Moving towards grapevine genotypes better adapted to abiotic constraints

Vitis spp., both in their cultivated and wild forms, have been growing in a large diversity of environments for thousands of years. As a result, they have developed many adaptive mechanisms controlled by a range of regulatory processes. The cultivated species, Vitis vinifera, is quite well adapted to semi-arid conditions and its cultivation can be used to produce crops on marginal lands. However, this is threatened by climate change, which is associated with increased temperature and CO2 atmospheric content, changes in water availability and an increased likelihood of extreme events, such as heat waves and early spring frosts. Indirect effects of climate change on solar radiation and soil minerals are also expected. Consequently, cultivated grapevines will presumably face more abiotic constraints occurring concomitantly or successively over one or more growing cycles. In addition to climate change, worldwide viticulture must reduce the use of pesticides. Adapting to climate change and reducing pesticide use are challenging, and increase the need to create new grapevine varieties that are more resistant to diseases and better adapted to abiotic constraints. For this purpose, the adaptive mechanisms of wild and cultivated Vitis spp. must be exploited. While major advances have already been made in exploiting wild alleles for disease resistance, the polygenic nature of adaptation to abiotic factors has slowed down research progress. To tackle this limitation, ambitious integrative strategies need to be undertaken from collection and characterization of genetic resources, investigations on genetic architecture and identification of underlying genes (including those involved in epigenetic regulation), to the implementation of new breeding technologies and the development of genomic selection. An update on the state-of-the-art regarding these aspects is presented

Multi-scale high-throughput phenotyping of apple architectural and functional traits in orchard reveals genotypic variability under contrasted watering regimes

Despite previous reports on the genotypic variation of architectural and functional traits in fruit trees, phenotyping large populations in the field remains challenging. In this study, we used high-throughput phenotyping methods on an apple tree core-collection (1000 individuals) grown under contrasted watering regimes. First, architectural phenotyping was achieved using T-LiDAR scans for estimating convex and alpha hull volumes and the silhouette to total leaf area ratio (STAR). Second, a semi-empirical index (IPL) was computed from chlorophyll fluorescence measurements, as a proxy for leaf photosynthesis. Last, thermal infrared and multispectral airborne imaging was used for computing canopy temperature variations, water deficit, and vegetation indices. All traits estimated by these methods were compared to low-throughput in planta measurements. Vegetation indices and alpha hull volumes were significantly correlated with tree leaf area and trunk cross sectional area, while IPL values showed strong correlations with photosynthesis measurements collected on an independent leaf dataset. By contrast, correlations between stomatal conductance and canopy temperature estimated from airborne images were lower, emphasizing discrepancies across measurement scales. High heritability values were obtained for almost all the traits except leaf photosynthesis, likely due to large intra-tree variation. Genotypic means were used in a clustering procedure that defined six classes of architectural and functional combinations. Differences between groups showed several combinations between architectural and functional traits, suggesting independent genetic controls. This study demonstrates the feasibility and relevance of combining multi-scale high-throughput methods and paves the way to explore the genetic bases of architectural and functional variations in woody crops in field conditions

Genetic and environmental dissection of biomass accumulation in multi-genotype maize canopies

International audienceMulti-genotype canopies are frequent in phenotyping experiments and are of increasing interest in agriculture. Radiation interception efficiency (RIE) and radiation use efficiency (RUE) have low heritabilities in such canopies. We propose a revised Monteith equation that identifies environmental and genetic components of RIE and RUE. An environmental term, a component of RIE, characterizes the effect of the presence or absence of neighbours on light interception. The ability of a given plant to compete with its neighbours is then identified, which accounts for the genetic variability of RIE of plants having similar leaf areas. This method was used in three experiments in a phenotyping platform with 765 plants of 255 maize hybrids. As expected, the heritability of the environmental term was near zero, whereas that of the competitiveness term increased with phenological stage, resulting in the identification of quantitative trait loci. In the same way, RUE was dissected as an effect of intercepted light and a genetic term. This approach was used for predicting the behaviour of individual genotypes in virtual multi-genotype canopies. A large effect of competitiveness was observed in multi-genotype but not in single-genotype canopies, resulting in a bias for genotype comparisons in breeding fields

