SNPs Associated with Foliar Phylloxera Tolerance in Hybrid Grape Populations Carrying Introgression from Muscadinia

Leaf-feeding phylloxera decreases the photosynthetic activity of a grape plant, leading to decreasing number of fruit buds. In addition, phylloxera larvae emerging from the leaf galls may colonize the roots, negatively affecting the growth of the grape plant. In this study, we evaluated host tolerance of three grapevine hybrid populations obtained from crossing of the same maternal grapevine M. no. 31-77-10 with interspecific hybrids carrying introgressions from Muscadinia and other North American Vitis species against leaf-feeding grape phylloxera. Combining genotyping data of the populations obtained with 12,734 SNPs and their resistance phenotypes evaluated in the laboratory experiment, we performed an association study. As the result of GWAS, nine SNPs with the lowest significant p-values were discovered in the whole sample of 139 hybrids as associated with variation of the scores ‘the percentage of infested leaves’ and ‘intensity of gall formation’. Three of the SNPs on LG 7 were located in the same chromosome interval where a major QTL (RDV6) for root phylloxera resistance was reported from Muscadine background. Two SNPs on LG 8 were detected within the gene, encoding E3 ubiquitin-protein ligase UPL4 involved in apoptosis. SNPs detected on LG 13 and LG 18 may overlap with the previously reported QTLs for phylloxera resistance inherited from V. cinerea.

Climate Change, Crop Wild Relatives and Genomic Data: The persistence and agronomic utility of five Vitis species

Crop wild relatives (CWRs) have the capacity to contribute novel traits to agriculture. Given climate change, these contributions may be especially vital for perennial crops, because perennials are often clonally propagated and consequently do not evolve rapidly. By studying the landscape genomics of five Vitis CWRs (V. arizonica, V. mustangensis, V. riparia, V. berlandieri and V. girdiana) in the context of projected climate change, we addressed two goals. The first was assessing the relative potential of different CWRs to persist in the context of climate change. By integrating species distribution models with adaptive genetic variation, additional genetic features such as genomic load, and a phenotype (resistance to Pierce Disease), we predicted that accessions of V. mustangensis are particularly well-suited to persist. The second goal was identifying candidate CWRs to contribute to bioclimatic adaptation for grapevine (V. vinifera) cultivation. To do so, we first estimated that ~40% of current viticulture sites in the United States will be vulnerable to climate change, based on species distribution models projected to 2070. We then predicted which CWRs have the genomic profile to contribute to bioclimatic adaptation at these vulnerable sites. We identified rootstock candidates from V. mustangensis, V. riparia and V. girdiana and hypothesized that they may prove useful for mitigating climate impacts on viticulture. By identifying candidate germplasm, this work takes a conceptual step toward mitigating the climate impacts on crops by utilizing the genomic and bioclimatic characteristics of CWRs.

Genetic Stability of in vitro Propagated Grapevine (Vitis vinifera L.) cv. Al-Bayadi

Grapevine (Vitis vinifera L.) fruit crops are a significant source of antioxidants, fibre, and nutrients; all are vital for a healthy diet and play a key role in the economy of several advanced and developing countries. It is of great importance to generate true-to-type plant products using in vitro propagation system. Thus, somaclonal variations can multiply very rapidly which leads to loss of the main features of parent rootstocks. In this research, a mixture of three Polymerase Chain Reaction (PCR)-based molecular marker methods – (conserved DNA derived polymorphism) CDDP, (Inter-simple sequence repeat) ISSR, and DNA barcoding – have been used to verify micro propagated grapevine genetic stability. Both ISSR and CDDP primer combinations produced scorable PCR fragments. The total number of bands was 98 and 109, with an average of 9.8 and 10.9 bands/primer in ISSR and CDDP assays, respectively. On the other hand, about 20 polymorphic bands were collected by CDDP primers, of CDDP-3 and CDDP-11produced 1 and 5 bands, with a polymorphism percentage of 11% and 33%, respectively. About 5 different unique PCR bands were detected in the mother plant (control) and were not observed in micro propagated plantlets (MP) samples of grapevine plant or vice versa. The phylogenetic trees were constructed using ISSR and CDDP assays diverged the control from MP samples at 1.3% and 7%, respectively. The phylogenetic tree constructed using (chloroplast gene RNA polymerase1) rpoC1 gene, multiple sequence alignment revealed that rpoC1 gene sequencing detected small genetic differences between control and MP samples of the grapevine and clustered grapevine control and MP samples to a single cluster with other Vitis species. This experiment reveals the potentiality of using CDDP, ISSR, and DNA barcoding in detecting the somaclonal variation of grapevine varieties subjected to tissue culture as a tool for plant conservation and breeding programs.

