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Clonal polymorphism mainly results from somatic mutations that occur naturally during plant growth. In grapevine, arrays of clones have been selected within varieties as a valuable source of diversity, among them clones showing berry color polymorphism. To identify mutations responsible for this color polymorphism, we studied a collection of 33 clones of Pinot noir, Pinot gris, and Pinot blanc. Haplotypes of the L2 cell layer of nine clones were resolved by genotyping self-progenies with molecular markers along a 10.07 Mb region of chromosome 2, including the color locus. We demonstrated that at least six haplotypes could account for the loss of anthocyanin biosynthesis. Four of them resulted from the replacement of sections of the 'colored' haplotype, sized from 31 kb to 4.4 Mb, by the homologous sections of the 'white' haplotype mutated at the color locus. This transfer of information between the two homologous sequences resulted in the partial homozygosity of chromosome 2, associated in one case with a large deletion of 108 kb-long. Moreover, we showed that, in most cases, somatic mutations do not affect the whole plant; instead, they affect only one cell layer, leading to periclinal chimeras associating two genotypes. Analysis of bud sports of Pinot gris support the hypothesis that cell layer rearrangements in the chimera lead to the homogenization of the genotype in the whole plant. Our findings shed new light on the way molecular and cellular mechanisms shape the grapevine genotypes during vegetative propagation, and enable us to propose a scheme of evolutionary mechanism of the Pinot clones.

The genome sequence of the diploid and highly homozygous Vitis vinifera genotype PN40024 serves as the reference for many grapevine studies. Despite several improvements to the PN40024 genome assembly, its current version PN12X.v2 is quite fragmented and only represents the haploid state of the genome with mixed haplotypes. In fact, being nearly homozygous, this genome contains several heterozygous regions that are yet to be resolved. Taking the opportunity of improvements that long-read sequencing technologies offer to fully discriminate haplotype sequences, an improved version of the reference, called PN40024.v4, was generated. Through incorporating long genomic sequencing reads to the assembly, the continuity of the 12X.v2 scaffolds was highly increased with a total number decreasing from 2,059 to 640 and a reduction in N bases of 88%. Additionally, the full alternative haplotype sequence was built for the first time, the chromosome anchoring was improved and the number of unplaced scaffolds was reduced by half. To obtain a high-quality gene annotation that outperforms previous versions, a liftover approach was complemented with an optimized annotation workflow for Vitis. Integration of the gene reference catalogue and its manual curation have also assisted in improving the annotation, while defining the most reliable estimation of 35,230 genes to date. Finally, we demonstrated that PN40024 resulted from 9 selfings of cv. “Helfensteiner” (cross of cv. “Pinot noir” and “Schiava grossa”) instead of a single “Pinot noir”. These advances will help maintain the PN40024 genome as a gold-standard reference, also contributing toward the eventual elaboration of the grapevine pangenome.

