, in a gene sequence according to SEQ ID 8 in the position between the sixth and seventh nucleotide. In an embodiment of the invention, an Erysiphe necator susceptibility gene comprising a resistance conferring mutation, a powdery mildew resistant protoplast, plant cell, tissue or grapevine plant is obtained by inserting a nucleotide, in particular an adenine, between the positions 201 bp and 202 bp in a DNA sequence with more than 70% identity, preferably more than 80% identity, more preferably more than 90% identity, and most preferably more than 95% identity with SEQ ID No.10. In a preferred embodiment of this method, the insertion is obtained by CRISPR/Cas9 genome editing using as gRNA a gRNA with the sequence according to SEQ ID No.7. This permits a precise cut and mutation.
200.2023 7 Preferably, the mutation is obtained in protoplasts. The protoplasts than can be regenerated to form the relative plant. The method can comprise further steps as described herein. In the invention, in a preferred embodiment, DNA-free genomic editing by transfecting protoplasts with CRISPR/Cas9 ribonucleoparticles was used for the functional inactivation of the VviMLO17 gene, which the inventors showed to be a susceptibility gene for the powdery mildew disease. It’s the first time that it was demonstrated that VviMLO17 works alone, and therefore the inventors are demonstrating for the first time that VviMLO17 it is indeed a true susceptibility gene. The practically complete silencing achievable introducing a respective mutation into VviMLO17 according to the invention, could not be expected from the results presented in EP 3320098. Yet another aspect of the invention, refers to a seed, fruit, or plant part of a grapevine plant comprising the gene according to the invention. Another aspect of the inventions refers to a method for the selection of mildew-resistant grapevine plants comprising the following steps: - selecting one or more powdery mildew-resistant mutants; - selecting among the powdery mildew-resistant mutants those that show ampelographic differences with respect to the wild-type plant. In particular, these ampelographic differences refer to the leave characteristics of the plant. This selection permits to have plants that can be easily identified. In fact, a further aspect of the invention refers to a method for identifying a powdery mildew resistant plant, in particular a grapevine plant, comprising the step of detecting the Erysiphe necator susceptibility gene comprising a resistance conferring mutation according to the invention and/or determining the ampelographic characteristics as defined in the invention. A last aspect of the invention concerns a kit for the preparation of a genome edited plant comprising: - a gRNA with the sequence according to SEQ ID No: 7. Preferably, the kit further comprises Cas9. The genome editing according to the invention permitted to obtain a mutation that heavily influenced morphological characteristics of the plant itself, to such an extent that it might even be possible to define a new cultivar while maintaining the other characteristics, primarily the organoleptic ones, of the wine by satisfying the traditionalist wine consumer.
200.2023 8 This particular modification surprisingly showed in an ampelographic analyses of certain morphological characters of the green organs the presence of significant differences between the leaf issued by the plant in which the genome editing was correctly carried out and other plants regenerated from embryogenic calli or from non-transfected protoplasts. These phenotype differences can easily be individuated by the person skilled in the art and help to individuate without genetic analysis for example counterfeited plants. The method for producing edited grapevine plants from protoplasts developed by the authors and described in EP 4151084 that significantly reduced the stress for the plant elements during production helped to obtain the targeted insertion point mutation avoiding further the formation of undesired other point mutations and subsequent soma clonal variations. The gRNA according to the invention was indeed no promising starting point, but led to the introduction of a point mutation in both alleles as a result of the gRNA/Cas9 cut and not point mutations as casual products of the in-vitro cultivation process. In a preferred embodiment of the invention, the transfected plants are obtained by the following steps: (I) preparation of a Cas9:gRNA complex with a molar ratio of 1:3 - 3: 1, in particular with a weight ratio between 1: 1 and 3:1, and incubating the ribonucleoprotein complex in the dark; (II) addition of the Cas9:gRNA complex prepared in the previous step to the protoplasts; (III) addition of a PEG 3000 - PEG 5000 solution, preferably PEG 4000, to the mixture obtained in step (II) and incubation, preferably at room temperature, in the dark; (IV) addition of a saline solution containing MES, in particular a W5 solution, stirring and incubation, preferably at room temperature, and preferably in the dark; (V) at least once repetition of step (IV), in particular with the doubled volume of saline solution; (VI) centrifugation of the transfected protoplasts washed in the previous steps preferably for 2 - 4 minutes at 80 - 120×g more preferably 3 min at 100×g and removal of the supernatant; (VII) proceed with the cultivation of the protoplasts without further incubation with incubation periods exceeding the duration of 10 min, in particular without any incubation. The above protocol allows a delicate transfection of the protoplasts in order to hardly stress them and make them suitable for the subsequent plant cultivation. gRNA is intended as any kind of guide RNA which functions as a guide for the Cas9 enzyme which targets RNA or DNA, with which it forms complexes. One or more component gRNAs, such as the cr/tracrRNA system, are conceivable. If incubations are to be performed in step (VII), these
