Characterization of genetic determinants of the resistance to phylloxera, Daktulosphaira vitifoliae, and the dagger nematode Xiphinema index from muscadine background

LiDAR Is Effective in Characterizing Vine Growth and Detecting Associated Genetic Loci

The strong societal demand to reduce pesticide use and adaptation to climate change challenges the capacities of phenotyping new varieties in the vineyard. High-throughput phenotyping is a way to obtain meaningful and reliable information on hundreds of genotypes in a limited period. We evaluated traits related to growth in 209 genotypes from an interspecific grapevine biparental cross, between IJ119, a local genitor, and Divona, both in summer and in winter, using several methods: fresh pruning wood weight, exposed leaf area calculated from digital images, leaf chlorophyll concentration, and LiDAR-derived apparent volumes. Using high-density genetic information obtained by the genotyping by sequencing technology (GBS), we detected 6 regions of the grapevine genome [quantitative trait loci (QTL)] associated with the variations of the traits in the progeny. The detection of statistically significant QTLs, as well as correlations (R2) with traditional methods above 0.46, shows that LiDAR technology is effective in characterizing the growth features of the grapevine. Heritabilities calculated with LiDAR-derived total canopy and pruning wood volumes were high, above 0.66, and stable between growing seasons. These variables provided genetic models explaining up to 47% of the phenotypic variance, which were better than models obtained with the exposed leaf area estimated from images and the destructive pruning weight measurements. Our results highlight the relevance of LiDAR-derived traits for characterizing genetically induced differences in grapevine growth and open new perspectives for high-throughput phenotyping of grapevines in the vineyard.

Establishment of Arthrobotrys flagrans as biocontrol agent against the root pathogenic nematode Xiphinema index

Plant-parasitic nematodes cause devastating agricultural damage worldwide. Only a few synthetic nematicides can be used and their application is limited in fields. Therefore, there is a need for sustainable and environment-friendly alternatives. Nematode-trapping fungi (NTF) are natural predators of nematodes. They capture and digest them with their hyphae and are starting to being used as bio-control agents. In this study, we applied the NTF Arthrobotrys flagrans (Duddingtonia flagrans) against the wine pathogenic nematode Xiphinema index. A. flagrans reduced the number of X. index juveniles in pot cultures of Ficus carica, an alternative host plant for X. index, significantly. Sodium-alginate pellets with A. flagrans spores were produced for vineyard soil inoculation under laboratory conditions. The NTF A. conoides, A. musiformis and A. superba were enriched from several soil samples, showing their natural presence. Trap formation is an energy-consuming process and depends upon various biotic and abiotic stimuli. Here, we show that bacteria of the genus Delftia, Bacillus, Pseudomonas, Enterobacter and Serratia induced trap formation in NTF like A. conoides and A. oligospora but not in A. flagrans in the absence of nematodes. The application of NTF along with such bacteria could be a combinatorial way of efficient biocontrol in nematode-infested soil.

Three Methods Assessing the Association of the Endophytic Entomopathogenic Fungus Metarhizium robertsii with Non-Grafted Grapevine Vitis vinifera

Characterizing the association of endophytic insect pathogenic fungi (EIPF) with plants is an important step in order to understand their ecology before using them in biological control programs. Since several methods are available, it is challenging to identify the most appropriate for such investigations. Here, we used two strains of Metarhizium robertsii: EF3.5(2) native to the French vineyard environment and ARSEF-2575-GFP a laboratory strain expressing a green fluorescent protein, to compare their potential of association with non-grafted grapevine Vitis vinifera. Three methods were used to evaluate the kinetics of rhizosphere and grapevine endospheric colonization: (i) Droplet Digital (ddPCR), a sensitive molecular method of M. robertsii DNA quantification in different plant parts, (ii) culture-based method to detect the live fungal propagules from plant tissues that grew on the medium, (iii) confocal imaging to observe roots segments. Both strains showed evidence of establishment in the rhizosphere of grapevines according to the culture-based and ddPCR methods, with a significantly higher establishment of strain EF3.5(2) (40% positive plants and quantified median of exp(4.61) c/μL) compared to strain ARSEF-2575-GFP (13% positive plants and quantified median of exp(2.25) c/μL) at 96-98 days post-inoculation. A low incidence of association of both strains in the grapevine root endosphere was found with no significant differences between strains and evaluation methods (15% positive plants inoculated with strain EF3.5(2) and 5% with strain ARSEF-2575-GFP according to culture-based method). ddPCR should be used more extensively to investigate the association between plants and EIPF but always accompanied with at least one method such as culture-based method or confocal microscopy.