Cet article comporte deux parties. La première est une description de l’aqueduc de la colonie romaine d’Arles. À l’époque d’Auguste, des sources situées au sud des Alpilles alimentaient deux canaux qui convergeaient à l’origine dans un bassin à l’amont d’un tronçon terminal. Au début du iie s., sa branche orientale a été affectée à l’alimentation des moulins de Barbegal. L’autre branche a été prolongée vers le nord pour capter des sources dans la vallée de la Durance. Des tunnels ont été creusés à cet effet dans la Petite Crau de Saint-Rémy-de-Provence et dans les interfluves des vallons du versant nord des Alpilles. Dans la seconde partie, la topographie des canaux est utilisée pour évaluer la pertinence du tracé, la place respective des compétences des entrepreneurs qui ont construit l’aqueduc, des contraintes techniques et des limites financières. Compte tenu de la topographie et des conditions géologiques, l’examen des différentes sections montre que l’ouvrage permettait un débit de 300 l/s, soit 26 000 m3 journaliers. Les conditions financières expliquent que des alternatives parfois mieux adaptées n’aient pas été retenues. La principale conclusion qui ressort de cette étude est la volonté de sécuriser l’approvisionnement en eau de la ville. En captant des sources alimentées par la nappe de la Durance, les Arlésiens se sont adaptés à une évolution du climat méditerranéen caractérisée par l’augmentation des épisodes de sécheresse. Ils ont anticipé le recours aux ressources hydriques alpines, qui est une spécificité de l’actuelle gestion de l’eau en Provence et distingue ce territoire des autres régions françaises. The Roman aqueduct of Arles is made up of three sections. The first two were fed by springs on either side of the Alpilles range, one around thirty kilometres to the north-east in the alluvial plain of the Durance, the other to the south of the massif at the foot of Les Baux, at a distance of fifteen kilometres from Arles. These two sections converged in the town of Fontvieille above the deep depression of the Vallée des Baux which separates the Alpilles from La Crau. The third successively crosses this plain and that of the Rhône until its end point in Arles. These three sections are of unequal length. The first measures 38 km from the first point where it is identified, the second 5.60 km from the village of Paradou where the channels bringing water from the two springs converged, and the third 12 km from the basin at this convergence point.They are not contemporary. In the 1990s, excavations established the chronology. The eastern branch dates from the time of Augustus. At the beginning of the 2nd century AD, it was assigned to supply the Barbegal mills while the other branch was extended into the Durance valley. Its 34 m level difference corresponds to an average slope of 0.68 m/km, significantly greater than that of the Nîmes aqueduct which has a level difference of 12.27 m over an equivalent distance, i.e. an average slope estimated at 0.248 m/km. However, these figures do not take into account adaptations to the topography. Differential GPS was used in order carry out georeferencing and hence to achieve accurate levelling. In two cases, the levelling of a section made an essential contribution to the dating of the aqueduct and the evaluation of its flow. At Paradou, it confirms the Augustan attribution by establishing the contemporaneity of the canal with the Aurelian Way, which dates back thousands of years. The slope of the channel was calculated to optimize water flow. It was greatest upstream of the crossing structure, then gradually diminished to prevent overflow caused by excessively rapid slowing. On the basis of the profile of the aqueduct’s route in La Crau, its maximum daily flow can be estimated at 300 l/s or 26,000 m3.In the second part, the altimetry of the canals is used to describe the topographical component of the specifications given to the teams that shared the construction operations, to assess the significance of the route, the skills of the contractors, the technical constraints and the financial restrictions. Since the available data is exclusively archaeological, this section begins by assessing the contribution of written sources and the debates they have prompted. Before the construction of an aqueduct channel, a specialist would determine the precise route, positioning crossing points on the basis of the altimetric factors. The route would then be divided into sections and the construction work allocated to contractors. When the slope was too steep, a drop was created. A bridge would be built or a tunnel dug to avoid the excessive fall loss entailed in going up a valley or around an interfluve. The cost of these operations would affect the choice of route by forcing the project manager to compromise relative to an ideal direct route. Hence, when a topographical feature separated two points from the planned route, the contractors might choose to bypass it rather than opening a deep trench or digging a tunnel. However, bypassing an obstacle would lengthen the channel, reduce the slope and flow speed, and diminish the flow rate. Where this happened, it is possible to observe the effect on the deposits left by the carbonated water: their volume and position are evidence of reduced flows caused by a decrease in the slope or by a counter-slope.The route of the eastern branch of the aqueduct was direct and its slope regular. Between the catchment and the basin where it converged with this eastern branch, the northern Alpilles branch transferred the water captured in the Durance valley to the south. In the northern foothills, the channel trench tunnelled through a height line separating the catchment in the Mollégès marsh from the village of Saint-Rémy. To bypass the western part of the range while losing as little slope as possible, the aqueduct used bridges to enter and cross the valleys cut into the slopes, and crossed the interfluves via tunnels with a cumulative length of 950 m.In the terminal section, which starts at an altitude of 24 m NGF (general levelling of France), the pipe had to maintain sufficient altitude to supply the Roman colony. It successively crossed the Vallon des Arcs on a bridge more than 300 m long and 4 to 5 m high. The deep depression of the Vallée des Baux was crossed by a bridge more than 1 km long comprising around sixty arches more than twenty metres high. Water crossed the subhorizontal plain of La Crau in a deep trench. The aqueduct then descended into the alluvial plain of the Rhône and arrived at Arles in channel supported on arches. It entered a tunnel at an altitude of 16.56 m NGF, 6 m below the highest point of the city.In the Alpilles, the reduced rate of flow in the terminal section crossing the range was caused by the difficulty of levelling an optimal route in a wooded and hilly environment. In La Crau, where this operation did not present any particular difficulty, the shallowness of the slope is explained by a desire to limit the cost of earthworks. During the Augustan period, the colony was satisfied with tapping into springs in the south of the Alpilles, which was enough to supply water to most of the city. At the beginning of the 2nd century, tapping into new sources north of the Alpilles offered the possibility of bringing water to the highest point of the city. But this would have entailed increasing the height of the structures in the final section, at a cost that must have seemed excessive. The most likely explanation for tapping into new sources lies either in an increase in the city’s needs or a drop in the flow of those captured by the southern branch.Financial conditions explain why different and sometimes more appropriate choices were not chosen. Overall, the main conclusion that emerges from this study is the primacy of the desire to secure the city’s water supply. By tapping springs fed by the Durance aquifer, the people of Arles were able to adapt to a change in the Mediterranean climate characterised by increased episodes of drought. They thus anticipated the use of Alpine water resources, which is a specific feature of current water management in Provence and distinguishes this territory from other French regions.

