Powdery mildew resistant grapevine plant

Provided herein are powdery mildew-resistant grapevine plants and methods for providing powdery mildew resistance to susceptible grapevine plants. Specifically, provided herein are grapevine plants including in their genome an impaired Erysiphe necator resistance-conferring gene, wherein the corresponding not impaired Erysiphe necator resistance conferring resistance-conferring gene designated VvMLO13 encodes a protein including the amino acid sequence of SEQ ID No. 1, or proteins having 95% sequence identity therewith. The impairment results in an absence of a protein comprising the amino acid sequence of SEQ ID No. 1, or proteins having 95% sequence identity therewith, in the grapevine plant and wherein the grapevine plant is resistant to powdery mildew.

1. 11. A powdery mildew-resistant grapevine plant comprising in its genome a mutation in a gene having the nucleotide sequence of SEQ ID No. 2, wherein the mutation results in the absence of a protein comprising the amino acid sequence of SEQ ID No. 1, or a protein having 95% sequence identity therewith, and confers resistance to Erysiphe necator in said grapevine plant.
2. 22. The grapevine plant according to claim 1, wherein the alleles of the gene with the mutation have the nucleotide sequences of SEQ ID No. 3, SEQ ID No. 4, and/or SEQ ID No. 5.
3. 33. The grapevine plant according to claim 2, wherein the plant comprises in its genome two alleles selected from the group consisting of SEQ ID No. 3 and SEQ ID No. 4, SEQ ID No. 3 and SEQ ID No. 5, SEQ ID No. 4 and SEQ ID No. 5, SEQ ID No. 3 and SEQ ID No. 3, SEQ ID No. 4 and SEQ ID No. 4, or SEQ ID No. 5 and SEQ ID No. 5.
4. 44. The grapevine plant according to claim 1, wherein the grapevine plant further comprises in its genome one or more Erysiphe necator resistance-conferring genes selected from the group consisting of VvMLO6, VvMLO7 and VvMLO11.
5. 55. A method for providing a powdery mildew-resistant grapevine plant, comprising mutating a gene having the nucleotide sequence of SEQ ID No. 2, wherein the mutation results in the absence of a protein comprising the amino acid sequence of SEQ ID No. 1, or a protein having 95% sequence identity therewith, in a powdery mildew-susceptible grapevine plant, thereby providing a grapevine plant that is resistant to powdery mildew.
6. 66. The method for providing a powdery mildew-resistant grapevine plant according to claim 5, wherein the step of mutating the gene encoding a protein comprising the amino acid sequence of SEQ ID No. 1 comprises introducing a deletion, insertion, or substitution in an endogenous sequence comprising the nucleotide sequence of SEQ ID No. 2.
7. 77. A seed, fruit, or plant part of a grapevine plant according to claim 1.

CROSS REFERENCE TO RELATED APPLICATION
This application is the United States national phase of International Patent Application No. PCT/EP2020/067007 filed Jun. 18, 2020, the disclosure of which is hereby incorporated by reference in its entirety.
The Sequence Listing associated with this application is filed in electronic format via EFS-Web and is hereby incorporated by reference into the specification in its entirety. The name of the text file containing the Sequence Listing is 2208066_ST25.txt. The size of the text file is 29,578 bytes, and the text file was created on Dec. 6, 2022.
BACKGROUND OF THE INVENTION
Field of the Invention
The present invention relates to powdery mildew resistant grapevine plants (Vitis spp.) and to methods and means for providing the present powdery mildew resistance to powdery mildew susceptible grapevine plants and to methods and means for providing the present powdery mildew resistant grapevine plants.
Description of Related Art
Erysiphe necator, also designated as Uncinula necator, is a fungus that causes powdery mildew disease symptoms in grapevine plants. The fungus is a common pathogen for Vitis species of which the most important species is Vitis vinifera. 
Grapevine plants require large amounts of pesticides, particularly fungicides, to prevent yield losses. Between 1992 and 2003, 73% of the fungicides sold in France, Italy, Spain and Germany, were used for grapevine protection, a crop that covers only 8% of the land used for agriculture in the considered countries (EUROSTAT, 2007).
Grapevine powdery mildew (PM) caused by the fungus Erysiphe necator, is one of the most economically relevant diseases of grapevine worldwide. Erysiphe necator is an obligate biotroph that can infect all green tissues of grapevine and causes significant losses in yield and berry quality. PM symptoms include a white or grey powder covering of the upper and lower surfaces of the leaves. Fruit infections result in shriveling or cracking of the berries. The quality of the fruit is severely damaged, with increased acidity and decreased anthocyanin and sugar content.
