In Vivo Human-Like Robotic Phenotyping of Leaf and Stem Traits in Maize and Sorghum in Greenhouse

In plant phenotyping, the measurement of morphological, physiological and chemical traits of leaves and stems is needed to investigate and monitor the condition of plants. The manual measurement of these properties is time consuming, tedious, error prone, and laborious. The use of robots is a new approach to accomplish such endeavors, which enables automatic monitoring with minimal human intervention. In this study, two plant phenotyping robotic systems were developed to realize automated measurement of plant leaf properties and stem diameter which could reduce the tediousness of data collection compare to manual measurements. The robotic systems comprised of a four degree of freedom (DOF) robotic manipulator and a Time-of-Flight (TOF) camera. Robotic grippers were developed to integrate an optical fiber cable (coupled to a portable spectrometer) for leaf spectral reflectance measurement, a thermistor for leaf temperature measurement, and a linear potentiometer for stem diameter measurement. An Image processing technique and deep learning method were used to identify grasping points on leaves and stems, respectively. The systems were tested in a greenhouse using maize and sorghum plants. The results from the leaf phenotyping robot experiment showed that leaf temperature measurements by the phenotyping robot were correlated with those measured manually by a human researcher (R2 = 0.58 for maize and 0.63 for sorghum). The leaf spectral measurements by the phenotyping robot predicted leaf chlorophyll, water content and potassium with moderate success (R2 ranged from 0.52 to 0.61), whereas the prediction for leaf nitrogen and phosphorus were poor. The total execution time to grasp and take measurements from one leaf was 35.5±4.4 s for maize and 38.5±5.7 s for sorghum. Furthermore, the test showed that the grasping success rate was 78% for maize and 48% for sorghum. The experimental results from the stem phenotyping robot demonstrated a high correlation between the manual and automated stem diameter measurements (R2 \u3e 0.98). The execution time for stem diameter measurement was 45.3 s. The system could successfully detect and localize, and also grasp the stem for all plants during the experiment. Both robots could decrease the tediousness of collecting phenotypes compare to manual measurements. The phenotyping robots can be useful to complement the traditional image-based high-throughput plant phenotyping in greenhouses by collecting in vivo morphological, physiological, and biochemical trait measurements for plant leaves and stems. Advisors: Yufeng Ge, Santosh Pitl

Impact of Accounting for Polygenic Effects on the Accuracy of Genomic Evaluations in Livestock Breeding

To investigate the accuracy of genomic breeding values, different scenarios were defined by accounting for polygenic effects, a different number of quantitative trait loci (30, 90, 150), and three levels of heritability (0.15, 0.25, and 0.4). The Bayes B method was used to estimate marker effects. A historical population was simulated stochastically, which consisted of 100 animals at first 100 generations, then the population size gradually increased to 1000 animals during the next 100 generations. The animals in generation 201 with known genotypic and phenotypic records were assigned as the reference population, and animals of generation 202 were considered as the validation population. The genome was comprised of one chromosome with 100 cM length and 500 markers that were distributed through the genome randomly. Picking up the information that was not captured by linkage disequilibrium (LD), including polygenic effects in the predictions increased the accuracy of genomic evaluations. As the trait heritability went from 0.15 to 0.40, the average genomic accuracy increased from 0.48 to 0.64. An increment in the number of quantitative trait loci (NQTL) declined the accuracy of the Bayes B method. This study suggests that the highest accuracy (0.74) was achieved when additive genotypic effects were coded by a few quantitative trait loci and a lot of small effects included in the prediction of genomic breeding values

Robotic Technologies for High-Throughput Plant Phenotyping: Contemporary Reviews and Future Perspectives

Phenotyping plants is an essential component of any effort to develop new crop varieties. As plant breeders seek to increase crop productivity and produce more food for the future, the amount of phenotype information they require will also increase. Traditional plant phenotyping relying on manual measurement is laborious, time-consuming, error-prone, and costly. Plant phenotyping robots have emerged as a high-throughput technology to measure morphological, chemical and physiological properties of large number of plants. Several robotic systems have been developed to fulfill different phenotyping missions. In particular, robotic phenotyping has the potential to enable efficient monitoring of changes in plant traits over time in both controlled environments and in the field. The operation of these robots can be challenging as a result of the dynamic nature of plants and the agricultural environments. Here we discuss developments in phenotyping robots, and the challenges which have been overcome and others which remain outstanding. In addition, some perspective applications of the phenotyping robots are also presented. We optimistically anticipate that autonomous and robotic systems will make great leaps forward in the next 10 years to advance the plant phenotyping research into a new era

