Single berry development – a new phenotyping and transcriptomics paradigm

Most present knowledge on berry development has been obtained from a random sampling of hundreds of berries to average their diversity of the experimental plot. According to recent studies, such heterogeneous samples formed from non-synchronized berries of mixed developmental stages are unsuitable for detecting fast physiological and molecular changes. Thus, it is necessary to revisit the physiological and transcriptional bases of berry ripening. Here we report the in-depth study of the late-ripening program in three genotypes. Berry expansion during the second growth phase was characterized on-vine through image analysis. Hundreds of sampled berries were individually analyzed for primary metabolites to calculate their respective accumulation rates with high precision. These primary individual fluxes and the growth kinetics allowed us to distinguish targeted developmental stages further investigated through RNA profiling. Single berry monitoring evidenced sharp developmental phases during which specific genes or pathways are quickly switched ON or OFF. The comparison between Syrah and the two microvines showed phenotypic differences in late-ripening stages in vines grown in the field (Syrah) and microvines (MV032 and MV102) grown in the greenhouse. This study shows that new high-throughput single berry phenotyping methods are required to compare unambiguous developmental stages in physiological or genetic studies

The Microvine: A Versatile Plant Model to Boost Grapevine Studies in Physiology and Genetics

The microvine is a grapevine somatic variant. The Vvgai1 mutation results in a miniaturization of the vegetative organs of the plant keeping fruit size intact and a systematic conversion of tendrils into inflorescences. The physiological characterization of the vegetative and reproductive development of the microvine makes it possible to infer kinetic data from spatial phenotypes. This biological model allows experiments on vine and grape development in tightly controlled conditions, which greatly accelerate physiology, molecular biology, as well as genetic studies. After introducing the main biological properties of the microvine, main results from various research programs performed with the microvine model will be presented

Day and night heat stress trigger different transcriptomic responses in green and ripening grapevine (vitis vinifera) fruit

Background: Global climate change will noticeably affect plant vegetative and reproductive development. The recent increase in temperatures has already impacted yields and composition of berries in many grapevine-growing regions. Physiological processes underlying temperature response and tolerance of the grapevine fruit have not been extensively investigated. To date, all studies investigating the molecular regulation of fleshly fruit response to abiotic stress were only conducted during the day, overlooking possible critical night-specific variations. The present study explores the night and day transcriptomic response of grapevine fruit to heat stress at several developmental stages. Short heat stresses (2 h) were applied at day and night to vines bearing clusters sequentially ordered according to the developmental stages along their vertical axes. The recently proposed microvine model (DRCF-Dwarf Rapid Cycling and Continuous Flowering) was grown in climatic chambers in order to circumvent common constraints and biases inevitable in field experiments with perennial macrovines. Post-véraison berry heterogeneity within clusters was avoided by constituting homogenous batches following organic acids and sugars measurements of individual berries. A whole genome transcriptomic approach was subsequently conducted using NimbleGen 090818 Vitis 12X (30 K) microarrays. Results: Present work reveals significant differences in heat stress responsive pathways according to day or night treatment, in particular regarding genes associated with acidity and phenylpropanoid metabolism. Precise distinction of ripening stages led to stage-specific detection of malic acid and anthocyanin-related transcripts modulated by heat stress. Important changes in cell wall modification related processes as well as indications for heat-induced delay of ripening and sugar accumulation were observed at véraison, an effect that was reversed at later stages. Conclusions: This first day - night study on heat stress adaption of the grapevine berry shows that the transcriptome of fleshy fruits is differentially affected by abiotic stress at night. The present results emphasize the necessity of including different developmental stages and especially several daytime points in transcriptomic studies

Birth Weight, Body Silhouette Over the Life Course, and Incident Diabetes in 91,453 Middle-Aged Women From the French Etude Epidemiologique de Femmes de la Mutuelle Générale de l'Education Nationale (E3N) Cohort