Target enrichment sequencing coupled with GWAS identifies MdPRX10 as a candidate gene in the control of budbreak in apple

The timing of floral budbreak in apple has a significant effect on fruit production and quality. Budbreak occurs as a result of a complex molecular mechanism that relies on accurate integration of external environmental cues, principally temperature. In the pursuit of understanding this mechanism, especially with respect to aiding adaptation to climate change, a QTL at the top of linkage group (LG) 9 has been identified by many studies on budbreak, but the genes underlying it remain elusive. Here, together with a dessert apple core collection of 239 cultivars, we used a targeted capture sequencing approach to increase SNP resolution in apple orthologues of known or suspected A. thaliana flowering time-related genes, as well as approximately 200 genes within the LG9 QTL interval. This increased the 275 223 SNP Axiom® Apple 480 K array dataset by an additional 40 857 markers. Robust GWAS analyses identified MdPRX10, a peroxidase superfamily gene, as a strong candidate that demonstrated a dormancy-related expression pattern and down-regulation in response to chilling. In-silico analyses also predicted the residue change resulting from the SNP allele associated with late budbreak could alter protein conformation and likely function. Late budbreak cultivars homozygous for this SNP allele also showed significantly up-regulated expression of C-REPEAT BINDING FACTOR (CBF) genes, which are involved in cold tolerance and perception, compared to reference cultivars, such as Gala. Taken together, these results indicate a role for MdPRX10 in budbreak, potentially via redox-mediated signaling and CBF gene regulation. Moving forward, this provides a focus for developing our understanding of the effects of temperature on flowering time and how redox processes may influence integration of external cues in dormancy pathways

Physiological and genetic determinisms of water-use in grapevine

La raréfaction des ressources en eau associée au changement climatique menace particulièrement la durabilité de la viticulture en climat Méditerranéen. Pour y faire face, la création ou le choix de cépages économes en eau et suffisamment vigoureux en cas de déficit hydrique se présente comme un levier important. Une compréhension approfondie des mécanismes qui gouvernent le maintien de l'état hydrique par la plante est indispensable pour avancer dans cette direction. Dans ce travail les déterminants génétiques et physiologiques de l'utilisation de l'eau ont été explorés chez la vigne. Une descendance F1, issue d'un croisement entre les cépages Syrah et Grenache, a été soumise à deux scénarios hydriques dans des pots (bonne irrigation et déficit modéré) en combinant de nouveaux outils de phénotypage, une démarche de génétique quantitative (pour la détection de QTLs) et des approches physiologiques. L'analyse de l'architecture génétique du maintien du potentiel hydrique par la plante, plus ou moins efficace en cas de déficit hydrique (i.e. iso- ou aniso-hydrique), a révélé un double déterminisme, impliquant non seulement la régulation stomatique de la transpiration mais également le maintien de la conductance hydraulique à travers la plante. Nous avons démontré l'existence d'une action indirecte de l'acide abscissique sur la fermeture stomatique à travers une diminution de la conductance hydraulique dans la feuille avec une variabilité génétique reliée aux comportements iso- ou aniso-hydriques. Par ailleurs, nous avons mis en évidence une variabilité génétique importante de la transpiration nocturne, liée à celle de l'efficience d'utilisation de l'eau, avec des déterminants génétiques et physiologiques que nous avons identifiés. Au-delà de l'utilité des QTLs détectés pour l'amélioration variétale, les résultats originaux de ce travail démontrent l'intérêt de la génétique quantitative pour progresser dans la compréhension de mécanismes physiologiques.In Mediterranean regions, water scarcity associated with climate change particularly threatens the sustainability of viticulture. Breeding grapevine for reduced water use and maintained production is therefore of major interest. This requires a comprehensive knowledge of the plant physiological responses to drought. In this study we focused on the determinism of transpiration rate as a key trait regulating water status in plant tissues, and on its relationship with water-use efficiency (WUE). We used a F1 progeny from a cross between cultivars Syrah and Grenache and combined powerful phenotyping tools on potted plants submitted to either well-watered or mild deficit conditions with quantitative genetics (for QTL detection) and physiological experiments. Analysis of the genetic control of water status maintenance in the plant, more or less efficient under soil water deficit (i.e. iso- or anisohydric), revealed a dual physiological determinism with a key role for plant hydraulic conductance beside that of stomatal control of transpiration. An indirect role of abscisic acid on stomatal conductance was also evidenced, mediated by the downregulation of leaf hydraulic conductance, with a genetic variability which correlated with genetic variation in iso- or aniso-hydric behaviour. We then revealed wide genetic variations in nocturnal transpiration, which correlated with variations in water use efficiency, and identified corresponding genetic and physiological determinants. In a final switch to the field, we showed consistency between QTLs detected for daytime WUE in pots and in the vineyard. Beyond the potential interest of the QTLs detected in this study for breeding prospects, this work demonstrated the benefits of quantitative genetics to shed light on ecophysiological and physiological processes

