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Research paper thumbnail of Additional file 1 of Wheat physiology predictor: predicting physiological traits in wheat from hyperspectral reflectance measurements using deep learning

Additional file 1. Effect of optimsing number of training epochs and expanding training sets by d... more Additional file 1. Effect of optimsing number of training epochs and expanding training sets by data augmentation on model prediction.

Research paper thumbnail of Effect of light and temperature on plant canopy growth

Umwelt-Bedingungen haben einen grosen Einfluss auf das Pflanzenwachstum und-entwicklung. Pflanzen... more Umwelt-Bedingungen haben einen grosen Einfluss auf das Pflanzenwachstum und-entwicklung. Pflanzen haben, um die bestmogliche Nutzung der verfugbaren Ressourcen, um ihr volles Potential und maximalen Ertrag zu erzielen. Wenn Umgebungsbedingungen suboptimal sind fur bestimmte Arten dann mussen diese mehr Mittel investieren, um zu uberleben was zu geringerer Ausbeute fuhrt. Diese Arbeit soll das Wissen uber die Auswirkungen von Temperatur und Licht in Labor-Experimenten auf pflanzliche Wachstumsdynamik erhohen. Viele aktuelle wissenschaftliche Studien basieren auf der Annahme, dass Laborbedingungen vergleichbar mit Feldbedingungen sind und dass eine direkte Umsetzung der gewonnenen Erkenntnisse aus dem Labor auf das Feld moglich ist. Feldbedingungen sind nur sehr schwer kunstlich zu reproduzieren und Laborbedingungen sind oft unrealistisch. Die klimatischen Unterschiede konnen zu falschen Aussagen uber pflanzliche Reaktionen auf ihre Umwelt fuhren. Es ist ein Ziel dieser Studie, Antwor...

Research paper thumbnail of Wheat physiology predictor: predicting physiological traits in wheat from hyperspectral reflectance measurements using deep learning

Plant Methods

Background The need for rapid in-field measurement of key traits contributing to yield over many ... more Background The need for rapid in-field measurement of key traits contributing to yield over many thousands of genotypes is a major roadblock in crop breeding. Recently, leaf hyperspectral reflectance data has been used to train machine learning models using partial least squares regression (PLSR) to rapidly predict genetic variation in photosynthetic and leaf traits across wheat populations, among other species. However, the application of published PLSR spectral models is limited by a fixed spectral wavelength range as input and the requirement of separate custom-built models for each trait and wavelength range. In addition, the use of reflectance spectra from the short-wave infrared region requires expensive multiple detector spectrometers. The ability to train a model that can accommodate input from different spectral ranges would potentially make such models extensible to more affordable sensors. Here we compare the accuracy of prediction of PLSR with various deep learning appro...

Research paper thumbnail of Measuring CO2 and HCO3− permeabilities of isolated chloroplasts using a MIMS-18O approach

Journal of Experimental Botany

Research paper thumbnail of Root cooling strongly affects diel leaf growth dynamics, water and carbohydrate relations in Ricinus communis

Plant, Cell & Environment, 2010

Research paper thumbnail of Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon

Journal of Integrative Plant Biology, 2014

Research paper thumbnail of Diel time-courses of leaf growth in monocot and dicot species: endogenous rhythms and temperature effects

Journal of Experimental Botany, 2010

Research paper thumbnail of Rapid adjustment in chrysanthemum carbohydrate turnover and growth activity to a change in time-of-day application of light and daylength

Functional Plant Biology, 2012

Diel (24 h) rhythms are believed to be of great importance to plant growth and carbohydrate metab... more Diel (24 h) rhythms are believed to be of great importance to plant growth and carbohydrate metabolism in fluctuating environments. However, it is unclear how plants that have evolved to experience regular day–night patterns will respond to irregular light environments that disturb diurnally-regulated parameters related to growth. In this study, chrysanthemum plants were exposed to a change in the time-of-day application of light followed by short days or long days with a night interruption of light. We observed a clear shift in the diel cycle of sucrose turnover and relative leaf expansion, indicating a resetting of these activities with a temporal trigger in the early morning. The starch pool was relatively stable in long-day plants and marginally affected by the change in the time-of-day application in light followed by long days with a night interruption. This was in contrast with an onset of a daily starch turnover by a shift to short days. These results confirm findings from m...