200.2023 9 preferably occur without the addition of further washing solutions. Very advantageously, no further incubation occurs in step (VII), greatly reducing the stress for the protoplasts. The various steps performed in the dark further reduce the stress for the protoplasts, an effect which makes them more "available" to plant cultivation. In a preferred embodiment of the invention, the final volume of the mixture of step (I) is 15-25 µL and/or the incubation time in step (I) is 10 min. Higher volumes should preferably be avoided. Preferably, the protoplasts for the addition of the Cas9-gRNA complex were re-suspended in a concentration of 2 × 105 protoplasts in 200 µL of a MMG solution and in step (III) 200 - 225 µL, preferably 200 µL of PEG 3000 - PEG 5000 solution, preferably PEG 4000, preferably at 40% by weight by volume, are added. The above concentration is to be understood as concentration and can thus be expressed in concentrations referring to other volumes of solution (for example: 1 × 105 protoplasts in 100 µL of a MMG solution), correspondingly varies the volume of added PEG solution. PEG 4000 gave the best results, even if the protocol works equally with PEGs of different molecular weight. Dark conditions during PEG-treatment in DNA-free genome editing protocols in Brassica oleracea have been described by Park et al in 2019. Advantageously, under these particular conditions, in step (IV) a volume of saline solution containing MES is added, in particular a W5 solution, which is twice the volume of the MMG solution and for which the incubation time is about 8-12 min, in particular 10 min. Preferably, in step (VII) a concentration of 1×105 ppt/mL on petri is used. Obtaining the protoplasts themselves allows the application of different methods also known in the state of the art. Different sources of cells are conceivable, such as for example also floral stamens. The flower organ that gives the best results for inducing the proliferation of embryogenic calli that can then give crops that can be maintained and propagated over time are the stamens. The inventors found that for the induction of embryogenic calli of the Chardonnay clone 76, the most suitable substrate is MSII medium (Dhekney, et al., 2009): MS macronutrients, MS micronutrients, MS vitamins, 5,0 µM 6-BAP, 2,5 µM 2,4 D; 2,5 µM NOA; 0,1 g/L inositol; 2% sucrose; 7 g/L Agar-TC at a pH of 6,0. Preferably, said protoplasts can be obtained from the following steps:
200.2023 10 (0-1) obtaining embryogenic calli from apical leaves of plants grown in vitro; (0-2) proliferation of embryogenic calli and regeneration of somatic embryos; (0-3) from embryos, possibly transgenic embryos, induction of embryogenic callus and isolation of protoplasts. In case of a Chardonnay variety, it has been shown that a modified procedure for obtaining protoplasts is advantageous: (0-1) obtaining embryogenic calli from flower organs; (0-2) proliferation of embryogenic calli; (0-3) isolation of protoplasts from embryogenic calli. The possibility of obtaining plants from transfected protoplasts can be further improved by intervening on the steps of the method which relate to the preparation of protoplasts for the cultivation of seedlings. In this regard, advantageously, the following preparatory steps are added for regenerating grapevine plants from the transfected protoplasts: (VIII) a culture medium, preferably of the Nitsch type, is added to the transfected protoplasts, wherein the liquefied medium is preferably added at a temperature above 35°C and below 48°C; (IX) the same volume of culture medium, preferably of the Nitsch type, in the liquid state is added to the culture medium after solidification; (X) incubation of the protoplasts, preferably at 27-28°C, in the dark until regeneration of embryos at the cotyledonary stage; (XI) germination of the embryos and subsequent development of the seedlings. The concentrations and quantities applied play a significant role. Preferably, in step (VIII) 2 mL of culture medium is added to 800-µL of the protoplast solution and the medium is separated into two halves, after solidification the same amount of culture medium is added as a reserve, and in step (VIII) and (IX) the culture medium is preferably of the Nitsch type supplemented with 2 mg/L 1-naphthaleneacetic acid (NAA), 0.5 mg/L 6-benzylaminopurine (6-BAP), 0.3 M glucose, 0.09 M sucrose and 2 g/L gellan gum (pH 5,7) wherein in step (IX) the medium was supplemented with 0.3% activated carbon or similar, e.g., glutathione; where during step (X) the liquid medium was replaced every 10-20 days, preferably every 12-18 days with fresh medium as defined above but without glucose, after 3-4 months of culture, the somatic embryos at the cotyledonary stage derived from protoplasts, were transferred to a solid preferably of the Nitsch type supplemented with 30 g/L sucrose and 2 g/L gellan gum (pH 5,7) and kept in the dark for 3-5 weeks, preferably 4-5 weeks to allow complete germination. The