Grapevine Shoot Tip Cryopreservation and Cryotherapy: Secure Storage of Disease-Free Plants

Grapevine (Vitis spp.) is one of the most economically important temperate fruit crops. Grapevine breeding programs require access to high-quality Vitis cultivars and wild species, which may be maintained within genebanks. Shoot tip cryopreservation is a valuable technique for the safe, long-term conservation of Vitis genetic resources that complements traditional field and in vitro germplasm collections. Vitis is highly susceptible to virus infections. Virus-free plants are required as propagation material for clonally propagated germplasm, and also for the global exchange of grapevine genetic resources. Shoot tip cryotherapy, a method based on cryopreservation, has proven to be effective in eradicating viruses from infected plants, including grapevine. This comprehensive review outlines/documents the advances in Vitis shoot tip cryopreservation and cryotherapy that have resulted in healthy plants with high regrowth levels across diverse Vitis species.

Horizontal Transfer of LTR Retrotransposons Contributes to the Genome Diversity of Vitis

While horizontally transferred transposable elements (TEs) have been reported in several groups of plants, their importance for genome evolution remains poorly understood. To understand how horizontally transferred TEs contribute to plant genome evolution, we investigated the composition and activity of horizontally transferred TEs in the genomes of four Vitis species. A total of 35 horizontal transfer (HT) events were identified between the four Vitis species and 21 other plant species belonging to 14 different families. We determined the donor and recipient species for 28 of these HTs, with the Vitis species being recipients of 15 of them. As a result of HTs, 8–10 LTR retrotransposon clusters were newly formed in the genomes of the four Vitis species. The activities of the horizontally acquired LTR retrotransposons differed among Vitis species, showing that the consequences of HTs vary during the diversification of the recipient lineage. Our study provides the first evidence that the HT of TEs contributes to the diversification of plant genomes by generating additional TE subfamilies and causing their differential proliferation in host genomes.

Vitis Species from the Southwestern United States Vary in Their Susceptibility to Powdery Mildew

The European grapevine (Vitis vinifera L.) has been cultivated in North America for about 500 years. One of the major limitations to its culture is the powdery mildew (PM) fungus, Erysiphe necator Schw. This study reports on the most extensive screening of Vitis species from the southwestern United States and northern Mexico for resistance to PM, testing 147 accessions of 13 Vitis species. In addition, Vitis vinifera cv. Carignane, a highly susceptible wine grape cultivar, was used as a reference to evaluate the effect of the inoculum 14 days postinoculation. Inoculation was done with a vacuum-operated settling tower using a broadly virulent isolate of E. necator, the C-strain. Resistant accessions (nine), moderately susceptible accessions (39), and highly susceptible accessions (99) were detected. The resistant accessions were then inoculated with an additional fungal isolate, e1-101, and they retained their resistance. Vitis species susceptibility was not associated with a North-South gradation, but Western species were more susceptible than Midwestern and Eastern species. All five of the V. monticola accessions were susceptible, as were the accessions of V. treleasei. The species V. acerifolia, V. candicans, V. cinerea, and V. × doaniana had significantly more resistant to moderately susceptible accessions compared with V. arizonica, V. berlandieri, V. californica, V. × champinii, V. girdiana, V. riparia, and V. rupestris, which had relatively more susceptible accessions than the other species. This research identified new sources of PM resistance in Vitis from the southwestern United States that could be incorporated into PM resistance breeding programs throughout the world.

Tannin Content in Vitis Species Red Wines Quantified Using Three Analytical Methods

Tannin content in red wines is positively correlated with astringency perception and wine grade; however, tannin quantification is one of the main challenges. In this study, tannin content was quantified using three analytical methods in commercial red wines from Vitis vinifera and interspecific cold-hardy hybrids including Marquette, Frontenac, and Petite pearl cultivars. Protein (PP) and methylcellulose precipitation (MCP) methods were compared to a HPLC-DAD method, which is based on the interaction between tannins and a hydrophobic surface (RPC). Frontenac wines were the poorest in tannins and Cabernet sauvignon wines were the richest regardless of the method used. In cold-hardy red wines, the tannin content was higher in Marquette with high alcohol content, which suggested that the tannins were extracted from seeds rather than skins. The high limit of quantification of the PP method and the presence of anthocyanin di-glucosides in cold-hardy wines were parameters suggesting that protein and methylcellulose precipitation methods were neither suitable nor reliable for the quantification of tannins in cold-hardy red wines. The tannin content quantified by RPC was positively correlated to tannin quantified by MCP, suggesting that the RPC method would be relevant for the quantification of tannins in red wines.

