Elisa Marguerit

Understanding how grafts form has fascinated scientists for over a century, and numerous transcription regulators involved in wound healing, callus formation, and grafting have been identified in model plants. However, the genetic architecture underlying grafting traits remains poorly characterized. To address this gap, we aimed to identify quantitative trait loci (QTLs) associated with grafting success rates and grafting-related traits (including callus formation, mechanical strength of the graft union, and post-grafting growth) in a grapevine rootstock mapping population, Vitis berlandieri × V. rupestris . Although no QTLs were identified for grafting success rate, QTLs were identified for component traits revealing a genetic architecture that would have remained hidden when considering grafting success as a single composite phenotype. By integrating QTL and transcriptome data, we identified regulators potentially mediating grafting-related traits. We then showed that one transcription factor that regulates callus formation and grafting in Arabidopsis potentially has a similar role in grapevine by silencing with exogenous double-stranded RNAs and that exogenous application of methyl jasmonate increases callus development at the graft interface. Candidate transcriptional regulators located within QTLs and evidence from gene silencing and hormone treatments suggest the conservation of regulatory mechanisms underlying wound-induced callus formation across plant species. Highlight: Grafting success is a complex phenotype that can be dissected into component traits. The combination of genetics, genomics and hormone treatments identified regulators controlling callus and potentially graft development.

Deciphering the genetic architecture of complex quantitative phenotypes remains challenging in quantitative genetics. These traits not only depend of multiple genetic factors but are also established over time and environments. Although quantitative genetics has investigated the genetic determinism of phenotypic plasticity in contrasted environmental conditions, the time related phenotypic plasticity has received less attention. Here we proposed a multivariate Bayesian framework, the Bayesian Varying Coefficient Model, designed for analysing the genetic architecture of the time related phenotypic plasticity by a multilocus approach. We applied the BVCM to time series phenotypes measured at various time scales (daily, monthly, yearly) across a diverse set of biological species. We included in this study: yeast (Saccharomyces cerevisiae), fungi (Fusarium graminearum), eucalyptus (Eucalyptus urophylla x E. grandis), and sweet cherry tree (Prunus avium). The BVCM results were compared with those obtained with a known genome-wide association method carried out time by time. For all species and traits, the BVCM was able to detect the major QTL identified by marker-trait association methods and revealed additional genetic regions of weak effect. It also increased the phenotypic variance explained for most of the phenotypes considered. It revealed dynamic QTLs with transitory, increasing or decreasing effects over time. By considering both the temporal and genetic multivariate structures in a single statistical model, we increased our understanding of the genetic architecture of complex traits notably by reducing the issue of missing heritability. More broadly, this work raises the foundation for extended applications in functional genomics, evolutionary ecology, and crop breeding programs, in which time-related phenotypic plasticity remains crucial for predicting and selecting key quantitative complex traits.

Dans le contexte de raréfaction de la ressource en eau, il est nécessaire de prendre en compte le caractère de tolérance à la sécheresse dans les programmes d’amélioration variétale, en particulier pour les porte-greffes de vigne. L’objectif de cette thèse est d’analyser, à l’échelle de la plante entière, le déterminisme génétique des effets du porte-greffe sur les réponses de la tranpiration et de la croissance, au niveau de la partie aérienne, en conditions de déficit hydrique édaphique. L’étude de ces caractères complexes, soumis à une forte interaction génotype × environnement, a été conduite à partir d’une approche de génétique quantitative où ces interactions ont été intégrées par deux approches : l’utilisation des paramètres de courbes de réponses comme caractère quantitatif et la mise en oeuvre d’une analyse QTL pluriannuelle. Une population de type F1, issu du croisement Vitis vinifera Cabernet Sauvignon × Vitis riparia Gloire de Montpellier, constituée de 138 individus, a été cartographiée génétiquement avec des marqueurs microsatellites. Cette descendance a été ensuite phénotypée en position de porte-greffe, avec un greffon unique. A partir de cet outil, des QTL ont été recherchés et identifiés pour la transpiration, l’efficience d’utilisation de l’eau et la plasticité de la transpiration induite par le porte-greffe, ainsi que pour plusieurs paramètres de la croissance et de l’allocation de la biomasse au sein de la plante entière. La plasticité de la transpiration réponse à l’état hydrique du substrat est déterminée génétiquement par des régions distinctes des autres caractères descriptifs de la consommation en eau. La colocalisation de gènes candidats dans les intervalles de confiance des QTL, impliqués dans la signalisation chimique (ABA) ou hydraulique (aquaporines) permet de formuler des hypothèses sur la signalisation porte-greffe/ greffon en condition de déficit hydrique. Des régions spécifiques du génome paraissent contrôler la croissance et la vigueur conférée par le porte-greffe en conditions de déficit hydrique. Ces régions sont également indépendantes de celles contrôlant la transpiration ou l’efficience d’utilisation de l’eau. Ce résultat permet d’envisager un travail de sélection pour ces deux catégories de caractères de manière indépendante