200.2023 11 indication of the amount of medium and of the protoplast solution is not to be only understood as an absolute value, but more a ratio that is maintained: 2 mL medium/800-µL protoplast solution is equivalent for example to 1 mL medium/400 µL protoplast solution. Embryogenic calli for certain varieties can be obtained from young apical leaves of plants grown in vitro, following for example the protocol reported in the work of Dhekney et al. (2009). After proliferation of the embryogenic callus, somatic embryos can be regenerated. Those skilled in the art know other manners for producing somatic embryos. In the case of Chardonnay, for example, embryogenic calli can be obtained from flower organs, as mentioned above. One of the best sprouting medium proved to be medium C2D5B:C2D macro; C2D micro; C2D vitamins; 5 mL/L 6-BAP; 30 g/L sucrose; 7 g/L Agar-TC at a pH of 5.8. The sprouting phase is the most critical as it shows a much lower yield than the germination phase. The features described for one aspect of the invention can be transferred mutatis mutandis to any other aspect of the invention. Summing up, it can be seen that the invention achieves the intended objects, and in particular provides a gene and corresponding edited plant with powdery-mildew resistance, provides the gRNA necessary for its production and further gives the possibility to recognize the edited plant without genetic analysis simply controlling some ampelographic characteristics. The gene according to the invention can also be obtained independently of the steps concerning the application of the CRISPR/Cas9 system by replacing it with other systems such as ZNF (zinc finger proteins) and TALEN (transcription activator-like effector nucleases) to obtain the specified mutation or by selecting it among naturally occurring mutations or mutations obtained by biological processes. Said objects and advantages will be further highlighted during the description of preferred embodiment examples of the invention given by way of example and not of limitation. Variant embodiments of the invention are the object of the dependent claims. The description of the preferred embodiment examples according to the invention is given by way of non- limiting example, in particular it is possible to replace the described features with equivalent features. DESCRIPTION OF PREFERRED EMBODIMENT EXAMPLES
200.2023 12 Figure 1: shows above the target site of a Chardonnay VviMLO17 gene (wild-type) and below the Cas9/gRNA induced mutation in edited protoplasts. Figure 2A: shows the sequencing results of a portion of the VviMLO17 gene within which the gRNA target site is located. Figure 2B: shows the sequencing results of a portion of the VviMLO17 gene with the insertion mutation with respect to Fig.2A. Figure 3: shows the alignment of the sequences of Figures 2A and 2B. Figure 4: shows the photos of a non-edited control plant regenerated from protoplasts (left) and of an edited plant (right) with the mutation according to the invention followed by the respective analysis of four OIV characteristics. Figure 5: shows for the same plants as illustrated in Figure 4 the results of powdery mildew infections. Figure 6: shows microscope images (10X) of leaves of non-edited control plant regenerated from protoplasts (left) and of an edited plant (right) 8 days after artificial powdery mildew infection. Figure 7: shows in a columnar diagram the difference in the number of fungal conidia per cm2 of leaf of control plants and the edited plant after natural infection. Figure 8A: shows the amino acid sequence (SEQ ID No.12) coded from the DNA sequence represented in Figure 2A (SEQ ID No.10). Figure 8B: shows the amino acid sequence (SEQ ID No.13) coded from the DNA sequence represented in Figure 2B (SEQ ID No.11). Figure 9: shows the alignment between the amino acid sequences of Figures 8A and 8B. For the isolation and subsequent cultivation of the transfected protoplasts, the protocol reported in Bertini et al. (2019) can be used, which was improved in some points by the inventors. The modified protocol is applicable to any type of protoplast, whether modified with the CRISPR/Cas9 system or with other systems known in the state of the art, such as ZFN (Zinc Finger Nucleases), TALEN (Transcription activator-like effector nucleases) systems, etc. To analyse the sequence of any vine gene, it is possible to consult the sequence from the reference genome, resulting from the sequencing of a genotype called PN40024; which was obtained following self-fertilisation of the pinot noir variety until approaching almost complete homozygosity (93%) (The French & Italian Public Consortium for Grapevine Genome
200.2023 13 Characterization, 2007). Consequently, before designing the guide RNAs and applying the CRISPR/Cas9 system, it is necessary to sequence the gene taken into consideration directly from the genotype of interest (in the example presented here: Chardonnay clone 76), and then, on the basis of the sequence obtained, proceed with the design of the guide RNAs. To correctly amplify the gene, the primers shown in Table 1 were used. Table 1
After purification by electrophoresis, sequencing was done according to the Sanger method using the primers indicated in table 2: Table 2
