What is cost-efficient phenotyping? Optimizing costs for different scenarios

Progress in remote sensing and robotic technologies decreases the hardware costs of phenotyping. Here, we first review cost-effective imaging devices and environmental sensors, and present a trade-off between investment and manpower costs. We then discuss the structure of costs in various real-world scenarios. Hand-held low-cost sensors are suitable for quick and infrequent plant diagnostic measurements. In experiments for genetic or agronomic analyses, (i) major costs arise from plant handling and manpower; (ii) the total costs per plant/microplot are similar in robotized platform or field experiments with drones, hand-held or robotized ground vehicles; (iii) the cost of vehicles carrying sensors represents only 5–26% of the total costs. These conclusions depend on the context, in particular for labor cost, the quantitative demand of phenotyping and the number of days available for phenotypic measurements due to climatic constraints. Data analysis represents 10–20% of total cost if pipelines have already been developed. A trade-off exists between the initial high cost of pipeline development and labor cost of manual operations. Overall, depending on the context and objsectives, “cost-effective” phenotyping may involve either low investment (“affordable phenotyping”), or initial high investments in sensors, vehicles and pipelines that result in higher quality and lower operational costs

Maize yields over Europe may increase in spite of climate change, with an appropriate use of the genetic variability of flowering time

Projections based on invariant genotypes and agronomic practices indicate that climate change will largely decrease crop yields. The comparatively few studies considering farmers’ adaptation result in a diversity of impacts depending on their assumptions. We combined experiments and process-based modeling for analyzing the consequences of climate change on European maize yields if farmers made the best use of the current genetic variability of cycle duration, based on practices they currently use. We first showed that the genetic variability of maize flowering time is sufficient for identifying a cycle duration that maximizes yield in a range of European climatic conditions. This was observed in six field experiments with a panel of 121 accessions and extended to 59 European sites over 36 years with a crop model. The assumption that farmers use optimal cycle duration and sowing date was supported by comparison with historical data. Simulations were then carried out for 2050 with 3 million combinations of crop cycle durations, climate scenarios, management practices, and modeling hypotheses. Simulated grain production over Europe in 2050 was stable (−1 to +1%) compared with the 1975–2010 baseline period under the hypotheses of unchanged cycle duration, whereas it was increased (+4–7%) when crop cycle duration and sowing dates were optimized in each local environment. The combined effects of climate change and farmer adaptation reduced the yield gradient between south and north of Europe and increased European maize production if farmers continued to make the best use of the genetic variability of crop cycle duration

Pneumocystis jiroveci Dihydropteroate Synthase Genotypes in Immunocompetent Infants and Immunosuppressed Adults, Amiens, France

To date, investigations of Pneumocystis jiroveci circulation in the human reservoir through the dihydropteroate synthase (DHPS) locus analysis have only been conducted by examining P. jirovecii isolates from immunosuppressed patients with Pneumocystis pneumonia (PCP). Our study identifies P. jirovecii genotypes at this locus in 33 immunocompetent infants colonized with P. jirovecii contemporaneously with a bronchiolitis episode and in 13 adults with PCP; both groups of patients were monitored in Amiens, France. The results have pointed out identical features of P. jirovecii DHPS genotypes in the two groups, suggesting that in these two groups, transmission cycles of P. jirovecii infections are linked. If these two groups represent sentinel populations for P. jirovecii infections, our results suggest that all persons parasitized by P. jirovecii, whatever their risk factor for infection and the form of parasitism they have, act as interwoven circulation networks of P. jirovecii

A phenomics-based dynamic model of growth and yield to simulate hundreds of maize hybrids in the diversity of European environments

Sous contrainte hydrique, les plantes limitent leur transpiration en diminuant leur croissance foliaire, économisant ainsi l’eau pour la fin du cycle de culture. Une forte variabilité génétique a été observée chez le maïs pour les processus impliqués dans cette réponse. Le compromis entre transpiration et photosynthèse implique qu’une forte plasticité n’est pas toujours avantageuse car elle diminue aussi l’accumulation de biomasse et le rendement. Un génotype qui maximise la production dans un environnement sec n’est donc pas le meilleur dans un autre environnement sec. Le but de cette thèse était de prédire quelles combinaisons de traits reliés à la croissance foliaire aboutissent aux meilleurs rendements dans différents environnements européens. Pour cela, (i) j’ai montré que les contrôles environnementaux et génétiques diffèrent entre l’élongation et l’élargissement foliaires, et établi/testé les équations décrivant ces contrôles. (ii) J’ai développé un modèle de croissance foliaire, en restant parcimonieux en paramètres et en veillant à ce que les paramètres soient mesurables en plateformes de phénotypage. (iii) J’ai développé un cadre de simulation qui inclut 36 ans de conditions climatiques et les pratiques agricoles dans 59 sites de culture du maïs en Europe, ainsi que la paramétré 254 hybrides de maïs qui maximisent la diversité génétique. (iv) Ce cadre d’analyse a été utilisé pour prédire la durée de cycle optimale dans chacun des environnements étudiés, sous les conditions climatiques présentes et futures. (v) J’ai utilisé le cadre de simulation et ces durées de cycle adaptées pour déterminer les meilleurs idéotypes de croissance foliaire adaptés aux différent scenarios environnementaux. Les résultats montrent que les variétés sensibles sont adaptées à l’Europe du sud en condition non-irriguées alors que l’opposé est adapté au nord ou en condition irriguée. Cependant, les meilleures combinaisons de paramètres déterminées dans un espace phénotypique non contraint n’étaient pas disponible dans la diversité génétique observée. Cette thèse fournit aux sélectionneurs des éléments sur les combinaisons de traits qui fournissent un avantage comparatif dans chaque environnement ainsi que le contour des possibles dans la diversité génétique observée.Under soil water deficit, plants limit transpiration by decreasing leaf area to save water for the end of the crop cycle. A large genetic diversity has been observed in maize for the processes involved in this response. Because of the trade-off between transpiration and photosynthesis, a high plasticity is not always beneficial because it also reduces biomass accumulation and grain yield. The genotype that maximises production in one dry environment therefore does not always perform the best in another dry environment. The aim of this thesis was to predict which combination of trait values related to leaf growth would be beneficial in the diversity of European environments. For this purpose, (i) I have shown that genetic and environmental controls differ between leaf elongation and widening, and established/tested the equations that describe these controls. (ii) I have developed a model of leaf development and expansion, with a particular attention to the parsimony for parameter number and to the possibility of measuring parameter values in phenotyping platforms. (iii) I have developed a simulation framework including 36 years of environmental conditions and management practices of 59 European fields, together with the parameterisation of 254 maize hybrids maximising the maize genetic diversity. (iv) This framework has been used to simulate the optimum crop cycle duration for each site and management practice in current and future conditions. (v) The simulation framework and the adapted cycle duration were then used to determine ideotypes of leaf growth adapted to the different environmental scenarios. Results indicate that sensitive hybrids perform better in southern Europe under rainfed conditions while less-sensitive genotypes perform better in northern Europe or in irrigated fields. However, the best combinations of parameters determined in an unconstrained phenotypic space were not available in the observed genetic diversity. Overall, this study provides elements on where and when a combination of trait values can give a comparative advantage on yield, together with the boundary of possibilities within the current genetic diversity