International audienceOBJECTIVE: Obesity and increases in body weight in adults are considered to be among the most important risk factors for type 2 diabetes. Low birth weight is also associated with a higher diabetes incidence. We aimed to examine to what extent the evolution of body shape, from childhood to adulthood, is related to incident diabetes in late adulthood. RESEARCH DESIGN AND METHODS: Etude Epidemiologique de Femmes de la Mutuelle Générale de l'Education Nationale (E3N) is a cohort study of French women born in 1925-1950 and followed by questionnaire every 2 years. At baseline, in 1990, women were asked to report their current weight, height, and body silhouette at various ages. Birth weight was recorded in 2002. Cases of diabetes were self-reported or obtained by drug reimbursement record linkage and further validated. RESULTS: Of the 91,453 women who were nondiabetic at baseline, 2,534 developed diabetes over the 15 years of follow-up. Birth weight and body silhouette at 8 years, at menarche, and in young adulthood (20-25 years) were inversely associated with the risk of diabetes, independently of adult BMI during follow-up (all P(trend) < 0.001). In mid-adulthood (35-40 years), the association was reversed, with an increase in risk related to a larger body silhouette. An increase in body silhouette from childhood to mid-adulthood amplified the risk of diabetes. CONCLUSIONS: Low birth weight and thinness until young adulthood may increase the risk of diabetes, independently of adult BMI during follow-up. Young women who were lean children should be especially warned against weight gain

The sugarless grape trait characterised by single berry phenotyping

In grape production, the selection of varieties well-adapted to climate fluctuations, especially warming, is based on achieving a balance between fruit sugars and acidity. In recent decades, temperature has been constantly rising during ripening causing excessive sugar concentrations and insufficient acidity in wine grapes in the warmest regions. There is thus an increasing interest in breeding new cultivars able to ripen at lower sugar concentration while preserving fruit acidity. However, the phenotyping of berry composition challenges both methodological and conceptual issues. Indeed, most authors predetermine either average harvest date, ripening duration, thermal time or even the hexoses concentration threshold itself to compare accessions at a hopefully similar ripe stage. In this study, we phenotyped the fruit development and composition of 6 genotypes, including 3 new disease-tolerant varieties known to produce wines with low alcoholic contents. The study was performed at single berry level from the end of the green growth stage to the end of phloem unloading, when water and solute contents reach a maximum per berry. The results confirm that sugarless genotypes achieve fruit ripening with 20-30 % less hexoses than the classical varieties, Grenache N and Merlot N, without impacting berry growth, total acidity or cation accumulation. The sugarless genotypes displayed a higher malic acid/tartaric acid balance than the other genotypes, but similar sucrose/H+ exchanges at the onset of ripening. Data suggest that the sugarless phenotype results from a specific plasticity in the relationship between growth and the turgor imposed by organic acid accumulation and sugar loading. This opens interesting perspectives for the understanding of the mechanism of grapevine berry growth and for breeding varieties that will cope better with climate warming

New stable QTLs for berry weight do not colocalize with QTLs for seed traits in cultivated grapevine (Vitis vinifera L.)

International audienceBACKGROUND: In grapevine, as in other fruit crops, fruit size and seed content are key components of yield and quality; however, very few Quantitative Trait Loci (QTLs) for berry weight and seed content (number, weight, and dry matter percentage) have been discovered so far. To identify new stable QTLs for marker-assisted selection and candidate gene identification, we performed simultaneous QTL detection in four mapping populations (seeded or seedless) with various genetic backgrounds. RESULTS: For berry weight, we identified five new QTLs, on linkage groups (LGs) 1, 8, 11, 17 and 18, in addition to the known major QTL on LG 18. The QTL with the largest effect explained up to 31% of total variance and was found in two genetically distant populations on LG 17, where it colocalized with a published putative domestication locus. For seed traits, besides the major QTLs on LG 18 previously reported, we found four new QTLs explaining up to 51% of total variance, on LGs 4, 5, 12 and 14. The previously published QTL for seed number on LG 2 was found related in fact to sex. We found colocalizations between seed and berry weight QTLs only for the major QTL on LG 18 in a seedless background, and on LGs 1 and 13 in a seeded background. Candidate genes belonging to the cell number regulator CNR or cytochrome P450 families were found under the berry weight QTLs on LGs 1, 8, and 17. The involvement of these gene families in fruit weight was first described in tomato using a QTL-cloning approach. Several other interesting candidate genes related to cell wall modifications, water import, auxin and ethylene signalling, transcription control, or organ identity were also found under berry weight QTLs. CONCLUSION: We discovered a total of nine new QTLs for berry weight or seed traits in grapevine, thereby increasing more than twofold the number of reliable QTLs for these traits available for marker assisted selection or candidate gene studies. The lack of colocalization between berry and seed QTLs suggests that these traits may be partly dissociated

Delayed grape ripening by intermittent shading to counter global warming depends on carry-over effects and water deficit conditions