After having obtained the correct sequence of the gene to be targeted, it is possible to design the guide RNA sequence. To proceed with the design, it is preferable to consider the sequence of the exon to be targeted, the genome of the organism to which the gene to be targeted belongs and the type of nuclease to be used to apply the cut, for example the Cas9 enzyme derived from Streptococcus pyogenes. The market offers a large variety of software packages to design gRNA proposals, but the difficulty remains in selecting the right gRNA among those proposed. The GeneArtTM Precision gRNA Synthesis Kit (Invitrogen, catalogue A29377) is used for the synthesis of guide RNA. First a pair of partially overlapping oligonucleotides (target F1 primer target R1 primer) were designed to contain the sequence of the target DNA fragment. The oligonucleotides useful for the synthesis of the gRNA targeting the VviMLO17 gene are represented in table 3. Table 3
200.2023 14
The gRNA then designed corresponds to GGAGTTGATGGATCCCAT (SEQ ID No: 7), and the corresponding PAM sequence is AGG. The oligonucleotides are purified from gRNA/DNA. To verify if the synthesized gRNA are functional, an in vitro cut of the VviMLO17 gene is done, directly mixing the RNP (ribonucleoprotein) with the amplicon of the sequence of the target gene. In particular, the primers used only delimit the first 1959 base pairs (bp) and not the entire gene. This was motivated by the fact that for the design of guide RNAs, the inventors decided to focus on the first exons, as in this way it is more likely that a mutation at these sites will create a non- functional protein. Within the sequence recognised by the selected gRNA, it is possible to observe a SNP (single- nucleotide polymorphism), which theoretically could generate recognition problems. Despite these expected difficulties, the inventors decided to proceed with this gRNA. Figure 1 shows that the gRNA/Cas9 complex induced an adenine insertion that occurred three nucleotides upstream of the sequence PAM (highlighted by a square). In this case the chromatogram, not presenting overlapping peaks, shows that the mutation occurs on both alleles. The patent application EP 3320098 describes the importance of the VviMLO17 gene in the context of powdery mildew resistance and provides mutants that seem to silence this gene to some extent, but almost casually targeting other genes, since they did not obtain a silenced gene by directly targeting the VviMLO17 gene. Targeted silencing of other MLO genes (particularly MLO13) was not specific and also silenced the MLO07 gene (corresponding to VviMLO17). The inventors of the present invention were able to design a gRNA directly targeting VviMLO17, and have chosen it despite expected technical difficulties. The authors of EP 3320 098 used the name VvMLO07 according to Winterhagen, that corresponds to VviMLO17 according to Feechan used herein. In the invention described in EP 3320098, the VviMLO17 gene (corresponding to VvMLO07 in EP 3 320 098), contrarily to the gene of the present invention, was not mutated (non- functioning protein), but simply silenced, with the RNA interference system. Moreover, the
200.2023 15 silencing does not appear to be complete, as the expression is about half that of non-transgenic plants. The transfection of the protoplasts is performed with Cas9-gRNA ribonucleotides (RNPs). The scientific literature knows several protocols for performing the transfection of protoplasts, such as those described by Woo et al. (2015), optimized for Arabidopsis, rice, lettuce and tobacco, or Osakabe et al. (2018), optimized for apples and grapevines. Specifically, by grapevine the authors do not describe the regeneration of plants from protoplasts transformed with CRISPR/Cas9. With the protocol herein described, the regeneration efficiency of grapevine protoplasts has been greatly increased. In a first step, the Cas9:gRNA complex was prepared with a ratio of 1:1 - 3:1 (w/v) in a final volume of 20-25 µL and the ribonucleoprotein complex was incubated at room temperature for 10 minutes in the dark.2 × 105 protoplasts were used for the transfection, resuspended in 200 µL MMG solution. The MMG solution preferably comprises 0,5 M mannitol, 4 mM MES (2- N-morpholino ethanesulfonic acid) and 15 mM MgCl2 in distilled H2O. The gRNA, prepared in the previous step, are added to the protoplasts. The most favourable ratio of Cas9 : gRNA in terms of yield was 1:1, in particular using a ratio of 60 µg : 60 µg. 200 µL 40% (w/v) PEG 4000 solution was then added to the protoplast-RNP mixture. The mixing occurred by pipetting gently, for example with tips with the top cut to avoid breaking the cells, followed by incubation at room temperature for 20 minutes in the dark. In a first wash 400 µL W5 solution was added, mixed and then incubated at room temperature for a further 10 minutes in the dark. A W5 solution comprises 5 mM glucose, 2 mM MES (pH 5.7), 154 mM NaCl, 125 mM CaCl2, and 5 mM KCl in distilled H2O. Advantageously, the solution is prepared fresh before use. In a second wash, 800 µL W5 solution was added, mixed and then incubated again for 10 minutes at room temperature in the dark. At the end of the washings, the transfected protoplasts were centrifuged for 3 minutes at 100×g and the supernatant was removed. To further reduce the stress, after centrifugation, the rest position was reached by inertia and not abruptly stopping the centrifugal machine. Proceeding immediately with the cultivation of the protoplasts, for example at a concentration of 1×105 ppt/mL, without an incubation, in particular without an overnight incubation, a higher regeneration efficiency was observed.