Un modèle dynamique de croissance et rendement basé sur la phénomique pour simuler la variabilité de centaines d’hybrides de maïs dans la diversité des environnements Européens

Under soil water deficit, plants limit transpiration by decreasing leaf area to save water for the end of the crop cycle. A large genetic diversity has been observed in maize for the processes involved in this response. Because of the trade-off between transpiration and photosynthesis, a high plasticity is not always beneficial because it also reduces biomass accumulation and grain yield. The genotype that maximises production in one dry environment therefore does not always perform the best in another dry environment. The aim of this thesis was to predict which combination of trait values related to leaf growth would be beneficial in the diversity of European environments. For this purpose, (i) I have shown that genetic and environmental controls differ between leaf elongation and widening, and established/tested the equations that describe these controls. (ii) I have developed a model of leaf development and expansion, with a particular attention to the parsimony for parameter number and to the possibility of measuring parameter values in phenotyping platforms. (iii) I have developed a simulation framework including 36 years of environmental conditions and management practices of 59 European fields, together with the parameterisation of 254 maize hybrids maximising the maize genetic diversity. (iv) This framework has been used to simulate the optimum crop cycle duration for each site and management practice in current and future conditions. (v) The simulation framework and the adapted cycle duration were then used to determine ideotypes of leaf growth adapted to the different environmental scenarios. Results indicate that sensitive hybrids perform better in southern Europe under rainfed conditions while less-sensitive genotypes perform better in northern Europe or in irrigated fields. However, the best combinations of parameters determined in an unconstrained phenotypic space were not available in the observed genetic diversity. Overall, this study provides elements on where and when a combination of trait values can give a comparative advantage on yield, together with the boundary of possibilities within the current genetic diversity.Sous contrainte hydrique, les plantes limitent leur transpiration en diminuant leur croissance foliaire, économisant ainsi l’eau pour la fin du cycle de culture. Une forte variabilité génétique a été observée chez le maïs pour les processus impliqués dans cette réponse. Le compromis entre transpiration et photosynthèse implique qu’une forte plasticité n’est pas toujours avantageuse car elle diminue aussi l’accumulation de biomasse et le rendement. Un génotype qui maximise la production dans un environnement sec n’est donc pas le meilleur dans un autre environnement sec. Le but de cette thèse était de prédire quelles combinaisons de traits reliés à la croissance foliaire aboutissent aux meilleurs rendements dans différents environnements européens. Pour cela, (i) j’ai montré que les contrôles environnementaux et génétiques diffèrent entre l’élongation et l’élargissement foliaires, et établi/testé les équations décrivant ces contrôles. (ii) J’ai développé un modèle de croissance foliaire, en restant parcimonieux en paramètres et en veillant à ce que les paramètres soient mesurables en plateformes de phénotypage. (iii) J’ai développé un cadre de simulation qui inclut 36 ans de conditions climatiques et les pratiques agricoles dans 59 sites de culture du maïs en Europe, ainsi que la paramétré 254 hybrides de maïs qui maximisent la diversité génétique. (iv) Ce cadre d’analyse a été utilisé pour prédire la durée de cycle optimale dans chacun des environnements étudiés, sous les conditions climatiques présentes et futures. (v) J’ai utilisé le cadre de simulation et ces durées de cycle adaptées pour déterminer les meilleurs idéotypes de croissance foliaire adaptés aux différent scenarios environnementaux. Les résultats montrent que les variétés sensibles sont adaptées à l’Europe du sud en condition non-irriguées alors que l’opposé est adapté au nord ou en condition irriguée. Cependant, les meilleures combinaisons de paramètres déterminées dans un espace phénotypique non contraint n’étaient pas disponible dans la diversité génétique observée. Cette thèse fournit aux sélectionneurs des éléments sur les combinaisons de traits qui fournissent un avantage comparatif dans chaque environnement ainsi que le contour des possibles dans la diversité génétique observée