Research paper thumbnail of Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon

Journal of Integrative Plant Biology, 2014

Research paper thumbnail of Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon

Journal of Integrative Plant Biology, 2014

This work evaluates the phenotypic response of the model grass (Brachypodium distachyon (L.) P. B... more This work evaluates the phenotypic response of the model grass (Brachypodium distachyon (L.) P. Beauv.) to nitrogen and phosphorus nutrition using a combination of imaging techniques and destructive harvest of shoots and roots. Reference line Bd21-3 was grown in pots using 11 phosphorus and 11 nitrogen concentrations to establish a dose-response curve. Shoot biovolume and biomass, root length and biomass, and tissue phosphorus and nitrogen concentrations increased with nutrient concentration. Shoot biovolume, estimated by imaging, was highly correlated with dry weight (R 2 > 0.92) and both biovolume and growth rate responded strongly to nutrient availability. Higher nutrient supply increased nodal root length more than other root types. Photochemical efficiency was strongly reduced by low phosphorus concentrations as early as 1 week after germination, suggesting that this measurement may be suitable for high throughput screening of phosphorus response. In contrast, nitrogen concentration had little effect on photochemical efficiency. Changes in biovolume over time were used to compare growth rates of four accessions in response to nitrogen and phosphorus supply. We demonstrate that a time series image-based approach coupled with mathematical modeling provides higher resolution of genotypic response to nutrient supply than traditional destructive techniques and shows promise for high throughput screening and determination of genomic regions associated with superior nutrient use efficiency. (2014) Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon.

Research paper thumbnail of Additional file 1 of Wheat physiology predictor: predicting physiological traits in wheat from hyperspectral reflectance measurements using deep learning

Additional file 1. Effect of optimsing number of training epochs and expanding training sets by d... more Additional file 1. Effect of optimsing number of training epochs and expanding training sets by data augmentation on model prediction.

Research paper thumbnail of Effect of light and temperature on plant canopy growth

Umwelt-Bedingungen haben einen grosen Einfluss auf das Pflanzenwachstum und-entwicklung. Pflanzen... more Umwelt-Bedingungen haben einen grosen Einfluss auf das Pflanzenwachstum und-entwicklung. Pflanzen haben, um die bestmogliche Nutzung der verfugbaren Ressourcen, um ihr volles Potential und maximalen Ertrag zu erzielen. Wenn Umgebungsbedingungen suboptimal sind fur bestimmte Arten dann mussen diese mehr Mittel investieren, um zu uberleben was zu geringerer Ausbeute fuhrt. Diese Arbeit soll das Wissen uber die Auswirkungen von Temperatur und Licht in Labor-Experimenten auf pflanzliche Wachstumsdynamik erhohen. Viele aktuelle wissenschaftliche Studien basieren auf der Annahme, dass Laborbedingungen vergleichbar mit Feldbedingungen sind und dass eine direkte Umsetzung der gewonnenen Erkenntnisse aus dem Labor auf das Feld moglich ist. Feldbedingungen sind nur sehr schwer kunstlich zu reproduzieren und Laborbedingungen sind oft unrealistisch. Die klimatischen Unterschiede konnen zu falschen Aussagen uber pflanzliche Reaktionen auf ihre Umwelt fuhren. Es ist ein Ziel dieser Studie, Antwor...