Powdery mildew is controlled with frequent applications of chemical fungicides. However, the intense application of chemical fungicides has several drawbacks. First of all, the effects on the environment of fungicides are well documented. Secondly, the costs of the chemicals and their applications can reach up to 20% of the total expenses for grape production in some areas. Thirdly, the development of resistant populations of the pathogen was already documented by Baudoin et al. (2008) and Dufour et al. (2011), strongly reducing the efficacy of chemical treatments. Therefore, there is increasing interest in the development of new alternative methods to chemical treatments.
The generation of PM-resistant varieties is one of the best options to make sustainable grapevine cultivation a realistic possibility, preserving at the same time the incomes of the growers. A study carried out on “Chardonnay” production in California, showed that the use of a PM-resistant variety could save the growers around $720 per hectare, with a significant reduction of fungicide usage (Fuller et al., 2014).
Most cultivars of the European grapevine (Vitis vinifera), which includes the world's finest and most widely planted wine and table grapevine cultivars, are highly susceptible to PM (Gadoury et al. 2003). In contrast, North American Vitis species co-evolved with E. necator and possess various levels of resistance to the pathogen (Fung et al., 2008). This resistance could be introgressed by crossing Vitis vinifera with one of the resistant American Vitis species, but breeding is a slow process in grapevine and the acceptance of resistant hybrids by producers and consumers has been limited in the past (Fuller et al., 2014). The use of technologies like genetic transformation or high-throughput marker-assisted selection can be used to obtain resistant grapevine cultivars with desirable grape properties for producers and consumers (Feechan et al., 2013a).
The most common strategy to develop resistant plants is focused on the introgression of resistance genes (R-genes). R-genes encode proteins that recognize pathogen effectors and trigger a defense response, mediated by a signaling network in which plant hormones play a major role (Pavan et al., 2010). Resistance is manifested as a localized hypersensitive response at the site of infection (Bari and Jones, 2009). Resistance conferred by R-genes is scarcely durable, as mutations of pathogen effectors allow it to overcome resistance (Parlevliet et al., 1993).
An alternative approach is based on the inactivation of susceptibility genes (S-genes), defined as genes whose loss-of-function results in recessively inherited resistance (Pavan et al., 2010). Some pathogens are able to suppress plant defense by activating plant proteins whose function is the negative regulation of plant immunity system. The genes encoding these plant proteins are known as susceptibility genes (S-genes) and their knock-out releases the suppression of plant defense and leads to resistance (Pavan et al., 2010). The disadvantage of S-genes is the pleiotropic phenotypes sometimes associated to their knock-out (Pavan et al. 2011).
Mildew Locus O (MLO) genes are a typical example of PM S-genes. Resistance due to the knock-out of an MLO gene (mlo resistance) was discovered in barley in 1992 (Jørgensen, 1992) and for a long time was considered as a unique form of resistance. However, further studies revealed that MLO genes are largely conserved across the plant kingdom and their loss-of-function resulted in resistance in several species, such as Arabidopsis (Consonni et al., 2006), pea (Pavan et al., 2011), tomato (Bai et al., 2008), and pepper (Zheng et al., 2013). Not all MLO genes are S-genes and MLO family members are divided in seven clades (Acevedo-Garcia et al., 2014; Pessina et al., 2014). Only two clades contain S-genes: clade IV contains all monocots S-genes (Panstruga et al., 2005; Reinstädler et al., 2010); and clade V contains all dicots S-genes (Consonni et al., 2006; Bai et al., 2008; Feechan et al., 2008; Winterhagen et al., 2008). Not all the members of clades IV and V are S-genes.
International patent application WO 2017/005747 discloses four MLO genes designated VvMLO6, VvMLO7, VvMLO11 and VvMLO13. According to WO 2017/005747, VvMLO7 is a major powdery mildew resistance providing gene while VvMLO6 and VvMLO11 are identified as genes providing additive resistance. WO 2017/005747 discloses that downregulation of VvMLO13 expression does not provide powdery mildew resistance in grapevine.
Considering the economic impact of an Erysiphe necator infection on grape production, there is a continuing need in the art for Erysiphe necator resistance providing genes.
SUMMARY OF THE INVENTION
It is an objective of the present invention, amongst other objectives, to meet this need of the art.
According to the present invention, the above objective, amongst other objectives, is met by providing impaired Erysiphe necator resistance providing genes as outlined in the appended claims.
Specifically, the above objective, amongst other objectives, is met according to a first aspect of the present invention by a grapevine plant (Vitis spp.) comprising in its genome an impaired E. necator resistance-conferring gene, wherein the corresponding not impaired E. necator resistance-conferring gene designated VvMLO13 encodes a protein comprising the amino acid sequence of SEQ ID No. 1, or proteins having 95% sequence identity therewith, wherein the impairment results in an absence of a protein comprising the amino acid sequence of SEQ ID No. 1, or proteins having 95% sequence identity therewith, in said grapevine plant and wherein the grapevine plant is resistant to powdery mildew.