200.2023 16 For the subsequent cultivation of the protoplasts and the regeneration of embryos, the protocol described in Bertini et al. (2019) was used in modified form. In particular, the following modifications have been identified which can generally be applied to the regeneration of any type of plant from any type of protoplast, in particular Vitis vinifera L. Particular attention is paid to the amount of culture medium.2 mL of culture medium are added to the transfected protoplasts, cultivated by the disc-culture method. To achieve the maximum homogeneity of the protoplasts in the solid culture medium, the liquefied medium is added at a temperature above 35°C and below 48°C. The 2 mL are divided into two petri dishes, placing a 1 mL culture drop in each, adding the same volume of culture medium in the liquid state in each petri after solidification. By putting a single drop, the cells have greater contact with the liquid nutrient medium. The plates are then incubated at 28°C in the dark until the regeneration of cotyledonary stage embryos. For the subsequent regeneration steps of the germinated embryos until the development of the entire plants, the protocol described by Bertini et al. (2019) was followed, but here other protocols known from the state of art are also applicable since they are even less delicate and critical steps. The entire method, applied here to Chardonnay, and the application of the gRNA according to the invention, in particular the transfection of protoplasts, is transferable to other types of grapevines or plants. The biological material of plant origin used is a table grapevine of the species Vitis vinifera subsp. vinifera with the name Chardonnay widely present and available on the markets, since it is one of the most important vine grapes, number 2455 in the Vitis International Variety Catalogue. In the present case, the plants from which the biological material was taken were cultivated in Italy. Figure 1 illustrates above the result of the sequencing of the target site of a Chardonnay VviMLO17 gene (wild-type) and below the Cas9/gRNA induced mutation in edited protoplasts. The sequencing of the gene at the gRNA target site revealed the insertion of a 3-base-pair adenine, confirming the occurrence of genome editing. The adenine insertion in the edited sequence represented (CCTATGAGGATCCA) corresponds to SEQ ID No. 9, while the represented control sequence (CCTATGGGATCCATCA) corresponds to SEQ ID No.8. The
200.2023 17 mutation is present in both alleles. The square indicates the PAM sequence, the arrow the mutation site. Figures 2A and 2B show a greater portion of the VviMLO17 gene within which the gRNA target site is located. The portion of the gene contains a part of the third exon, the entire sequence of the fourth and fifth exons and the two introns between them. Figure 2A refers to the non-edited gene portion which corresponds to SEQ ID No: 10, while Figure 2B illustrates the gene portion of the edited plant corresponding to SEQ ID No: 11. The arrow indicates the mutation. The sequences SEQ ID No. 10 and 11 represent part of the third exon, the fourth and fifth complete exons with the two introns between the third and fourth exon and the other between the fourth and fifth exon; in the fourth exon is the mutation. To better highlight the nature and location of the mutation in the gene, Figure 3 shows the alignment of the two gene portions represented in Figures 2A and 2B. The consensus sequence corresponds exactly to the sequence of the wild-type plant (SEQ ID No: 10). The mutation is an adenine insertion in position 202 bp. Figure 4 shows the photos of a non-edited control plant regenerated from protoplasts (left) and of an edited plant (right) followed by the respective analysis of four OIV characteristics. To perform the ampelographic analyses, the inventors used the OIV “Descriptive character code for vine varieties and Vitis species”, i.e., a guide produced by the International Organisation of Vine and Vine that provides a large number of morphological descriptors that can be used to describe varieties of the genus Vitis and proceed with their recognition on the basis of the observable phenotype (OIV, 2021). The guide provides numerical scores corresponding to the level of character expression and each of these is accompanied by a picture describing it and reference cultivars, i.e. cultivars that clearly express a certain level of expression for that character. The plants here described are plants grown in a controlled environment and have one or at most two shoots of small size and growth. Differences with respect to the wild type in terms of leaves have been observed for: - OIV 067: Shape of the adult leaf blade The shape of the adult or mature leaf is wedge-shaped in plants regenerated from callus and protoplast, whereas in the edited plant the shape changes and becomes kidney- shaped.
