Characterization of the grape powdery mildew genetic resistance loci in Muscadinia rotundifolia Trayshed

Muscadinia rotundifolia cv. Trayshed is a valuable source of resistance to grape powdery mildew (PM). It carries two PM resistance (R) loci, Run1.2 on chromosome 12 and Run2.2 on chromosome 18. This study identified the nucleotide-binding leucine-rich repeat (NLR) genes composing each R locus and their associated defense mechanisms. Evaluation of PM disease development showed that introgression of both loci confers resistance to PM in a V. vinifera background, but with varying speed and intensity of the response. To better understand the effect of NLR composition on PM resistance, both haplotypes of each R locus were reconstructed and the gene models within each haplotype were manually refined. We found that the number and classes of NLR genes differed between Run1.2 and Run2.2 loci and between the haplotypes of each R locus. In addition, NLR genes composing Run1.2b or Run2.2 loci exhibited different levels of gene expression, pointing to candidate NLR genes responsible for PM resistance in Trayshed. Finally, a transcriptomic analysis that included six additional R loci showed differences in the defense mechanisms associated with Run1.2b and Run2.2 in response to PM and at constitutive level. Altogether, our results reveal that Trayshed's R loci are composed of distinct NLRs that trigger different plant defense mechanisms in response to PM and at constitutive level, which would explain the variation of pathogen restriction between the two loci.

Viticultura biologică - o necesitate a dezvoltării durabile

The primary imperative of the sustainable development of the wine sector is to obtain organic pro-ducts, with low consumption of resources, in conditions of increased economic efficiency and the use of tec-hnological links that contribute to reducing energy consumption and protecting the environment. As a result of crossing Vitis vinifera L. with Muscadinia rotundifolia Michx. interspecific vine genotypes have been obtai-ned and identified that can be multiplied by pruning, without grafting, thus obtaining rhizogenic propagating material that contributes to reducing the costs of setting up vineyards. They were approved as table grape vari-eties: "Malena", "Nistreana" and "Algumax" and grape varieties for fresh consumption and processing: "Au-gustina", "Alexandrina" and "Amethyst". By creating plantations, it will contribute to the extension of the area to the northern limit of vine cultivation and obtaining products derived from the "organic" category.

The Assessment of Agrobiological and Disease Resistance Traits of Grapevine Hybrid Populations (Vitis vinifera L. × Muscadinia rotundifolia Michx.) in the Climatic Conditions of Crimea

The Crimean autochthonous grape varieties are unique by their origin and serve as a valuable source for breeding new cultivars with increased salt and frost resistance, as well as high-quality berries. However, they suffer from fungal pathogens, as the dry and hot summer months contribute to the epiphytotic course of diseases. An increase in the resistance of Crimean grape varieties is currently achieved through interspecific hybridization. In this study, we describe the genetic and agrobiological diversity of three hybrid populations obtained using the Vitis interspecific hybrid ‘Magarach 31-77-10′ as a female parent and Muscadinia rotundifolia × Vitis vinifera BC5 hybrid plants as male parents. The hybrid nature of the populations was assessed using RADseq high-throughput genotyping. We discovered 12,734 SNPs, which were common to all three hybrid populations. We also proved with the SSR markers that the strong powdery and downy mildew resistance of the paternal genotypes is determined by the dominant Run1/Rpv1 locus inherited from M. rotundifolia. As a result, the disease development score (R, %) for both mildew diseases in the female parent ‘Magarach 31-77-10’ was three times higher than in male parents 2000-305-143 and 2000-305-163 over two years of phytopathological assessment. The highest values of yield-contributing traits (average bunch weight ~197 g and 1.3 kg as yield per plant) were detected in the population 4-11 (♀M. No. 31-77-10 × 2000-305-163). Despite the epiphytotic development of PM, the spread of oidium to the vegetative organs of hybrids 4-11 did not exceed 20%. Some hybrid genotypes with high productivity and resistance to pathogens were selected for further assessment as promising candidates for new varieties.