Background Many available interventions to reduce challenges of natural caregivers of people living with dementia have limited efficacy since they do not meet the caregiver’s individual needs. This study aims to evaluate caregivers’ needs with the future goal of developing a tailored, multicomponent intervention to ease caregiver challenges through appropriate caregiver-centred interventions. Methods Mixed method study using a convergent design with quantitative and qualitative data collection and analysis performed at similar times. For the cross-sectional quantitative study, questionnaires were sent to natural adult caregivers of a person with dementia identified by local healthcare professionals and general practitioners exercising in a rural and an urban department. For the qualitative descriptive study, individual caregiver interviews and healthcare professional focus groups were conducted in two primary healthcare territories in both departments. Data about screening for caregiver challenges and any help provided to the caregiver were collected. Quantitative data were analysed using descriptive statistics and qualitative data underwent thematic analysis using the grounded theory approach. Quantitative and qualitative results were described using a narrative discussion approach, then results were combined on a theme-by-theme basis using the weaving approach enabling integrated analysis. Results A total of 199 general practitioners and 67 caregivers participated in the quantitative study. In the qualitative study, 10 caregivers from the urban area and 12 caregivers from the rural area participated in the individual interviews, and 9 healthcare professionals participated in the focus groups. Our broad categories of caregiver needs were identified: awareness and early diagnosis, information and training, practical, coordinated support, and psychological support. The integrated analysis highlighted areas for improvement in meeting these needs, especially a better identification of the caregiver role, caregiver distress, better information about what the caregiver has to expect in terms of the disease’s progression and daily management, ways to improve awareness in general population, acceptation of practical support and its coordination and adaptation. Conclusions Identified needs were concordant with those in the literature. The mixed method used enabled expectations to be explored by analysing together the points of view of both patients and healthcare professionals in order to identify ways of improving their care. Trial registration Not applicable.

Muscadinia rotundifolia , a species closely related to cultivated grapevine Vitis vinifera , is a major source of resistance to grapevine downy and powdery mildew, two major threats to cultivated traditional cultivars of V. vinifera respectively caused by the oomycete Plasmopara viticola and the ascomycete Erisyphe necator . The aim of the present work was to develop a reference genetic linkage map based on simple sequence repeat (SSR) markers for M. rotundifolia . This map was created using S1 M. rotundifolia cv. Regale progeny, and covers 948 cM on 20 linkage groups, which corresponds to the expected chromosome number for muscadine. The comparison of the genetic maps of V. vinifera and M. rotundifolia revealed a high macrosynteny between the genomes of both species. The S1 progeny was used to assess the general level of resistance of M. rotundifolia to P. viticola and E. necator , by scoring different parameters of pathogen development. A quantitative trait locus (QTL) analysis allowed us to highlight a major QTL on linkage group 14 controlling resistance to powdery mildew, which explained up to 58 % of the total phenotypic variance. This QTL was named ‘Resistance to Erysiphe Necator 5 ’ ( Ren5 ). A microscopic evaluation E. necator mycelium development on resistant and susceptible genotypes of the S1 progeny showed that Ren5 exerts its action after the formation of the first appressorium, and acts by delaying, and then stopping, mycelium development.