Background: Deciphering the genetic basis of above and below ground organs communication is essential for plant adaptation. In grafted perennial crops, such as grapevine, identifying genes from the roots system controlling the expression of shoot traits is essential to improve plant adaptation to environmental conditions through rootstock breeding. However, the grapevine rootstocks genetic control on conferred scion traits has rarely been explored and even less considering genetic diversity at the intra-species level through GWAS. In this study we used a Vitis berlandieri natural population comprising 211 genotypes, grafted with a single scion genotype, to identify genetic regions associated with water use efficiency and shoot biomass conferred to the scion using GWAS in field conditions. Water use efficiency was evaluated by δ ¹³ C over three years and the shoot biomass produced every year during the first two years of growth after plantation. Results: δ ¹³ C and shoot biomass were not correlated. δ ¹³ C indicated a moderate broad sense heritability from 0.34 to 0.46 in the absence or under moderate water deficit. Heritability falls to zero under strong water deficit indicating a major contribution of environmental conditions. The shoot biomass heritability was moderate to strong from 0.34 to 0.70. One QTL for δ ¹³ C explained 54% of the genetic variance. The QTL was associated with a gene homolog to AT4G22790 , coding for a mate family protein involved in stomatal aperture regulation in response to carbon dioxide concentration. Four QTL for shoot biomass were linked with genes homologous to AT5G19350, AT4G37130, AT1G22020, and AT1G15780 known to be involved in vegetative growth and root development, hormonal signalling, photorespiration, and response to light, respectively. Conclusion: This study represents the first GWAS carried out for scion traits conferred by a natural Vitis berlandieri rootstock population in a field experiment. It contributes to the understanding of the genetic basis of shoot plant performance regulated by roots. Ultimately, these outcomes provide valuable targets for breeding programs suggesting that rootstocks selection based on genetic information and morphological traits could improve crop adaptation to future environments, contributing to sustainable agriculture.

Root traits are fundamental to plant establishment and survival, influencing resource acquisition, anchorage, and stress resilience. In grapevine, a perennial grafted fruit crop, early growth-related traits, such as rooting and grafting success, are crucial for both vineyard establishment and nursery production, which require well-developed rootstock mother vines and grafted plants. An understanding of the genetic variability underlying these traits is therefore important. We investigated the genetic architecture of early growth-related traits in a Vitis berlandieri × V. rupestris mapping population of 449 genotypes, using hardwood cuttings and grafted plants with two scion cultivars: V. vinifera cvs. Cabernet Sauvignon and Riesling. Our results indicate that the genetic control of these traits was polygenic and varied with the method of propagation (cuttings vs grafts), with individual QTLs explaining from 3.1% to 14.1% of the phenotypic variance. In particular, we detected largely non-overlapping genomic regions associated with similar traits across propagation methods and observed rootstock × scion interactions, suggesting an influence of scion genotype on root development. Two overlapping roots number QTLs were identified in grafts with different scions accounted for 7 and 14% of the variance in Cabernet Sauvignon and Riesling, respectively. Our results highlight the challenge of applying marker-assisted selection in rootstock breeding programs, due to the different genetic determinants underlying the same traits across the different propagation methods. Here, we found that QTLs colocalized with genes involved in growth and stress responses. Finally, eight genotypes with root-related performance superior to that of commercial rootstocks were identified, providing promising candidates for further evaluation in grapevine rootstock breeding programs.

Field experiments are complex to interpret due to interactions between genotypes, environment, plant development and cultivation practices. This complexity challenges the accurate phenotyping of individual plant traits over the season. Here, we quantified the primary sources of seasonal variation in stomatal conductance (gs) across 15 grapevine cultivar–rootstock combinations within a large-scale phenotyping platform, comprising over 6000 observations. Environment-related traits and date of measurement accounted for up to 76% of the variance, potentially obscuring cultivar–rootstock effects. Therefore, we integrated machine learning, spatiotemporal normalization of the gs response, and the use of mixed models to disentangle the influences of environmental factors, plant material and crop performance related traits. After spatio-temporal normalization, cultivar and cultivar–rootstock interactions explained over 25% of the variation in gs, and Grenache exhibited the most conservative water-use behavior resulting in high water-use efficiency. Specific rootstock–scion combinations also exhibited smaller, but still significant, differences in gs and water-use efficiency, highlighting the specificity arising from the interaction within each rootstock–scion combination. The high variability in gs indicates that accurate quantification of rootstock–scion contributions to key traits in field studies is complex and requires accounting for spatial heterogeneity driven by the environment.