Tolerance of Muscadine grapes (Vitis rotundifolia) to alkaline soil

Muscadine (Muscadinia rotundifolia) grapes have been used in grape variety and rootstock development due to their inherent pest and disease resistance, but little is known about their alkaline soil tolerance. In this study, Muscadine varieties, commercialrootstock and interspecific hybrid grape (Vitis spp.) cultivars were evaluated for alkaline soil tolerance under field conditions to determine the potential suitability of muscadines for rootstock development. Thirty-one muscadine and eleven interspecific hybridgrape cultivars were grown in a moderately alkaline soil (pH = 8.1) over a three-year period. Alkaline soil tolerance wasdetermined by relative vine vigour (shoot length), vine nutrient status (whole leaf tissue testing) and visual chlorosis. Additional data were collected on the timing of budbreak. Overall, the muscadines studied expressed low vigour and had greater chlorosissymptoms than the interspecific hybrid rootstocks (Paulsen 1103, Millardet et de Grasset 101-14, Millardet et de Grasset 420A,Ruggeri 140, Schwarzmann, and Matador). These parameters were not correlated with the concentration in any specific nutrient, although nutrient deficiencies (nitrogen, copper) and excesses (calcium, boron) were observed in the muscadine varieties.Overall, the muscadine grapes expressed poor alkaline soil tolerance compared to interspecific hybrid grape rootstocks (1103P, 101-14 MGt., 140Ru, Schwarzmann, 420A, and Matador), even the ones having poor alkaline soil tolerance (101-14 MGt., Schwarzmann) and own-rooted cultivars (Black Spanish, Blanc Du Bois, Dunstan’s Dream and Victoria Red). Nevertheless, some variability in chlorosis symptoms and nutrition was observed across the muscadine group, suggesting some interests to select Muscadine hybrid rootstocks less sensitive to iron chlorosis.

Silicon Alleviate Hypoxia Stress by Improving Enzymatic and Non-enzymatic Antioxidants and Regulating Nutrient Uptake in Muscadine Grape (Muscadinia rotundifolia Michx.)

Flooding induces low oxygen (hypoxia) stress to plants, and this scenario is mounting due to hurricanes followed by heavy rains, especially in subtropical regions. Hypoxia stress results in the reduction of green pigments, gas exchange (stomatal conductance and internal CO2 concentration), and photosynthetic activity in the plant leaves. In addition, hypoxia stress causes oxidative damage by accelerating lipid peroxidation due to the hyperproduction of reactive oxygen species (ROS) in leaf and root tissues. Furthermore, osmolyte accumulation and antioxidant activity increase, whereas micronutrient uptake decreases under hypoxia stress. Plant physiology and development get severely compromised by hypoxia stress. This investigation was, therefore, aimed at appraising the effects of regular silicon (Si) and Si nanoparticles (SiNPs) to mitigate hypoxia stress in muscadine (Muscadinia rotundifolia Michx.) plants. Our results demonstrated that hypoxia stress reduced muscadine plants’ growth by limiting the production of root and shoot dry biomass, whereas the root zone application of both Si and SiNP effectively mitigated oxidative and osmotic cell damage. Compared to Si, SiNP yielded better efficiency by improving the activity of enzymatic antioxidants [including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)], non-enzymatic antioxidants [ascorbic acid (AsA) and glutathione contents], and accumulation of organic osmolytes [proline and glycinebetaine (GB)]. SiNP also regulated the nutrient profile of the plants by increasing N, P, K, and Zn contents while limiting Mn and Fe concentration to a less toxic level. A negative correlation between antioxidant activities and lipid peroxidation rates was observed in SiNP-treated plants under hypoxia stress. Conclusively, SiNP-treated plants combat hypoxia more efficiently stress than conventional Si by boosting antioxidant activities, osmoprotectant accumulation, and micronutrient regulation.

Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence

Muscadinia rotundifolia, the muscadine grape, has been cultivated for centuries in the southeastern United States. M. rotundifolia is resistant to many of the pathogens that detrimentally affect Vitis vinifera, the grape species commonly used for winemaking. For this reason, M. rotundifolia is a valuable genetic resource for breeding. Single-molecule real-time reads were combined with optical maps to reconstruct the two haplotypes of each of the 20 M. rotundifolia cv. Trayshed chromosomes. The completeness and accuracy of the assembly were confirmed using a high-density linkage map of M. rotundifolia. Protein-coding genes were annotated using an integrated and comprehensive approach. This included using Full-length cDNA sequencing (Iso-Seq) to improve gene structure and hypothetical spliced variant predictions. Our data strongly support that Muscadinia chromosomes 7 and 20 are fused in Vitis and pinpoint the location of the fusion in Cabernet Sauvignon and PN40024 chromosome 7. Disease-related gene numbers in Trayshed and Cabernet Sauvignon were similar, but their clustering locations were different. A dramatic expansion of the Toll/Interleukin-1 Receptor-like Nucleotide-Binding Site Leucine-Rich Repeat (TIR-NBS-LRR) class was detected on Trayshed chromosome 12 at the Resistance to Uncinula necator 1 (RUN1)/ Resistance to Plasmopara viticola 1 (RPV1) locus, which confers strong dominant resistance to powdery and downy mildews. A genome browser for Trayshed, its annotation, and an associated Blast tool are available at .www.grapegenomics.com