Grapevine phenology is continuously advancing due to global warming, exposing berry ripening to increasingly drier and hotter episodes that can dramatically affect yield and berry quality. This study aimed to analyse whether intermittent shading produced by panels placed over the plants can delay berry ripening to counter the impact of global warning on phenology. A two-year outdoor trial repeated on two batches of young potted grapevine (cv. Syrah) was conducted in Montpellier (South of France). Shading was created in a row using 2 m-wide horizontal panels placed 2.4 m above the ground. A moderate water deficit was also applied at the start of veraison to half the plants in both full sun (without panels) and shaded conditions to mimic usual field conditions. Variables related to budburst, flowering, veraison and sugar at harvest were analysed in all treatments. Although intermittent shading did not significantly modify air temperature within the canopy when cumulated over the growing season, the panels substantially delayed veraison by up to more than 30 days under well-watered conditions. The most marked phenological shifts were noted in the second year of treatment between flowering and veraison when carbon demand sharply increased during berry formation, suggesting there was a carry-over effect likely due to limited carbon assimilation. This was accompanied by sharp decreases in berry diameter and sugar content per berry at harvest. Higher berry growth and sugar loading were maintained when shading was combined with water deficit. However, the trigger effect of water deficit on veraison almost halved the phenological delay caused by the panels. Overall, a cooler period for ripening could be achieved with panels over the vines but at the expense of berry size and sugar amount in berries. It can be concluded that shading intensity and duration should be adapted to evaporative and soil water conditions to benefit from the phenological delay caused by panels, without altering production in the long term

Field investigation with real-time virus genetic characterisation support of a cluster of Ebola virus disease cases in Dubréka, Guinea, April to June 2015

On 11 May 2015, the Dubréka prefecture, Guinea, reported nine laboratory-confirmed cases of Ebola virus disease (EVD). None could be epidemiologically linked to cases previously reported in the prefecture. We describe the epidemiological and molecular investigations of this event. We used the Dubréka EVD registers and the Ebola treatment centre’s (ETC) records to characterise chains of transmission. Real-time field Ebola virus sequencing was employed to support epidemiological results. An epidemiological cluster of 32 cases was found, of which 27 were laboratory confirmed, 24 were isolated and 20 died. Real-time viral sequencing on 12 cases demonstrated SL3 lineage viruses with sequences differing by one to three nt inside a single phylogenetic cluster. For isolated cases, the average time between symptom onset and ETC referral was 2.8 days (interquartile range (IQR): 1–4). The average time between sample collection and molecular results’ availability was 3 days (IQR: 2–5). In an area with scarce resources, the genetic characterisation supported the outbreak investigations in real time, linking cases where epidemiological investigation was limited and reassuring that the responsible strain was already circulating in Guinea. We recommend coupling thorough epidemiological and genomic investigations to control EVD clusters.Peer Reviewe

Evolution of coastal zone vulnerability to marine inundation in a global change context. Application to Languedoc Roussillon (France)

The coastal system is likely to suffer increasing costal risk in a global change context. Its management implies to consider those risks in a holistic approach of the different vulnerability components of the coastal zone, by improving knowledge of hazard and exposure as well as analyzing and quantifying present day and future territory vulnerability. The ANR/VMC2007/MISEEVA project (2008-2011) has applied this approach on Languedoc Roussillon region in France. MISEEVA approach relies on several scenarios for 2030 and 2100, in terms of meteorology (driver of coastal hazard), sea level rise, and also considering further trends in demography and economy, and possible adaption strategies Hazard has been modeled (SWAN, MARS and SURFWB), on the base of the presentday situation, sea level rise hypotheses, and existing or modeled data, of extreme meteorological driving f. It allowed to assess the possible surges ranges and map coastal zone exposure to: - a permanent inundation (considering sea level rise in 2030 and 2100, - a recurrent inundation (considering sea level rise and extreme tidal range) - an exceptional inundation (adding extreme storm surge to sea level rise and tidal range). In 2030, exposure will be comparable to present day exposure. In 2100, extreme condition will affect a larger zone. Present days social and economic components of the coastal zone have been analyzed in terms of vulnerability and potential damaging. Adaptation capacity was approached by public inquiries and interviews of stakeholders and policy makers, based on existing planning documents The knowledge of the present day system is then compared to the possible management strategies that could be chosen in the future, so to imagine what would be the evolution of vulnerability to marine inundation, in regards to these possible strategies