Impact of Accounting for Polygenic Effects on the Accuracy of Genomic Evaluations in Livestock Breeding

To investigate the accuracy of genomic breeding values, different scenarios were defined by accounting for polygenic effects, a different number of quantitative trait loci (30, 90, 150), and three levels of heritability (0.15, 0.25, and 0.4). The Bayes B method was used to estimate marker effects. A historical population was simulated stochastically, which consisted of 100 animals at first 100 generations, then the population size gradually increased to 1000 animals during the next 100 generations. The animals in generation 201 with known genotypic and phenotypic records were assigned as the reference population, and animals of generation 202 were considered as the validation population. The genome was comprised of one chromosome with 100 cM length and 500 markers that were distributed through the genome randomly. Picking up the information that was not captured by linkage disequilibrium (LD), including polygenic effects in the predictions increased the accuracy of genomic evaluations. As the trait heritability went from 0.15 to 0.40, the average genomic accuracy increased from 0.48 to 0.64. An increment in the number of quantitative trait loci (NQTL) declined the accuracy of the Bayes B method. This study suggests that the highest accuracy (0.74) was achieved when additive genotypic effects were coded by a few quantitative trait loci and a lot of small effects included in the prediction of genomic breeding values

High throughput analysis of leaf chlorophyll content in sorghum using RGB, hyperspectral, and fluorescence imaging and sensor fusion

Background: Leaf chlorophyll content plays an important role in indicating plant stresses and nutrient status. Traditional approaches for the quantification of chlorophyll content mainly include acetone ethanol extraction, spectrophotometry and high-performance liquid chromatography. Such destructive methods based on laboratory procedures are time consuming, expensive, and not suitable for high-throughput analysis. High throughput imaging techniques are now widely used for non-destructive analysis of plant phenotypic traits. In this study three imaging modules (RGB, hyperspectral, and fluorescence imaging) were, separately and in combination, used to estimate chlorophyll content of sorghum plants in a greenhouse environment. Color features, spectral indices, and chlorophyll fluorescence intensity were extracted from these three types of images, and multiple linear regression models and PLSR (partial least squares regression) models were built to predict leaf chlorophyll content (measured by a handheld leaf chlorophyll meter) from the image features. Results: The models with a single color feature from RGB images predicted chlorophyll content with R2 ranging from 0.67 to 0.88. The models using the three spectral indices extracted from hyperspectral images (Ration Vegetation Index, Normalized Difference Vegetation Index, and Modified Chlorophyll Absorption Ratio Index) predicted chlorophyll content with R2 ranging from 0.77 to 0.78. The model using the fluorescence intensity extracted from fluorescence images predicted chlorophyll content with R2 of 0.79. The PLSR model that involved all the image features extracted from the three different imaging modules exhibited the best performance for predicting chlorophyll content, with R2 of 0.90. It was also found that inclusion of SLW (Specific Leaf Weight) into the image-based models further improved the chlorophyll prediction accuracy. Conclusion: All three imaging modules (RGB, hyperspectral, and fluorescence) tested in our study alone could estimate chlorophyll content of sorghum plants reasonably well. Fusing image features from different imaging modules with PLSR modeling significantly improved the predictive performance. Image-based phenotyping could provide a rapid and non-destructive approach for estimating chlorophyll content in sorghum

High throughput analysis of leaf chlorophyll content in sorghum using RGB, hyperspectral, and fluorescence imaging and sensor fusion