A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia

The gardenia is a traditional medicinal horticultural plant in China, but its molecular genetic research has been largely hysteretic. Here, we constructed an F₁ population with 200 true hybrid individuals. Using the genotyping-by-sequencing method, a high-density sex-average genetic map was generated that contained 4,249 SNPs with a total length of 1956.28 cM and an average genetic distance of 0.46 cM. We developed 17 SNP-based Kompetitive Allele-Specific PCR markers and found that 15 SNPs were successfully genotyped, of which 13 single-nucleotide polymorphism genotypings of 96 F₁ individuals showed genotypes consistent with GBS-mined genotypes. A genomic collinearity analysis between gardenia and the Rubiaceae species Coffea arabica, Coffea canephora and Ophiorrhiza pumila showed the relativity strong conservation of LG11 with NC_039,919.1, HG974438.1 and Bliw01000011.1, respectively. Lastly, a quantitative trait loci analysis at three phenotyping time points (2019, 2020, and 2021) yielded 18 QTLs for growth-related traits and 31 QTLs for leaf-related traits, of which qBSBN7-1, qCD8 and qLNP2-1 could be repeatably detected. Five QTL regions (qCD8 and qSBD8, qBSBN7 and qSI7, qCD4-1 and qLLLS4, qLNP10 and qSLWS10-2, qSBD10 and qLLLS10) with potential pleiotropic effects were also observed. This study provides novel insight into molecular genetic research and could be helpful for further gene cloning and marker-assisted selection for early growth and development traits in the gardenia.

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.

Selected Genotypes with the Genetic Background of Vitis aestivalis and Vitis labrusca Are Resistant to Xiphinema index

The ectoparasitic nematode Xiphinema index transmits grapevine fanleaf virus (GFLV) during feeding on grapevine roots, causing fanleaf degeneration in the plant. Hence, resistance breeding is a key to develop novel rootstocks to overcome such threats. In past years, various grapevine species were screened, and a few candidates with partial resistance were identified. However, they were hardly sufficient for viticulture because of their many agronomical defects. To develop reliably resistant rootstocks applicable in viticulture, multiple Vitis spp. genotypes were analyzed using root inoculation with nematodes in glass vials as an early and easy evaluation test. Resistance levels were evaluated 35 days after inoculation based on nematode reproduction factors, focusing on juveniles and eggs. Infection of grapevines with GFLV was analyzed after inoculation with viruliferous X. index. With this fast screening system, putative candidates with resistances against X. index have been identified for future breeding programs. Particularly, genotypes with the genetic background of Vitis aestivalis and Vitis labrusca were found to be nematode-resistant.

Evidence of Sexual Reproduction Events in the Dagger Nematode Xiphinema index in Grapevine Resistance Experiments Under Controlled Conditions

The dagger nematode Xiphinema index has a major economic impact because of its transmission of Grapevine fanleaf virus to grapevines. This vector nematode, which was introduced into Western countries from the Middle East together with the domesticated grapevine, mostly reproduces by meiotic parthenogenesis, but microsatellite multilocus genotype (MLG) analysis has revealed the occurrence of rare sexual reproduction events in field conditions. In a previous 6-year study under controlled conditions, we evaluated the durability of resistance to X. index in accessions derived from a muscadine resistance source and reference accessions. In this previous study, we used an equal-proportion mixture of four lines (from Spain, Italy, Greece, and Iran) representative of X. index diversity as the inoculum, and we collected random samples in 3-, 4-, 5-, and 6-year-old vines. Here, we genotyped the individuals from these samples using the MLG technique, and we analyzed the changes in line frequency and the occurrence of sexual reproduction events between lines over time. The nematode lines differed in aggressiveness and hybrids between lines were detected at a low, but apparently increasing rate. Hybridization events were recovered in all accessions, regardless of resistance status and propagation type. Finally, our data provide the first evidence of sexual reproduction in the nematode X. index under controlled conditions.