200.2023 18 - OIV 079: Degree of opening/overlapping of the edges of the petiolar sinus of the adult leaf The degree of openness of the petiolar sinus would clearly appear to be a distinguishing character of the genomically edited plant on VviMLO17, since, in this one, the petiolar sinus appears to be very open when compared to the unedited plant. - OIV 080: Shape of the base of the petiolar sinus of the adult leaf The shape of the petiolar sinus base also changes, as in callus- and protoplast- regenerated plants, a U-shaped opening can be seen, whereas in the edited plant it is more like a brace. - OIV 094: Depth of the upper lateral sinuses of the adult leaf Again with regard to the upper lateral sinuses, their degree of depth is clearly more important in plants regenerated from callus and protoplast than in plants edited on the VviMLO17 gene, where sometimes very shallow sinuses are found generating even indecision as to the level of expression to be attributed to the OIV 067 character. The mature leaf is more similar to Vitis vinifera silvestris grapevine types than to Vitis vinifera sativa. Table 4 indicates the scores for these four OIV characters: Table 4
Figure 4 relating to the ampelographic characters uses an “a” to designate elements belonging to the wild-type plant, while “b” designates the edited plant. Same numerals refer to the same elements in the compared plants.10a and 10b, respectively, denominate the leaf itself.12a and 12b, respectively, denominate the shape that best corresponds to the outline of the leaf. In the case of the wild-type it is wedge-shaped, in the case of the edited plant kidney-shaped.14a and 14b, respectively, indicate the aperture of the petiolar sinus, while also 16a and 16b, respectively, indicate again the petiolar sinus, but refer to its basis, that has a specific shape in
200.2023 19 its base zone Za or Zb, respectively, on the left side a U-shape, on the right side a brace-shape. Numerals 20a and 20b show the lateral sinuses, the depth of which is analysed, the right leaf has no clear lateral sinuses, they are absent or at least very shallow. These results seem to provide clues that this gene could also control the shape of the leaf and these morphological changes perhaps ensure a lower susceptibility during infections by Erysiphe Necator. The CPVO (Community Plant Variety Office) and the UPOV (International Union for the Protection of New Varieties of Plants) offer similar classifications in their technical protocols for distinctness, uniformity and stability tests. The above OIV classification corresponds as indicated in table 5. Table 5
Figure 5 shows for the same plants as illustrated in Figure 4 the results of powdery mildew infections, in particular the effect of natural powdery mildew infection approximately 40 days after the onset of infection on protoplast regenerated plants and edited plants in homozygosity. The plants grew in close contact in an environment with controlled light and temperature conditions in which powdery mildew developed. The figure shows the seventh leaf from the apex of a plant regenerated from protoplast (left) and the plant edited in the S gene in homozygosis (right). The image highlights that the leaf of the plant on the left shows widespread growth and development of the fungus, while the plant on the right is characterised by rare and circumscribed areas of infection. To better monitor the infection process, microscopic studies have been done and illustrated in Figure 6, that shows the development of the hyphae of the fungus on leaves of a non-edited control plant regenerated from protoplasts (left) and of an edited plant (right) 8 days after artificial powdery mildew infection. The hyphae are stained with aniline blue. A clear reduction
200.2023 20 can be seen in the extension of mycelial growth and in conidiation on the edited plant, which has been quantified in the diagram of Figure 7. Figure 7 shows in a column chart the difference in the number of fungal conidia per cm2 of leaf of control plants and the edited plant about 20 days after the onset of natural infection. There is a significant decrease between the conidia counted on the control leaves and that on the leaves of the edited plant (asterisk). Statistics were done with t-test (Student's t-test; p < 0.01). The microscopic images illustrate the initial infectious process, while the photos of the leaves show the infectious state after about one month. Figure 8A and 8B show, respectively, the amino acid sequence (SEQ ID No.12) coded from the DNA sequence represented in Figure 2A (SEQ ID No. 10) and the amino acid sequence (SEQ ID No.13) coded from the DNA sequence represented in Figure 2B (SEQ ID No.11), while Figure 9 shows the alignment between the amino acid sequences of Figures 8A and 8B. The adenine insertion resulted in two stop codons (TAA and TGA, positions 413-415 bp and 422-424 bp) that were premature with the consequent change in the reading frame resulting in a very different amino acid sequence. During implementation, further embodiment modifications or variants of the gene, plants, kit and methods not described herein can be introduced. If such modifications or such variants should fall within the scope of the following claims, they should all be considered protected under the present patent. REFERENCES Bertini, Edoardo; Tornielli, Giovanni Battista; Pezzotti, Mario; Zenoni, Sara; Regeneration of plants from embryogenic callus-derived protoplasts of Garganega and Sangiovese grapevine (Vitis vinifera L.) cultivars, Plant Cell, Tissue and Organ Culture (2019) 138: 239-246 (doi: 10.1007/s 11240-019-01619-1). Buchanan, Bob B.; Gruissem, Wilhelm; Jones, Russell L.; Biochemistry and Molecular Biology of Plants, 2° edition; John Wiley & Sons (2015). Devoto, Alessandra; Piffanelli, Pietro; Nilsson, IngMarie; Wallin, Erik; Panstruga, Ralph; Heijne, Gunnar von; Schulze-Lefert, Paul. Topology, Subcellular Localization, and Sequence Diversity of the Mlo Family in Plants. The journal of biological chemistry; 274; 49; (1999); 34993–35004.