Leaf chlorophyll content plays an important role in indicating plant stresses and nutrient status. Traditional approaches for the quantification of chlorophyll content mainly include acetone ethanol extraction, spectrophotometry and high-performance liquid chromatography. Such destructive methods based on laboratory procedures are time consuming, expensive, and not suitable for high-throughput analysis. High throughput imaging techniques are now widely used for non-destructive analysis of plant phenotypic traits. In this study three imaging modules (RGB, hyperspectral, and fluorescence imaging) were, separately and in combination, used to estimate chlorophyll content of sorghum plants in a greenhouse environment. Color features, spectral indices, and chlorophyll fluorescence intensity were extracted from these three types of images, and multiple linear regression models and PLSR (partial least squares regression) models were built to predict leaf chlorophyll content (measured by a handheld leaf chlorophyll meter) from the image features. Results: The models with a single color feature from RGB images predicted chlorophyll content with R2 ranging from 0.67 to 0.88. The models using the three spectral indices extracted from hyperspectral images (Ration Vegetation Index, Normalized Difference Vegetation Index, and Modified Chlorophyll Absorption Ratio Index) predicted chlorophyll content with R2 ranging from 0.77 to 0.78. The model using the fluorescence intensity extracted from fluorescence images predicted chlorophyll content with R2 of 0.79. The PLSR model that involved all the image features extracted from the three different imaging modules exhibited the best performance for predicting chlorophyll content, with R2 of 0.90. It was also found that inclusion of SLW (Specific Leaf Weight) into the image-based models further improved the chlorophyll prediction accuracy. Conclusion: All three imaging modules (RGB, hyperspectral, and fluorescence) tested in our study alone could estimate chlorophyll content of sorghum plants reasonably well. Fusing image features from different imaging modules with PLSR modeling significantly improved the predictive performance. Image-based phenotyping could provide a rapid and non-destructive approach for estimating chlorophyll content in sorghum

High‑throughput analysis of leaf physiological and chemical traits with VIS–NIR–SWIR spectroscopy: a case study with a maize diversity panel

Hyperspectral reflectance data in the visible, near infrared and shortwave infrared range (VIS–NIR– SWIR, 400–2500 nm) are commonly used to nondestructively measure plant leaf properties. We investigated the usefulness of VIS–NIR–SWIR as a high-throughput tool to measure six leaf properties of maize plants including chlorophyll content (CHL), leaf water content (LWC), specific leaf area (SLA), nitrogen (N), phosphorus (P), and potassium (K). This assessment was performed using the lines of the maize diversity panel. Data were collected from plants grown in greenhouse condition, as well as in the field under two nitrogen application regimes. Leaf-level hyperspectral data were collected with a VIS–NIR–SWIR spectroradiometer at tasseling. Two multivariate modeling approaches, partial least squares regression (PLSR) and support vector regression (SVR), were employed to estimate the leaf properties from hyperspectral data. Several common vegetation indices (VIs: GNDVI, RENDVI, and NDWI), which were calculated from hyperspectral data, were also assessed to estimate these leaf properties

Variation in morpho‑physiological and metabolic responses to low nitrogen stress across the sorghum association panel

Background: Access to biologically available nitrogen is a key constraint on plant growth in both natural and agricultural settings. Variation in tolerance to nitrogen deficit stress and productivity in nitrogen limited conditions exists both within and between plant species. However, our understanding of changes in different phenotypes under long term low nitrogen stress and their impact on important agronomic traits, such as yield, is still limited. Results: Here we quantified variation in the metabolic, physiological, and morphological responses of a sorghum association panel assembled to represent global genetic diversity to long term, nitrogen deficit stress and the relationship of these responses to grain yield under both conditions. Grain yield exhibits substantial genotype by environment interaction while many other morphological and physiological traits exhibited consistent responses to nitrogen stress across the population. Large scale nontargeted metabolic profiling for a subset of lines in both conditions identified a range of metabolic responses to long term nitrogen deficit stress. Several metabolites were associated with yield under high and low nitrogen conditions. Conclusion: Our results highlight that grain yield in sorghum, unlike many morpho-physiological traits, exhibits substantial variability of genotype specific responses to long term low severity nitrogen deficit stress. Metabolic response to long term nitrogen stress shown higher proportion of variability explained by genotype specific responses than did morpho-pysiological traits and several metabolites were correlated with yield. This suggest, that it might be possible to build predictive models using metabolite abundance to estimate which sorghum genotypes will exhibit greater or lesser decreases in yield in response to nitrogen deficit, however further research needs to be done to evaluate such model

In Vivo Human-Like Robotic Phenotyping of Leaf and Stem Traits in Maize and Sorghum in Greenhouse

