Earbox, an open tool for high-throughput measurement of the spatial organization of maize ears and inference of novel traits.

BACKGROUND: Characterizing plant genetic resources and their response to the environment through accurate measurement of relevant traits is crucial to genetics and breeding. Spatial organization of the maize ear provides insights into the response of grain yield to environmental conditions. Current automated methods for phenotyping the maize ear do not capture these spatial features. RESULTS: We developed EARBOX, a low-cost, open-source system for automated phenotyping of maize ears. EARBOX integrates open-source technologies for both software and hardware that facilitate its deployment and improvement for specific research questions. The imaging platform consists of a customized box in which ears are repeatedly imaged as they rotate via motorized rollers. With deep learning based on convolutional neural networks, the image analysis algorithm uses a two-step procedure: ear-specific grain masks are first created and subsequently used to extract a range of trait data per ear, including ear shape and dimensions, the number of grains and their spatial organisation, and the distribution of grain dimensions along the ear. The reliability of each trait was validated against ground-truth data from manual measurements. Moreover, EARBOX derives novel traits, inaccessible through conventional methods, especially the distribution of grain dimensions along grain cohorts, relevant for ear morphogenesis, and the distribution of abortion frequency along the ear, relevant for plant response to stress, especially soil water deficit. CONCLUSIONS: The proposed system provides robust and accurate measurements of maize ear traits including spatial features. Future developments include grain type and colour categorisation. This method opens avenues for high-throughput genetic or functional studies in the context of plant adaptation to a changing environment.

Modelling temperature-compensated physiological rates, based on the co-ordination of responses to temperature of developmental processes.

Temperature fluctuates rapidly and affects all developmental and metabolic processes. This often obscures the effects of developmental trends or of other environmental conditions when temperature fluctuates naturally. A method is proposed for modelling temperature-compensated rates, based on the coordination of temperature responses of developmental processes. In a data set comprising 41 experiments in the greenhouse, growth chamber, or the field, the temperature responses in the range of 6-36 degrees C for different processes were compared in three species, maize, rice, and Arabidopsis thaliana. Germination, cell division, expansive growth rate, leaf initiation, and phenology showed coordinated temperature responses and followed common laws within each species. The activities of 10 enzymes involved in carbon metabolism exhibited monotonous exponential responses across the whole range 10-40 degrees C. Hence, the temperature dependence of developmental processes is not explained by a simple relationship to central metabolism. Temperature-compensated rates of development were calculated from the equations of response curve, by expressing rates per unit equivalent time at 20 degrees C. This resulted in stable rates when temperatures fluctuated over a large range (for which classical thermal time was inefficient), and in time courses of leaf development which were common to several experiments with different temperature scenarios.

Co-Ordination of Cell Division and Tissue Expansion in Sunflower, Tobacco, and Pea Leaves: Dependence or Independence of Both Processes?

Temporal analyses of cell division and tissue expansion in pea, tobacco, and sunflower leaves reveal that both processes follow similar patterns during leaf development. Relative cell division and relative tissue expansion rates are maximal and constant during early leaf development, but they decline later. In contrast, relative cell expansion rate follows a bell-shaped curve during leaf growth. Cell division and tissue expansion have common responses to temperature, intercepted radiation, and water deficit. As a consequence, final leaf area and cell number remain highly correlated throughout a large range of environmental conditions for these different plant species, indicating that cell division and tissue expansion are co-ordinated during leaf development. This co-ordination between processes has long been explained by dependence between both processes. Most studies on dicotyledonous leaf development indicate that leaf expansion rate depends on the number of cells in the leaf. We tested this hypothesis with a large range of environmental conditions and different plant species. Accordingly, we found a strong correlation between both absolute leaf expansion rate and leaf cell number. However, we showed that this relationship is not necessarily causal because it can be simulated by the hypothesis of independence between cell division and tissue expansion according to Green's theory of growth (1976).