Research paper thumbnail of Wheat physiology predictor: predicting physiological traits in wheat from hyperspectral reflectance measurements using deep learning

Plant Methods

Background The need for rapid in-field measurement of key traits contributing to yield over many ... more Background The need for rapid in-field measurement of key traits contributing to yield over many thousands of genotypes is a major roadblock in crop breeding. Recently, leaf hyperspectral reflectance data has been used to train machine learning models using partial least squares regression (PLSR) to rapidly predict genetic variation in photosynthetic and leaf traits across wheat populations, among other species. However, the application of published PLSR spectral models is limited by a fixed spectral wavelength range as input and the requirement of separate custom-built models for each trait and wavelength range. In addition, the use of reflectance spectra from the short-wave infrared region requires expensive multiple detector spectrometers. The ability to train a model that can accommodate input from different spectral ranges would potentially make such models extensible to more affordable sensors. Here we compare the accuracy of prediction of PLSR with various deep learning appro...

Research paper thumbnail of Measuring CO2 and HCO3− permeabilities of isolated chloroplasts using a MIMS-18O approach

Journal of Experimental Botany

Research paper thumbnail of Root cooling strongly affects diel leaf growth dynamics, water and carbohydrate relations in Ricinus communis

Plant, Cell & Environment, 2010

Research paper thumbnail of Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon

Journal of Integrative Plant Biology, 2014

Research paper thumbnail of Diel time-courses of leaf growth in monocot and dicot species: endogenous rhythms and temperature effects

Journal of Experimental Botany, 2010

Research paper thumbnail of Rapid adjustment in chrysanthemum carbohydrate turnover and growth activity to a change in time-of-day application of light and daylength

Functional Plant Biology, 2012

Diel (24 h) rhythms are believed to be of great importance to plant growth and carbohydrate metab... more Diel (24 h) rhythms are believed to be of great importance to plant growth and carbohydrate metabolism in fluctuating environments. However, it is unclear how plants that have evolved to experience regular day–night patterns will respond to irregular light environments that disturb diurnally-regulated parameters related to growth. In this study, chrysanthemum plants were exposed to a change in the time-of-day application of light followed by short days or long days with a night interruption of light. We observed a clear shift in the diel cycle of sucrose turnover and relative leaf expansion, indicating a resetting of these activities with a temporal trigger in the early morning. The starch pool was relatively stable in long-day plants and marginally affected by the change in the time-of-day application in light followed by long days with a night interruption. This was in contrast with an onset of a daily starch turnover by a shift to short days. These results confirm findings from m...

Research paper thumbnail of Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon

Journal of Integrative Plant Biology, 2014

Research paper thumbnail of Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon

Journal of Integrative Plant Biology, 2014

This work evaluates the phenotypic response of the model grass (Brachypodium distachyon (L.) P. B... more This work evaluates the phenotypic response of the model grass (Brachypodium distachyon (L.) P. Beauv.) to nitrogen and phosphorus nutrition using a combination of imaging techniques and destructive harvest of shoots and roots. Reference line Bd21-3 was grown in pots using 11 phosphorus and 11 nitrogen concentrations to establish a dose-response curve. Shoot biovolume and biomass, root length and biomass, and tissue phosphorus and nitrogen concentrations increased with nutrient concentration. Shoot biovolume, estimated by imaging, was highly correlated with dry weight (R 2 > 0.92) and both biovolume and growth rate responded strongly to nutrient availability. Higher nutrient supply increased nodal root length more than other root types. Photochemical efficiency was strongly reduced by low phosphorus concentrations as early as 1 week after germination, suggesting that this measurement may be suitable for high throughput screening of phosphorus response. In contrast, nitrogen concentration had little effect on photochemical efficiency. Changes in biovolume over time were used to compare growth rates of four accessions in response to nitrogen and phosphorus supply. We demonstrate that a time series image-based approach coupled with mathematical modeling provides higher resolution of genotypic response to nutrient supply than traditional destructive techniques and shows promise for high throughput screening and determination of genomic regions associated with superior nutrient use efficiency. (2014) Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon.

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