Déterminismes physiologique et génétique de l’utilisation de l’eau chez la vigne

In Mediterranean regions, water scarcity associated with climate change particularly threatens the sustainability of viticulture. Breeding grapevine for reduced water use and maintained production is therefore of major interest. This requires a comprehensive knowledge of the plant physiological responses to drought. In this study we focused on the determinism of transpiration rate as a key trait regulating water status in plant tissues, and on its relationship with water-use efficiency (WUE). We used a F1 progeny from a cross between cultivars Syrah and Grenache and combined powerful phenotyping tools on potted plants submitted to either well-watered or mild deficit conditions with quantitative genetics (for QTL detection) and physiological experiments. Analysis of the genetic control of water status maintenance in the plant, more or less efficient under soil water deficit (i.e. iso- or anisohydric), revealed a dual physiological determinism with a key role for plant hydraulic conductance beside that of stomatal control of transpiration. An indirect role of abscisic acid on stomatal conductance was also evidenced, mediated by the downregulation of leaf hydraulic conductance, with a genetic variability which correlated with genetic variation in iso- or aniso-hydric behaviour. We then revealed wide genetic variations in nocturnal transpiration, which correlated with variations in water use efficiency, and identified corresponding genetic and physiological determinants. In a final switch to the field, we showed consistency between QTLs detected for daytime WUE in pots and in the vineyard. Beyond the potential interest of the QTLs detected in this study for breeding prospects, this work demonstrated the benefits of quantitative genetics to shed light on ecophysiological and physiological processes.La raréfaction des ressources en eau associée au changement climatique menace particulièrement la durabilité de la viticulture en climat Méditerranéen. Pour y faire face, la création ou le choix de cépages économes en eau et suffisamment vigoureux en cas de déficit hydrique se présente comme un levier important. Une compréhension approfondie des mécanismes qui gouvernent le maintien de l'état hydrique par la plante est indispensable pour avancer dans cette direction. Dans ce travail les déterminants génétiques et physiologiques de l'utilisation de l'eau ont été explorés chez la vigne. Une descendance F1, issue d'un croisement entre les cépages Syrah et Grenache, a été soumise à deux scénarios hydriques dans des pots (bonne irrigation et déficit modéré) en combinant de nouveaux outils de phénotypage, une démarche de génétique quantitative (pour la détection de QTLs) et des approches physiologiques. L'analyse de l'architecture génétique du maintien du potentiel hydrique par la plante, plus ou moins efficace en cas de déficit hydrique (i.e. iso- ou aniso-hydrique), a révélé un double déterminisme, impliquant non seulement la régulation stomatique de la transpiration mais également le maintien de la conductance hydraulique à travers la plante. Nous avons démontré l'existence d'une action indirecte de l'acide abscissique sur la fermeture stomatique à travers une diminution de la conductance hydraulique dans la feuille avec une variabilité génétique reliée aux comportements iso- ou aniso-hydriques. Par ailleurs, nous avons mis en évidence une variabilité génétique importante de la transpiration nocturne, liée à celle de l'efficience d'utilisation de l'eau, avec des déterminants génétiques et physiologiques que nous avons identifiés. Au-delà de l'utilité des QTLs détectés pour l'amélioration variétale, les résultats originaux de ce travail démontrent l'intérêt de la génétique quantitative pour progresser dans la compréhension de mécanismes physiologiques