Rootstocks play a crucial role in viticulture because of both their agronomic benefits and impact on grape and wine chemical composition. Their influence on vigor, yield, and phenolic maturity has been widely studied, but only recently have studies begun to examine their effects on wine aroma compounds and sensory profiles. This review compiles findings of studies investigating 33 rootstocks for their influence on wine aroma composition and 29 rootstocks for sensory evaluation across 10 red and four white grape varieties. The most studied rootstocks include 1103 Paulsen, 110 Richter, Sélection Oppenheim 4 and 101-14 Millardet et de Grasset. Shiraz, Merlot, and Cabernet-Sauvignon are the most frequently assessed varieties. Despite growing works in this research area, results are highly variable due to differences in experimental design, winemaking protocols, and sensory methodologies. Only five studies have simultaneously analyzed both wine aroma compounds and sensory attributes. While some consistent trends emerge for certain aroma compounds, such as β-damascenone or linalool, most findings remain context-dependent. This review emphasizes a lack of standardization, including that of winemaking conditions, and highlights the critical need for multi-site, multi-year studies to better understand rootstock effects on wine aroma and sensory quality.

Adaptation to drought is one of the most important challenges for agriculture. The root system, along with its integration with the soil, is fundamental in conferring drought tolerance. At the same time, it is extremely challenging to study. The result is that investigations aimed at increasing crop drought tolerance have mainly focused on above-ground traits, especially for perennial species. In this review, we explore the root trait syndromes that would constitute drought-tolerant ideotypes, taking the example of grapevine as a model perennial grafted plant. We introduce and discuss the complexity of root trait interactions across different spatial and temporal scales considering their diversity, plasticity, and possible trade-offs. Finally, we review future approaches for discovering hidden root trait syndromes conferring drought tolerance, such as state-of-the-art root phenotyping technologies, the use of modeling as a tool to upscale root traits to the field, and new strategies to link genes to phenotypes. Together these integrated approaches can improve the breeding of drought-tolerant grapevine rootstocks.

Rootstocks are an important means of adapting grapevine to environmental conditions whilst conserving the typical features of scion genotypes. Rootstocks not only provide tolerance to Phylloxera, but also ensure the supply of water and mineral nutrients to the scion. We take advantage of the large diversity of rootstocks used worldwide to facilitate this adaptation. The aim of this study was to characterise rootstock regulation of scion mineral status and its relationship with scion development.Vitis vinifera cvs. Cabernet-Sauvignon, Pinot noir, Syrah and Ugni blanc were grafted onto 55 different rootstock genotypes and planted as three replicates of five plants in sandy gravelly soil near Bordeaux, France. In 2020 and 2021, petiolar concentrations of 13 mineral elements (N, P, K, S, Mg, Ca, Na, B, Zn, Mn, Fe, Cu and Al) were measured at veraison. Winter pruning weight, shoot vigour, leaf chlorophyll content, bud fertility and yield were measured. Magnesium deficiency severity was visually scored for each plant. Rootstocks were grouped according to their Vitis parentage background when at least 50 % of a Vitis species was present in order to determine whether the petiole mineral composition could be related to the rootstock genetic parentage.Scion, rootstock, and their interactions had a significant influence on petiole mineral content and explained the same proportion of phenotypic variance for most mineral elements. Rootstock effect explained 9, 28 and 45 % of the mineral content variance for N, Mg and S respectively. This unique experimental design showed that the rootstock effect was higher than the scion effect on the petiole concentration of a large majority of mineral elements. The genetic background V. riparia increased the probability of low petiolar P and Mg contents. The severity of Mg deficiency symptoms varied depending on the rootstock. The differences in mineral status conferred by rootstocks were not significantly correlated with vigour or fertility.The evaluation of Mg levels by petiole analysis and the intensity of deficiency symptoms showed for the first time the variability of the thresholds of satisfactory mineral nutrition between rootstocks. Therefore, fertiliser management should take the rootstock variety into account.

French research on rootstocks is based on two strategies: the creation of new rootstocks and the evaluation of existing rootstocks (GreffAdapt facility). The search for traits associated with drought tolerance has not yet been brought to a successful conclusion, but work is continuing with the emphasis on field experiments, measurement of δ13C, consideration of yield, and study of trait plasticity as a function of the scion and the water status.