The present inventors have surprisingly discovered that despite prior art disclosures that VvMLO13 is not a powdery mildew resistance providing gene, absence of expression of this gene provides substantially complete resistance against Erysiphe necator in grapevine, i.e. the leaves of grapevine are substantially free of powdery mildew sporulation.
Within the context of the present invention, a grapevine is considered to be resistant to powdery mildew when detached leaves of a grapevine stem at a growth stadium of 7 to 11 leaves per stem show less than 10%, such as less than 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1% or 0% sporulation as compared to wild-type leaves at 5 to 15 dpi infection with Erysiphe necator. 
Without wishing to be limited to an underlying mechanism of the powdery mildew resistance observed, the presently disclosed powdery mildew resistance based on VvMLO13 appears to be due to a complete reduction of expression of VvMLO13 of both alleles (2n) either by complete disruption of transcription or mutation of the proteins encoded by both alleles rendering these proteins no longer capable of performing their function in grapevine.
Accordingly, the present invention, according to a preferred embodiment, relates to grapevine plants, wherein the absence of a protein comprising the amino acid sequence of SEQ ID No. 1 results from one or more mutations in the nucleotide sequence of a cDNA comprising SEQ ID No. 2.
Alternatively, the present invention, according to a preferred embodiment, relates to grapevine plants, wherein the absence of a protein comprising the amino acid sequence of SEQ ID No. 1 results from one or more mutations in the not impaired E. necator resistance-conferring gene designated VvMLO13 resulting in an absence of expression thereof.
According to the present invention, the present one or more mutations comprise deletions, insertions or substitutions in the nucleotide sequence of a cDNA comprising SEQ ID No. 2. Examples of such mutations are 1 or 2 base pair deletions or insertions in SEQ ID No. 2 causing frameshifts, base pair changes resulting in a triplet coding another amino acid, i.e. amino acid substitutions or deletion of a triplet.
According to another preferred embodiment, the present invention relates to grapevine plants, wherein the absence of a protein comprising the amino acid sequence of SEQ ID No. 1 results from the impaired E. necator resistance-conferring gene to encode a nucleotide sequence comprising SEQ ID No. 3 (1 base pair deletion in SEQ ID No. 2), SEQ ID No. 4 (triplet deletion in SEQ ID No. 2), or SEQ ID No. 5 (1 base pair insertion in SEQ ID No. 2), or combinations thereof or a protein comprising an amino acid sequence comprising SEQ ID No. 6 (encoded by SEQ ID No. 3), SEQ ID No. 7 (encoded by SEQ ID No. 4), or SEQ ID No. 8 (encoded by SEQ ID No. 5), or combinations thereof.
According to an especially preferred embodiment, the present invention relates to grapevine plants wherein the absence of a protein comprising the amino acid sequence of SEQ ID No. 1 results from the impaired E. necator resistance-conferring gene (2n) encoding a nucleotide sequence comprising SEQ ID No. 3 and SEQ ID No. 4, SEQ ID No. 3 and SEQ ID No. 5, SEQ ID No. 4 and SEQ ID No. 5, SEQ ID No. 3 and SEQ ID No. 3, SEQ ID No. 4 and SEQ ID No. 4, SEQ ID No. 5 and SEQ ID No. 5.
The present grapevine plants further preferably comprise in their genome one or more E. necator resistance-conferring genes, preferably one or more E. necator resistance-conferring genes selected from the group consisting of VvMLO6, VvMLO7 and VvMLO11.
The present invention also relates to methods for providing a powdery mildew resistant grapevine plant, the methods comprising the step of mutating a gene designated VvMLO13 to encode a protein comprising the amino acid sequence of SEQ ID No. 1 in a powdery mildew susceptible grapevine plant. The present methods preferably comprise mutating a gene designated VvMLO13 to encode a protein comprising the amino acid sequence of SEQ ID No. 1 by introducing a deletion, insertion, or substitution in a cDNA sequence comprising SEQ ID No. 2.
The present invention additionally relates to seeds, fruits or plant parts of the present grapevine plant.
The present invention further relates to impaired powdery mildew resistance-conferring genes designated VvMLO13, wherein the impaired powdery mildew resistance-conferring genes encode a protein comprising an amino acid sequence selected from the group consisting of SEQ ID No. 6, SEQ ID No. 7 and SEQ ID No. 8, powdery mildew resistance providing proteins, the proteins comprise an amino acid sequence selected from the group consisting of SEQ ID No. 6, SEQ ID No. 7 and SEQ ID No. 8 and use thereof for introducing or identifying powdery mildew resistance in a grapevine plant.