Genetic architecture of water use efficiency in grapevine: a key role for night transpiration

National audienceImproving water use efficiency (WUE, the balance between biomass production and water costs) in crops becomes crucial to match increasing needs for food in a context of global change. Reduction of water loss at night could be a good strategy to limit waste of water without altering photosynthesis rate in the daytime. However, genetic and physiological bases of night transpiration and its contribution to WUE remain poorly documented. This study first aimed at deciphering the genetic determinants of WUE in grapevine, a woody crop of economic importance in drought prone areas. It further explored a possible role for night transpiration in WUE variability. A four-year experiment was run on a F1 progeny from a cross between Shiraz and Grenache. A greenhouse phenotyping facility (PhenoArch, Montpellier) was used to dissect determinants of WUE in potted plants and results were compared to those obtained in vineyard conditions under two soil water regimes. In PhenoArch, a high genetic variability was found and QTLs were detected for whole plant WUE under both watering regimes. Interestingly, these QTLs co-localized with those found for proxys of WUE (Δ13C in musts) measured in the field, highlighting the promising avenues offered by phenotyping facilities. Furthermore, a genetic control of water losses at night was detected and supported for the first time by QTL detection. Night transpiration could reach 30% of daytime one depending on genotype and conditions. Furthermore, we found common QTLs to WUE and night transpiration. This, together with significant negative correlations between both traits, strongly suggested that lower WUE relies, at least partly, on higher water losses at night. Through further physiological characterization of the determinants of night transpiration, we showed that both residual stomatal aperture and cuticle losses are genetically controlled. These results open new avenues to breed grapevine for lower water losses at night

A Combination of Phenotyping, Genetic and Physiological Approaches to Guide Breeding for Efficient Water Use in Grapevine

International audienceWater scarcity associated with climate change particularly threatens the sustainability of viticulture in most cultivated, drought prone areas. Breeding grapevine for reduced water use and maintained production (that is high water-use efficiency) is therefore of major interest. This requires a comprehensive knowledge of the physiological impacts of drought which are the most influential on yield and quality. Special attention should be paid to those mechanisms involved in the regulation of water status in plant tissues as the primary parameter affected by drought. Transpiration rate, which has major influence on plant water status, together with water-use efficiency, therefore require special attention in breeding programs. To progress on the determinism of transpiration rate and water-use efficiency in grapevine, we used a F1 progeny made of 188 genotypes from a cross between two widespread cultivars, Syrah and Grenache, well-known for their contrasted water use. We showed the benefits of combining quantitative genetics (for QTL detection) and physiological experiments to study this population both in the vineyard and on potted plants. On the one hand, we developed an original experimental design in the field coupled to geostatistical modelling to take into account the spatial variability of soil water status inherent to vineyard conditions. This helped to identify significant genetic variability for the traits of interest. On the other hand, we combined powerful phenotyping tools on potted plants (high-throughput platform and controlled chambers) to control water deficit conditions and improve QTL detection. First, we found evidence that a dual physiological mechanism controls the decline of leaf water status under drought with a key role for plant hydraulic conductance beside that of stomatal control of transpiration. Contrasted combination of these two controls may lead to more or less efficient maintenance of leaf water status in response to soil drying (i.e. iso- or an isohydric behaviour). An indirect role of abscisic acid on stomatal conductance was also identified, mediated by the downregulation of leaf hydraulic conductance, with a genetic variability which correlated with genetic variation in iso- or aniso-hydric behaviour. We then revealed wide genetic variations in nocturnal transpiration, which correlated with variations in whole plant water-use efficiency (WUE), and identified corresponding genetic and physiological determinants. Lastly, we showed some consistency between QTLs detected for daytime WUE in pots and in the vineyard. Beyond the potential interest of the QTLs detected in this study for breeding prospects, this work demonstrated the interest of quantitative genetics to shed light on ecophysiological and physiological processes