A molecular marker set combining a retrotransposon insertion and SSR polymorphisms is useful for assessing diversity in Vitis

Molecular markers, based on DNA polymorphisms, are useful tools for identifying individuals, establishing phylogenetic relationships, managing collections of genetic material or assisting breeding. In the present study, we developed a marker set to differentiate Vitis species, grapevine varieties or clones belonging to the same variety. This novel marker set combines, in four PCR amplifications, the presence/absence of a remarkable retrotransposon, Tvv1-Δ3460, inserted at its single locus and the SSR polymorphism present within its two LTRs. By studying a collection of Vitaceaeaccessions, we showed the prevalence of two allelic forms of Tvv1-Δ3460 - one of which was partially truncated - in Vitis species. Out of the twenty-five studied Vitis species, the insertion of a Tvv1-Δ3460 element was detected in twenty, including Vitis vinifera. The homozygous vs heterozygous state of the element insertion was determined by amplifying the empty site. Additionally, each Tvv1-Δ3460 LTRs included a microsatellite sequence useful for designing markers based on LTR length. The LTR-SSR markers distinguished most of the fifty-two cultivars and revealed polymorphism within five of the seven varieties studied.

Plasmopara viticola causing downy mildew on Vitis davidii in Korea

Vitis davidii (Rom.Caill.) Foëx, commonly known as spine grape, is a deciduous climber native to China. Its fruits are consumed fresh or used to make wine in South and Central China. In recent years, spine grape has been cultivated in Korea. In July 2020, downy mildew was detected on spine grape vines in Jeongeup (35°42′17″N, 126°54′02″E), Korea, with a disease incidence of 70%. The symptoms appeared as yellowish, brownish, or reddish, vein-limited, poly-angular adaxial leaf spots, correspond to dense, white downy growth abaxially. A representative specimen was deposited in the Kunsan National University Herbarium (KSNUH679). Sporangiophores were tree-like, hyaline, mostly straight, and monopodially branched in orders of three to six; they measured (219.4–)273.2 to 435.1(–546.6) × (4.8–)6.7 to 9.0(–10.0) μm (n = 50). Ultimate branchlets were bi or trifurcate, straight to slightly curved, with truncate or, rarely, a swollen tip and measured 2.9 to 9.7 μm long and 0.8 to 2.5 μm wide at the base (n = 50). Sporangia were hyaline, ovoidal or lemon-shaped; they measured (16.8–)20.0 to 28.8(–34.2) × (11.4–)13.1 to 17.0(–20.1) μm with a length to width ratio of (1.28–)1.46 to 1.78(–2.07) (n = 50). This morphology was as described for Plasmopara viticola (Berk. & M. A. Curtis) Berl. & De Toni (Hall, 1989). Genomic DNA was extracted directly from infected V. davidii leaves. Three regions were PCR-amplified and sequenced: cox2 mtDNA with primers cox2F and cox2-RC4 (Choi et al., 2015), actin with primers pve04815-F and pve04815-R, and beta-tubulin with primers pvc389-F3 and pvc389-R4 (Rouxel et al., 2013). The resulting sequences were deposited in GenBank (accession nos. MT834527 for cox2, MT834525 for actin, and MT834526 for beta-tubulin). A BLASTn search revealed that the Korean sample was identical to P. viticola clade aestivalis originating from Vitis species: MK215072 for cox2 sequence, KY933800 for actin, and MK358393 for beta-tubulin. In all phylogenetic analyses of the three genes (cox2, actin, and beta-tubulin), KSNUH679 came out as phylogenetically place within P. viticola clade aestivalis, which has recently been reported on V. coignetiae and V. ficifolia var. sinuata in Korea (Kim et al., 2019). A pathogenicity test was performed twice by inoculating the leaves of 10 healthy spine grape plants with a sporangial suspension (~1 × 106 sporangia·mL-1) and incubating them in a growth chamber at 25 °C, 12-h day/night cycle, and 90% relative humidity; five non-inoculated plants served as controls. After two weeks, all inoculated plants developed typical downy mildew symptoms could be observed, whereas the controls remained symptomless. Morphology and molecular features confirmed the identity of the pathogen of spine grape to be P. viticola. To the best of our knowledge, this is the first report of downy mildew caused by P. viticola on V. davidii in Korea. Recently, downy mildew outbreaks caused by P. viticola have been recorded in spine grape plantations in southern China (Yi et al., 2019). Considering the potential of spine grape as a novel crop for Korea, P. viticola appears to represent a significant threat to this industry.