200.2023 21 Dhekney, Sadanand A.; Li, Zhijian T.; Compton, Michael E.; Gray, Dennis J.; Optimizing Initiation and Maintenance of Vitis Embryogenic Cultures, HortScience, (2009) 44(5): 1400- 1406. Dhekney, Sadanand A.; Li, Zhijian T.; Zimmerman, Thomas W.; J. Gray, Dennis; Factors Influencing Genetic Transformation and Plant Regeneration of Vitis. Am. J. Enol. Vitic.; 60; 3; (2009). Feechan Angela; Jermakow, Angelica M.; Torregrosa, Laurent; Panstruga, Ralph; Dry, Ian B.; Identification of grapevine MLO gene candidates involved in susceptibility to powdery mildew, Functional Plant Biology, (2008) 35: 1255-1266. Fregoni; Mario, Viticoltura di qualità.3° edizione. Tecniche Nuove: Milano (2013). Malnoy, Mickael; Viola, Roberto; Jung, Min-Hee; Koo, Ok-Jae; Kim, Seokjoong; Kim, Jin- Soo; Velasco, Riccardo; Kanchiswamy, Chidananda Nagamangala; DNA-Free Genetically Edited Grapevine and Apple Protoplast Using CRISPR/Cas9 Ribonucleoproteins, frontiers in Plant Science, (2016) 7:articolo 1904 (doi: 10.3389/fpls.2016.01904 ). OIV-International organization of vine and wine.2° edizione del codice di caratteri descrittivo OIV per le varietà di vite e specie di vitis. Documento tecnico (2021). Osakabe, Yuriko; Liang, Zhenchang; Ren, Chong; Nishitani, Chikako; Osakabe, Keishi; Wada, Masato; Komori, Sadao; Malnoy, Mickael; Velasco, Riccardo; Ploi, Michele; Jung, Min-Hee; Koo, Ok-Jae; Viola, Roberto; Kanchiswamy, Chidananda Nagamangala; CRISPR- Cas9-mediated genome editing in apple and grapevine, nature protocols, (2019) 13: 2844-2863 (doi: 10.1038/s41596-018-0067-9. ). Park Sung-Chul; Park, Suhyun; Jeong, Yu Jeong; Lee, Saet Buyl; Pyun, Jang Won; Kim, Soyoung; Kim, Tae Hee; Kim, Suk Weon; Jeong, Jae Cheol; Kim, Cha Young; DNA-free mutagenesis of GIGANTEA in Brassica oleracea var. capitata using CRISPR/Cas9 ribonucleoprotein complexes, Plant Biotechnology Reports, (2019) 13: 483-489. Pessina, Stefano; Lenzi, Luisa; Perazzolli, Michele; Campa, Manuela; Costa, Lorenza Dalla; Urso, Simona; Valè, Giampiero; Salamini, Francesco; Velasco, Riccardo; Malnoy, Mickael. Knockdown of MLO genes reduces susceptibility to powdery mildew in grapevine. Horticulture Research; 3, (2016); 16016. Reustle, Götz; Harst, Margit; Alleweldt, Gerhardt; Plant regeneration of grapevine (Vitis sp.) protoplasts isolated from embryogenic tissue, Plant Cell Reports (1995) 15:238-241 . Scintilla, Simone; Salvagnin, Umberto; Giacomelli, Lisa; Zeilmaker, Tieme; Malnoy, Mickael
200.2023 22 A.; van der Voort, Jeroen Rouppe; Moser, Claudio; Regeneration of Plants from DNA-free Edited Grapevine Protoplasts, bioRxiv preprint (2021) (doi: 10.1101/2021.07.16.452503 ). Van Schie, Chris C.N.; Takken, Frank L.W.; Susceptibility Genes 101: How to Be a Good Host. Annu. Rev. Phytopathol; 52; (2014); 551-581. Winterhagen, Patrick; Howard, Susanne F; Qui, Wenping; Kovács Laszlo G.; Transcriptional up- regulation of grapevine MLO genes in response to powdery mildew infection. American Journal of Enology and Viticulture (2008) 59 (2): 159–168 (doi:10.5344/ajev.2008.59.2.159). Woo, Je Wook; Kim, Jungeun; Kwon, Soon Il; Corvalán, Claudia; Cho, Seung Woo; Kim, Hyeran; Kim, Sang-Gyu; Kim, Sang-Tae; Choe, Sunghwa; Kim, Jin-Soo; DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins, Nature biotechnology, (2015) 33(11): 1162-1164 (doi: 10.1038/nbt3389). Zhu, Yan-Ming; Hoshino, Yoichiro; Nakano, Masaru; Takahashi, Eikichi; Mii, Masahiro; Highly efficient system of plant regeneration from protoplast of grapevine (Vitis vinifera L.) through somatic embryogenesis by using embryogenic callus culture and activated charcoal, Plant Science 123 (1997) 151-157. [0061] In the sequence listing SEQ. 1 and 2 report target DNAs for GFP guide RNA, while SEQ.7 reports a target DNA for MLO17 guide RNA.SEQ.3, 5 and 8 report Vitis vinifera DNA and SEQ.4, 6 and 8 report CRISPR/Cas9 edited Vitis vinifera DNA.