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.Djennane, Merdinoglu and colleagues identify a single genetic factor, rgflv1, in Riesling grapes that confers a resistance to grapevine fanleaf virus. This resistance factor may inform genetic solutions for control of this virus in many grape varieties.

The genetic determinism of developmental stages in grapevine was studied in the progeny of a cross between grapevine cultivars Riesling and Gewurztraminer by combining ecophysiological modelling, genetic analysis and data mining of the grapevine whole genome sequence. The dates of three phenological stages, budbreak, flowering and veraison, were recorded during four successive years for 120 genotypes in the vineyard. The phenotypic data analysed were the duration of three periods expressed in thermal time (degree-days): 15 February to budbreak (Bud), budbreak to flowering (Flo) and flowering to veraison (Ver). Parental and consensus genetic maps were built using 153 microsatellite markers on 188 individuals. Six independent quantitative trait loci (QTLs) were detected for the three phases. They were located on chromosomes 4 and 19 for Bud, chromosomes 7 and 14 for Flo and chromosomes 16 and 18 for Ver. Interactions were detected between loci and also between alleles at the same locus. Using the available grapevine whole-genome sequences, candidate genes underlying the QTLs were identified. VvFT , on chromosome 7, and a CONSTANS -like gene, on chromosome 14, were found to colocalise with the QTLs for flowering time. Genes related to the abscisic acid response and to sugar metabolism were detected within the confidence intervals of QTLs for veraison time. Their possible roles in the developmental process are discussed. These results raise new hypotheses for a better understanding of the physiological processes governing grapevine phenology and provide a framework for breeding new varieties adapted to the future predicted climatic conditions.

Climate change is expected to advance grapevine phenological stages. After the calibration and the validation of a degree-days model, we were able to accurately simulate dates of budbreak, flowering and véraison for Riesling and Gewurztraminer, 2 winegrape varieties grown in Alsace, France. Projected daily temperatures were calculated for the local meteorological station with the ARPEGE-Climat general circulation model using 3 distinct greenhouse gas emissions scenarios. Compared with its timing in 1976–2008, véraison is predicted to advance by up to 23 d and mean temperatures during the 35 d following véraison are projected to increase by more than 7°C by the end of the 21st century for both varieties. Such changes will likely have a significant impact on grape and wine quality. Using the same framework, the genetic variability of phenological parameters was explored with 120 genotypes of progeny from a Riesling × Gewurztraminer cross, along with 14 European varieties. In addition, we created a virtual late ripening genotype, derived from a cross between Riesling and Gewurztraminer. This modelled genotype was projected to undergo véraison 2 to 3 d before Muscat of Alexandria, one of the latest ripening varieties studied. Even with this virtual genotype, or with Muscat of Alexandria, grapes would ripen by the middle of the 21st century under higher temperatures than in the present years. This study highlights the important changes that viticulture will likely face in a future warmer climate and emphasises the need to create very late ripening genotypes or genotypes able to produce high quality wines under elevated temperatures.

Key messageIn a grapevine segregating population, genomic regions governing berry pH were identified, paving the way for breeding new grapevine varieties best adapted to a warming climate.As a consequence of global warming, grapevine berry acidity is expected to dramatically decrease. Adapting grapevine (Vitis vinifera L.) varieties to the climatic conditions of the future requires a better understanding of the genetic architecture of acidity-related traits. For this purpose, we studied during five growing seasons 120 individuals from a grapevine biparental cross. Each offspring was genotyped by simple sequence repeats markers and by hybridization on a 20-K Grapevine Illumina® SNP chip. Quantitative trait loci (QTLs) for pH colocalized with QTLs for the ratio between potassium and tartaric acid concentrations, on chromosomes 10, 11 and 13. Strong QTLs for malic acid concentration or for the malic acid-to-tartaric acid ratio, on chromosomes 6 and 8, were not associated with variations of pH but can be useful for controlling pH stability under high temperatures. Our study highlights the interdependency between acidity parameters and consequently the constraints and degrees of freedom for designing grapevine genotypes better adapted to the expected warmer climatic conditions. In particular, it is possible to create grapevine genotypes with a high berry acidity as the result of both high tartaric acid concentrations and low K+ accumulation capacities.