A single resistance factor to solve vineyard degeneration due to grapevine fanleaf virus

Grapevine fanleaf disease, caused by grapevine fanleaf virus (GFLV), transmitted by the soil-borne nematode Xiphinema index, provokes severe symptoms and economic losses, threatening vineyards worldwide. As no effective solution exists so far to control grapevine fanleaf disease in an environmentally friendly way, we investigated the presence of resistance to GFLV in grapevine genetic resources. We discovered that the Riesling variety displays resistance to GFLV, although it is susceptible to X. index. This resistance is determined by a single recessive factor located on grapevine chromosome 1, which we have named rgflv1. The discovery of rgflv1 paves the way for the first effective and environmentally friendly solution to control grapevine fanleaf disease through the development of new GFLV-resistant grapevine rootstocks, which was hitherto an unthinkable prospect. Moreover, rgflv1 is putatively distinct from the virus susceptibility factors already described in plants.

Potential Global Distribution of Daktulosphaira vitifoliae under Climate Change Based on MaxEnt

Simple Summary

Daktulosphaira vitifoliae (Fitch) or grape phylloxera is a small, invasive, and sap-sucking insect widely distribution in most viticultural areas of the world. In the current study, the potential distribution ranges of the leaf-feeding population under current and future environmental conditions were simulated by MaxEnt software. The highly suitable ranges of D. vitifoliae mainly focus on Europe, East and North China, Japan, the Eastern USA, Uruguay, and the Southeast of South America under current climatic conditions. The highly suitable ranges were obviously increased under future climate conditions.

Abstract

Grape phylloxera, Daktulosphaira vitifoliae, is a small, invasive, sap-sucking pest that is widely present in most viticulture regions all over the world. It is originally from North America and feeds on grapevine roots and leaves. In the current study, the potential distribution area of the leaf-feeding population was investigated with MaxEnt based on population occurrence data under different environmental variables. Results suggested that under current climatic conditions, Europe, East and North China, Japan, the Eastern USA, Uruguay, and the Southeast of South America are highly suitable areas for the occurrence of phylloxera leaf populations. The results showed that isothermality and precipitation of coldest quarter were major factors which contribute more than 60% of the model under current climate conditions. Our results provide important information for governmental decision makers and famers to develop control and management strategies against D. vitifoliae, and can also be used as a reference for studies on other invasive pest.

Behind the curtain of the compartmentalization process: Exploring how xylem vessel diameter impacts vascular pathogen resistance

A key determinant of plant resistance to vascular infections lies in the ability of the host to successfully compartmentalize invaders at the xylem level. Growing evidence supports that the structural properties of the vascular system impact host vulnerability towards vascular pathogens. The aim of this study was to provide further insight into the impact of xylem vessel diameter on compartmentalization efficiency and thus vascular pathogen movement, using the interaction between Vitis and Phaeomoniella chlamydospora as a model system. We showed experimentally that an increased number of xylem vessels above 100 μm of diameter resulted in a higher mean infection level of host tissue. This benchmark was validated within and across Vitis genotypes. Although the ability of genotypes to restore vascular cambium integrity upon infection was highly variable, this trait did not correlate with their ability to impede pathogen movement at the xylem level. The distribution of infection severity of cuttings across the range of genotype's susceptibility suggests that a risk-based mechanism is involved. We used this experimental data to calibrate a mechanistic stochastic model of the pathogen spread and we provide evidence that the efficiency of the compartmentalization process within a given xylem vessel is a function of its diameter.