Claims
200.2023 23 CLAIMS 1) An Erysiphe necator susceptibility gene comprising a resistance conferring mutation, comprising the DNA sequence according to SEQ ID No.9. 2) The Erysiphe necator susceptibility gene comprising a resistance conferring mutation according to claim 2 characterized in that the gene is designated VviMLO17. 3) An Erysiphe necator susceptibility gene comprising a resistance conferring mutation according to claim 1 or 2, characterized in that the Erysiphe necator resistance conferring gene, comprises a DNA sequence that has more than 70% identity, preferably more than 80% identity, more preferably more than 90% identity, and most preferably more than 95% identity with SEQ ID No.11 and - comprises inside said DNA sequence an insertion, in particular an adenine, at position 202 bp with respect to a DNA sequence that has more than 70% identity, preferably more than 80% identity, more preferably more than 90% identity, and most preferably more than 95% identity with SEQ ID No.10, or - comprises the sequence according to SEQ ID No.9. 4) An Erysiphe necator susceptibility gene, in particular VviMLO17, comprising a resistance conferring mutation wherein the mutation causes a shift in the codon reading window by insertion of one or two nucleotides or by deletion of one or two nucleotides into a DNA sequence that has more than 70% identity, preferably more than 80% identity, more preferably more than 90% identity, and most preferably more than 95% identity with SEQ ID No. 10 and wherein, preferably the insertion or deletion, in particular the insertion of one nucleotide, preferably adenine is present in the fourth exon. 5) A protoplast or plant cell that comprises the Erysiphe necator resistance conferring gene according to anyone of claims 1 – 4.
24 6) A powdery mildew resistant plant comprising in its genome the gene according to anyone of claims 1 – 4. 7) A powdery mildew resistant plant according to claim 6 characterized in that said plant is a Vitis vinifera plant, preferably of the Chardonnay type. 8) A powdery mildew resistant plant according to claim 7, characterized in that the adult leaves of the plant show the following ampelographic characteristics: - OIV 067 is 5; - OIV 079 is 1; - OIV 094 is 1; and preferably OIV 080 is 2, wherein OIV and the scores used are defined by the guidelines of the International Organization of Vine and Wine of 2021. 9) A method for providing an Erysiphe necator susceptibility gene comprising a resistance conferring mutation, a powdery mildew resistant protoplast, plant cell, tissue or grapevine plant, comprising the following steps: - mutating a gene designated VvMLO17 by insertion of an adenine nucleotide in a gene sequence according to SEQ ID 8 in the position between the sixth and seventh nucleotide. 10) The method according to claim 9, characterized in that the insertion is obtained by CRISPR/Cas9 genome editing using as gRNA a gRNA with the sequence according to SEQ ID No.7. 11) The method according to claim 9 or 10, characterized in that the mutation is obtained in protoplasts. 12) A seed, fruit, or plant part of a grapevine plant comprising a gene according to anyone of the claims 1-4.
.2023 25 13) A method for the selection of mildew-resistant grapevine plants comprising the following steps: - selecting one or more powdery mildew-resistant mutants; - selecting among the resistant mutants those that show ampelographic differences with respect to the wild-type plant. 14) A method for identifying a powdery mildew resistant grapevine plant comprising the step of detecting the Erysiphe necator susceptibility gene comprising a resistance conferring mutation according to anyone of claims 1 – 4 in the genome of a grapevine plant and/or the step of determining the ampelographic characteristics as defined in claim 8. 15) A kit for the preparation of a genome edited plant comprising: - a gRNA with the sequence according to SEQ ID No: 7. 16) The kit according to claim 15, characterized in that it further comprises Cas9.
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WO2017005323A1 (en) * | 2015-07-08 | 2017-01-12 | Fondazione Edmund Mach | Erysiphe necator resistence providing genes in vitis vinifera |
EP4151084A1 (en) | 2021-09-10 | 2023-03-22 | EdiVite S.r.l. | Transfection of protoplasts from grapevine plants with the cas9/grna complex and regeneration of relative edited grapevine plants |
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WO2017005323A1 (en) * | 2015-07-08 | 2017-01-12 | Fondazione Edmund Mach | Erysiphe necator resistence providing genes in vitis vinifera |
WO2017005747A1 (en) * | 2015-07-08 | 2017-01-12 | Fondazione Edmund Mach | Erysiphe necator resistence providing genes in vitis vinifera |
EP3320098A1 (en) | 2015-07-08 | 2018-05-16 | Fondazione Edmund Mach | Erysiphe necator |
EP4151084A1 (en) | 2021-09-10 | 2023-03-22 | EdiVite S.r.l. | Transfection of protoplasts from grapevine plants with the cas9/grna complex and regeneration of relative edited grapevine plants |
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