Grapevine Resistance to the Nematode Xiphinema index Is Durable in Muscadine-Derived Plants Obtained from Hardwood Cuttings but Not from In Vitro

Breeding for varieties carrying natural resistance (R) against plant-parasitic nematodes is a promising alternative to nematicide ban. In perennial crops, the long plant−nematode interaction increases the risk for R breaking and R durability is a real challenge. In grapevine, the nematode Xiphinema index has a high economic impact by transmitting Grapevine fanleaf virus (GFLV) and, to delay GFLV transmission, rootstocks resistant to this vector are being selected, using Muscadinia rotundifolia in particular as an R source. To optimize in fine this strategy, the durability has been studied under controlled conditions in F1 and BC1 muscadine-derived resistant accessions previously obtained from either hardwood-cutting or in vitro propagation. After inoculation with a mix, in equal proportions, of four lines representative of the X. index diversity, multiplication on plants has been monitored 3 to 6 years. The nematode reproduction factor remained lower than 1 in resistant plants obtained from hardwood cuttings while it increased at values far beyond 1 in resistant plants of in vitro origin. Data for nematode numbers per gram of roots mostly paralleled those obtained for the reproduction factor. The effect of the propagation type on resistance over years was also evaluated for the ratio female/juvenile and the frequency of males. Altogether our results illustrate that the muscadine-derived resistance based on hardwood cuttings is durable. By contrast, in resistant and reference accessions obtained from in vitro, our data suggest that the increased nematode multiplication might be mainly due to the modification of root architecture consecutive to this propagation method.

Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence

Muscadinia rotundifolia, the muscadine grape, has been cultivated for centuries in the southeastern United States. M. rotundifolia is resistant to many of the pathogens that detrimentally affect Vitis vinifera, the grape species commonly used for winemaking. For this reason, M. rotundifolia is a valuable genetic resource for breeding. Single-molecule real-time reads were combined with optical maps to reconstruct the two haplotypes of each of the 20 M. rotundifolia cv. Trayshed chromosomes. The completeness and accuracy of the assembly were confirmed using a high-density linkage map of M. rotundifolia. Protein-coding genes were annotated using an integrated and comprehensive approach. This included using Full-length cDNA sequencing (Iso-Seq) to improve gene structure and hypothetical spliced variant predictions. Our data strongly support that Muscadinia chromosomes 7 and 20 are fused in Vitis and pinpoint the location of the fusion in Cabernet Sauvignon and PN40024 chromosome 7. Disease-related gene numbers in Trayshed and Cabernet Sauvignon were similar, but their clustering locations were different. A dramatic expansion of the Toll/Interleukin-1 Receptor-like Nucleotide-Binding Site Leucine-Rich Repeat (TIR-NBS-LRR) class was detected on Trayshed chromosome 12 at the Resistance to Uncinula necator 1 (RUN1)/ Resistance to Plasmopara viticola 1 (RPV1) locus, which confers strong dominant resistance to powdery and downy mildews. A genome browser for Trayshed, its annotation, and an associated Blast tool are available at www.grapegenomics.com.

Disease resistant grapevine varieties and quality: the case of Bouquet varieties

The disease resistant grapevine varieties (ref A. Bouquet) were obtained by INRA from 4 or 5 generations of backcrossing between Muscadinia rotundifolia and Vitis vinifera and exhibit a high level of resistance against downy and powdery mildew. These varieties carry the resistance genes RUN 1 and RPV1, with several other secondary genes at one chromosomal locus. Agronomic criteria were studied for all these selections. Among the selected grapevine species, some have high levels of polyphenols. Some (white and red) have a high aromatic potential, while others have low sugar contents (135 g/L to 150 g/L) and adapted sugar/acidity ratio. All these characteristics were combined to design a new set of vine cultivars dedicated to the production of either low-alcohol wines, grape juices, or classical wines. Since 2012, within a France Agrimer/CIVL/INRA financial framework, 10 plots (0.5 ha each) were planted at INRA Pech Rouge with 8 resistant grape varieties (ref A. Bouquet) in order to examine long-term resistance to diseases and to define quality criteria for the classification of the wines obtained from these new grape varieties.