PHENOPSIS DB: an Information System for Arabidopsis thaliana phenotypic data in an environmental context

<p>Abstract</p> <p>Background</p> <p>Renewed interest in plant × environment interactions has risen in the post-genomic era. In this context, high-throughput phenotyping platforms have been developed to create reproducible environmental scenarios in which the phenotypic responses of multiple genotypes can be analysed in a reproducible way. These platforms benefit hugely from the development of suitable databases for storage, sharing and analysis of the large amount of data collected. In the model plant <it>Arabidopsis thaliana</it>, most databases available to the scientific community contain data related to genetic and molecular biology and are characterised by an inadequacy in the description of plant developmental stages and experimental metadata such as environmental conditions. Our goal was to develop a comprehensive information system for sharing of the data collected in PHENOPSIS, an automated platform for <it>Arabidopsis thaliana </it>phenotyping, with the scientific community.</p> <p>Description</p> <p>PHENOPSIS DB is a publicly available (URL: <url>http://bioweb.supagro.inra.fr/phenopsis/</url>) information system developed for storage, browsing and sharing of online data generated by the PHENOPSIS platform and offline data collected by experimenters and experimental metadata. It provides modules coupled to a Web interface for (i) the visualisation of environmental data of an experiment, (ii) the visualisation and statistical analysis of phenotypic data, and (iii) the analysis of <it>Arabidopsis thaliana </it>plant images.</p> <p>Conclusions</p> <p>Firstly, data stored in the PHENOPSIS DB are of interest to the <it>Arabidopsis thaliana </it>community, particularly in allowing phenotypic meta-analyses directly linked to environmental conditions on which publications are still scarce. Secondly, data or image analysis modules can be downloaded from the Web interface for direct usage or as the basis for modifications according to new requirements. Finally, the structure of PHENOPSIS DB provides a useful template for the development of other similar databases related to genotype × environment interactions.</p

Gradual responses of grapevine yield components and carbon status to nitrogen supply

Aim: Nitrogen is a major element conditioning grapevine growth, yield and aromatic profiles of berries and wines. Different tools can be used in order to detect differences in N status of the plant, including direct measurements of soil, plant nitrogen status (eg. petiole; must), or indirect observations of plant nutritional status such as leaf transmittance or reflectance (eg. SPAD; NDVI). However, the relationships between these indicators of nitrogen status and the overall plant functioning over vintages remain poorly known. The present study aimed at quantifying key vegetative and reproductive responses to plant nitrogen status over two successive seasons under different nitrogen supply levels. Methods and results: Potted plants of Sauvignon Blanc grafted onto SO4 were grown outdoors in 2017 and 2018 with no water limitation. Four mineral nitrogen fertilization levels (equivalent to 0 kg of N ha-1 or 0U, 20U, 40U, 80U) and one organic nitrogen fertilization level (40U) were imposed in 2017. These treatments were doubled in 2018 to increase the degree of nitrogen supply and consequently, the range of observed effects on plant growth and yield. Plant nitrogen status (SPAD) was monitored weekly during both growing cycles. Yield components were determined over the two seasons. Lastly, plant carbon status was addressed through dynamic measurement of plant development and photosynthesis, and destructive measurement of dry matter accumulation and carbon storage in annual and perennial organs at flowering, veraison and harvest. The SPAD values progressively decreased under lower N supply (0N) during the first year (from 31 to 16) and they were more than halved between the maximum and the minimum N treatments straight after budburst in year two (40 for 160N and 19 for 0N). Then, the differences in SPAD values among treatments were maintained up to harvest (2018). The gradient of N status resulted in a gradient of berry numbers per inflorescence (from 180 to 34 berries/inflorescence for 80N and 0N, respectively in 2018) and of individual berry dry matter at harvest (from 0.13 to 0.41 g for 160N and 0N, respectively in 2018). Quantitative relationships between N status and the relative reductions (% of reduction per %SPAD decrease) in terms of C gain (leaf area, photosynthesis), C growth (shoot, berry, trunk and root dry matter) and C storage (trunk and root) were fitted at flowering, veraison and harvest. The reduction in C gain under lower N supply was mainly related to the decrease in total leaf area before flowering (-1.64%). Although the photosynthesis rate tended to decrease under N deficiency over the season, it only poorly contributed to the reduction in C gain. The whole plant C growth was inhibited when N status decreased (-1.13% at harvest), due to the inhibition of shoot dry matter before veraison (-1.81%) and to a lower extent, to the lower dry matter in berries (-0.80%), trunks (-0.42%) and roots (-0.84%) at harvest. Part of the reduction in root dry matter was related to the lower starch reserves (-0.31%) at harvest. Interestingly, starch reserves tended to be higher under organic N supply than mineral N supply. Conclusion: The present results provided a general framework of carbon gain and use over time (within and between seasons) as impacted by N supply levels and form. Such a framework will be useful when building a model of the pluri-annual dynamics of carbon balance related to yield elaboration in grapevines