In plant phenotyping, the measurement of morphological, physiological and chemical traits of leaves and stems is needed to investigate and monitor the condition of plants. The manual measurement of these properties is time consuming, tedious, error prone, and laborious. The use of robots is a new approach to accomplish such endeavors, which enables automatic monitoring with minimal human intervention. In this study, two plant phenotyping robotic systems were developed to realize automated measurement of plant leaf properties and stem diameter which could reduce the tediousness of data collection compare to manual measurements. The robotic systems comprised of a four degree of freedom (DOF) robotic manipulator and a Time-of-Flight (TOF) camera. Robotic grippers were developed to integrate an optical fiber cable (coupled to a portable spectrometer) for leaf spectral reflectance measurement, a thermistor for leaf temperature measurement, and a linear potentiometer for stem diameter measurement. An Image processing technique and deep learning method were used to identify grasping points on leaves and stems, respectively. The systems were tested in a greenhouse using maize and sorghum plants. The results from the leaf phenotyping robot experiment showed that leaf temperature measurements by the phenotyping robot were correlated with those measured manually by a human researcher (R2 = 0.58 for maize and 0.63 for sorghum). The leaf spectral measurements by the phenotyping robot predicted leaf chlorophyll, water content and potassium with moderate success (R2 ranged from 0.52 to 0.61), whereas the prediction for leaf nitrogen and phosphorus were poor. The total execution time to grasp and take measurements from one leaf was 35.5±4.4 s for maize and 38.5±5.7 s for sorghum. Furthermore, the test showed that the grasping success rate was 78% for maize and 48% for sorghum. The experimental results from the stem phenotyping robot demonstrated a high correlation between the manual and automated stem diameter measurements (R2 \u3e 0.98). The execution time for stem diameter measurement was 45.3 s. The system could successfully detect and localize, and also grasp the stem for all plants during the experiment. Both robots could decrease the tediousness of collecting phenotypes compare to manual measurements. The phenotyping robots can be useful to complement the traditional image-based high-throughput plant phenotyping in greenhouses by collecting in vivo morphological, physiological, and biochemical trait measurements for plant leaves and stems. Advisors: Yufeng Ge, Santosh Pitl

In vivo Human-Like Robotic Phenotyping of Leaf and Stem Traits in Maize and Sorghum in Greenhouse

In plant phenotyping, the measurement of morphological, physiological and chemical traits of leaves and stems is needed to investigate and monitor the condition of plants. The manual measurement of these properties is time consuming, tedious, error prone, and laborious. The use of robots is a new approach to accomplish such endeavors, which enables automatic monitoring with minimal human intervention. In this study, two plant phenotyping robotic systems were developed to realize automated measurement of plant leaf properties and stem diameter which could reduce the tediousness of data collection compare to manual measurements. The robotic systems comprised of a four degree of freedom (DOF) robotic manipulator and a Time-of-Flight (TOF) camera. Robotic grippers were developed to integrate an optical fiber cable (coupled to a portable spectrometer) for leaf spectral reflectance measurement, a thermistor for leaf temperature measurement, and a linear potentiometer for stem diameter measurement. An Image processing technique and deep learning method were used to identify grasping points on leaves and stems, respectively. The systems were tested in a greenhouse using maize and sorghum plants. The results from the leaf phenotyping robot experiment showed that leaf temperature measurements by the phenotyping robot were correlated with those measured manually by a human researcher (R2 = 0.58 for maize and 0.63 for sorghum). The leaf spectral measurements by the phenotyping robot predicted leaf chlorophyll, water content and potassium with moderate success (R2 ranged from 0.52 to 0.61), whereas the prediction for leaf nitrogen and phosphorus were poor. The total execution time to grasp and take measurements from one leaf was 35.5±4.4 s for maize and 38.5±5.7 s for sorghum. Furthermore, the test showed that the grasping success rate was 78% for maize and 48% for sorghum. The experimental results from the stem phenotyping robot demonstrated a high correlation between the manual and automated stem diameter measurements (R2 \u3e 0.98). The execution time for stem diameter measurement was 45.3 s. The system could successfully detect and localize, and also grasp the stem for all plants during the experiment. Both robots could decrease the tediousness of collecting phenotypes compare to manual measurements. The phenotyping robots can be useful to complement the traditional image-based high-throughput plant phenotyping in greenhouses by collecting in vivo morphological, physiological, and biochemical trait measurements for plant leaves and stems