BRIEF DESCRIPTION OF THE DRAWINGS
The present invention will be further detailed in the example below. In the example, reference is made to figures wherein:
FIG. 1: shows the results of a PM assay on detached leaves of wild type and mlo13 plants. Wild type leaves show complete sporulation, mlo13 leaves are clean of PM sporulation at 14 dpi;
FIG. 2: shows hyphal growth of PM visualized using specific staining on a microscopic image. PM infection on leaves at 14 dpi in the wild type (on the right) and the mlo13 mutant (on the left). There is clearly less hyphal growth in the mutant compared to its wild type;
FIG. 3: shows a PM assay on detached leaves of wild type (on the left) and mlo13 leaves (on the right). Wild type leaves show complete sporulation, mlo13 leaves are clean of PM sporulation at 13 dpi;
FIG. 4: shows quantification of PM sporulation in wild type and mlo 13 mutant leaves. Percentage of leaf area covered by PM sporulation was determined for 3 wild type leaves and 3 mlo13 leaves 10 dpi.



DESCRIPTION OF THE INVENTION
Example
Material and Methods
Leaves to be tested in a detached-leaf-assay were taken from grapevine plants grown in pots until they reached a stage of at least 8-10 leaves per stem. From the top of each stem, the second, third and fourth leaf were used as test leaves. They were surface-sterilized in a bath of 1% bleach for 2 minutes, and then rinsed three times in sterile water, by soaking them for two minutes, and then left to dry in sterile conditions (laminar flow hood).
A 1% agar layer of about 1 cm was poured in a sterile plastic box, or sterile plates, and then covered by sterile filter paper. Test leaves were laid on the paper ensuring that the petiole is sticking in the underneath agar layer. Using a PM infected leaf with visible sporulation on its surface as inoculum, E. necator spores were distributed on the test leaves by the aid of an air pump.
Box/plates were covered by a lid and stored in a growth chamber with the following settings: 16 hour light period, 21° C. and 21% RH. Scoring was performed at several timepoints indicated in the figures by calculating the surface area of leaves covered by powdery mildew or making pictures of the leaves.
PM hyphae were visualized by aniline blue coloration on infected leaves previously treated with ethanol: (glacial) acetic acid 3:1 as described in detail in “Pessina et al., (2016)”. Leaf sections were mounted on glass slides and observed with a microscope Leica MZ16F.
Results
Mutant plants were generated by Agrobacterium-mediated transformation of young embryogenic calli of cv. Crimson seedless. Binary vectors constitutively expressing the CRISPR/Cas9 machinery were used to specifically target VvMLO13. Plants regenerated from such calli were then selected for kanamycin resistance and their DNA analyzed by next-generation sequencing (Illumina®).
Plants were obtained edited in MLO13 after NextGen sequencing confirmation (minimal sequencing depth 1000× coverage). Several mlo13 alleles were obtained after sequencing and used for these experiments. The mlo13 mutant used in experiment 1 is biallelic with 1 base pair insertion for one allele and 1 base pair deletion for the other allele both causing frame shift mutations. For experiment 2, another mlo13 was used, this mutant contains a 3 base pair deletion for one allele and a 1 base pair deletion for the other allele.
Detached leaves from Crimson seedless were used in a PM assay as described in the M & M section.
Experiment 1:
FIG. 1 shows 2 detached leaves of wild type and mlo13 mutant plants. Whereas the wild type shows PM sporulation, the mlo13 mutant does not show any sporulation. Picture was taken at 14 dpi. To further analyze the phenotype of the wild type and mlo13 mutants, histological analysis was performed on the same leaf material by visualizing PM hyphae using aniline blue. As seen in FIG. 2, in the wild type hyphae are present all over the leaf surface where they form dense structures, while on the mlo13 mutant, they are only visible in a limited number. This clearly illustrates that the mlo13 hardly supports pathogen growth.
Experiment 2:
FIG. 3 shows an example of wild type leaf and mlo13 leaf that were used in a PM assay. Picture of the leaves were taken 10 dpi and show severe sporulation on the wild type leaf. The mlo13 mutant is resistant to PM as seen by the strongly reduced or absence of sporulation. To further analyze this, 3 wild type leaves and 3 mlo13 leaves were used for quantitative analysis. FIG. 4 shows percentage of the leaf area covered with PM sporulation for 3 wild type leaves and 3 mlo13 mutant leaves. Wild type leaves have at least 80% of the surface area covered in PM sporulation while in the mlo13 this was absent or greatly reduced to a maximum of 5% of the surface area.