Multivariate genetic analysis of plant responses to water deficit and high temperature revealed contrasting adaptive strategies

How genetic factors control plant performance under stressful environmental conditions is a central question in ecology and for crop breeding. A multivariate framework was developed to examine the genetic architecture of performance-related traits in response to interacting environmental stresses. Ecophysiological and life history traits were quantified in the Arabidopsis thaliana Ler×Cvi mapping population exposed to constant soil water deficit and high air temperature. The plasticity of the genetic variance–covariance matrix (G-matrix) was examined using mixed-effects models after regression into principal components. Quantitative trait locus (QTL) analysis was performed on the predictors of genotype effects and genotype by environment interactions (G×E). Three QTLs previously identified for flowering time had antagonistic G×E effects on carbon acquisition and the other traits (phenology, growth, leaf morphology, and transpiration). This resulted in a size-dependent response of water use efficiency (WUE) to high temperature but not soil water deficit, indicating that most of the plasticity of carbon acquisition and WUE to temperature is controlled by the loci that control variation of development, size, growth, and transpiration. A fourth QTL, MSAT2.22, controlled the response of carbon acquisition to specific combinations of watering and temperature irrespective of plant size and development, growth, and transpiration rate, which resulted in size-independent plasticity of WUE. These findings highlight how the strategies to optimize plant performance may differ in response to water deficit and high temperature (or their combination), and how different G×E effects could be targeted to improve plant tolerance to these stresses

Structural assessment of the impact of environmental constraints on arabidopsis thaliana leaf growth: A 3D approach

Light and soil water content affect leaf surface area expansion through modifications in epidermal cell numbers and area, while effects on leaf thickness and mesophyll cell volumes are far less documented. Here, three-dimensional imaging was applied in a study of Arabidopsis thaliana leaf growth to determine leaf thickness and the cellular organization of mesophyll tissues under moderate soil water deficit and two cumulative light conditions. In contrast to surface area, thickness was highly conserved in response to water deficit under both low and high cumulative light regimes. Unlike epidermal and palisade mesophyll tissues, no reductions in cell number were observed in the spongy mesophyll; cells had rather changed in volume and shape. Furthermore, leaf features of a selection of genotypes affected in leaf functioning were analysed. The low-starch mutant pgm had very thick leaves because of unusually large palisade mesophyll cells, together with high levels of photosynthesis and stomatal conductance. By means of an open stomata mutant and a 9-cis-epoxycarotenoid dioxygenase overexpressor, it was shown that stomatal conductance does not necessarily have a major impact on leaf dimensions and cellular organization, pointing to additional mechanisms for the control of CO2 diffusion under high and low stomatal conductance, respectively. © 2012 Blackwell Publishing Ltd

Contribution a l'etude du determinisme du nombre de rangs.

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Développement d’un système d'information de phénotypage d’Arabidopsis thaliana

National audienceL'évolution de la démarche scientifique dans la plupart des champs d'investigation se traduit par une exigence de haut débit dont on ne peut tirer le meilleur profit sans un effort considérable d’archivage et de mise à disposition des données. Au laboratoire d’écophysiologie des plantes sous stress environnementaux (LEPSE) du centre Inra de Montpellier, le développement récent d’une plate-forme de phénotypage automatisée dédiée à la plante modèle Arabidopsis thaliana, la plate-forme PHENOPSIS, a permis d’augmenter de façon considérable les analyses phénotypiques effectuées sur cette espèce. Dans ce contexte, il est devenu nécessaire de développer une base de données associée à la plate-forme. Le travail présenté ici décrit les choix technologiques et le développement de la base de données et de l’interface Web qui établit le lien entre cette base de données et ses utilisateurs. Avec cet ensemble le travail d’insertion des données et de leur stockage ainsi que leur consultation et/ou téléchargement se fait de manière contrôlée