A Clustering Framework for Monitoring Circadian Rhythm in Structural Dynamics in Plants From Terrestrial Laser Scanning Time Series

Proximal and remote sensing in plant phenomics: 20 years of progress, challenges, and perspectives

Plant phenomics (PP) has been recognized as a bottleneck in studying the interactions of genomics and environment on plants, limiting the progress of smart breeding and precise cultivation. High-throughput plant phenotyping is challenging owing to the spatio-temporal dynamics of traits. Proximal and remote sensing (PRS) techniques are increasingly used for plant phenotyping because of their advantages in multi-dimensional data acquisition and analysis. Substantial progress of PRS applications in PP has been observed over the last two decades and is analyzed here from an interdisciplinary perspective based on 2972 publications. This progress covers most aspects of PRS application in PP, including patterns of global spatial distribution and temporal dynamics, specific PRS technologies, phenotypic research fields, working environments, species, and traits. Subsequently, we demonstrate how to link PRS to multi-omics studies, including how to achieve multi-dimensional PRS data acquisition and processing, how to systematically integrate all kinds of phenotypic information and derive phenotypic knowledge with biological significance, and how to link PP to multi-omics association analysis. Finally, we identify three future perspectives for PRS-based PP: (1) strengthening the spatial and temporal consistency of PRS data, (2) exploring novel phenotypic traits, and (3) facilitating multi-omics communication.

Understanding the dynamic properties of trees using the motions constructed from multi-beam flash light detection and ranging measurements

Measuring the three-dimensional motion of trees at every position remains challenging as it requires dynamic measurement technology with sufficient spatial and temporal resolution. Consequently, this study explores the use of a novel multi-beam flash light detection and ranging (LiDAR) sensor to tackle such a sensing barrier. A framework is proposed to record tree vibrations, to construct the motions of tree skeletons from the point-cloud frames recorded by the LiDAR sensor and to derive the dynamic properties of trees. The feasibility of the framework is justified through measurement on a Ficus microcarpa under pull-and-release tests. The relative differences for the first two modal frequencies between the LiDAR and linear variable differential transformer measurements in the displacement Fourier spectra are 0.1% and 2.5%, respectively. The framework is further adopted to study the dynamic response of different trees subjected to typhoons, including a Liquidambar formosana, three Araucaria heterophylla trees, a Sterculia lanceolata, a Celtis sinensis, a Tabebuia chrysantha and a Cinnamomum camphora. Results suggest that broadleaved trees might exhibit vibration in a wide frequency band, whereas the coniferous trees could follow a distinct dominant frequency.

Evaluation of the Moso Bamboo Age Determination Based on Laser Echo Intensity

Determination of bamboo age is an important task for bamboo forest management and bamboo utilization. However, the bamboo age is usually manually determined in the field, which is time-consuming and labor-intensive. Due to the ability to generate very high-density point clouds, terrestrial laser scanning (TLS) has been applied in forestry to acquire forest parameters. This study evaluated the potential of using the laser echo intensity data generated by TLS technology to determine the Moso bamboo age represented by “du.” The intensity data were first corrected for the distance and incidence angle effects using an intensity correction method that constructed an empirical correction model by fitting piecewise polynomials to the intensity data collected based on a reference target. Then the models expressing the relationship between intensity and bamboo culm section number were constructed for different bamboo du by fitting polynomials to the intensity data of individual bamboo culms through least-squares adjustment. For a bamboo plant whose age is determined, the bamboo du could be determined based on the constructed intensity-culm section models. The proposed bamboo age determination method was tested at a site in a managed Moso bamboo forest in Lin’an District, Hangzhou City, Zhejiang Province, China. From the test site, 56 and 120 bamboo plants with known bamboo ages were selected to construct the intensity-culm section models and to validate the bamboo age determination method, respectively. The bamboo age determination accuracies for each bamboo du were all above 90%. The result indicates a great potential for automatic determination of bamboo age in practice using TLS technology.

Tree Water Status Affects Tree Branch Position

Physiological processes cause movements of tree stems and branches that occur in a circadian rhythm and over longer time periods, but there is a lack of quantitative understanding of the cause-and-effect relationships. We investigated the movement of tree branches in a long-term drought experiment and at a circadian time scale using time-series of terrestrial laser scanning measurements coupled with measurements of environmental drivers and tree water status. Our results showed that movement of branches was largely explained by leaf water status measured as leaf water potential in a controlled environment for both measured trees (R2 = 0.86 and R2 = 0.75). Our hypothesis is that changes in leaf and branch water status would cause branch movements was further supported by strong relationship between vapor pressure deficit and overnight branch movement (R2 = [0.57–0.74]). Due to lower atmospheric water demand during the nighttime, tree branches settle down as the amount of water in leaves increases. The results indicate that the quantified movement of tree branches could help us to further monitor and understand the water relations of tree communities.

Exploring Seasonal and Circadian Rhythms in Structural Traits of Field Maize from LiDAR Time Series

Plant growth rhythm in structural traits is important for better understanding plant response to the ever-changing environment. Terrestrial laser scanning (TLS) is a well-suited tool to study structural rhythm under field conditions. Recent studies have used TLS to describe the structural rhythm of trees, but no consistent patterns have been drawn. Meanwhile, whether TLS can capture structural rhythm in crops is unclear. Here, we aim to explore the seasonal and circadian rhythms in maize structural traits at both the plant and leaf levels from time-series TLS. The seasonal rhythm was studied using TLS data collected at four key growth periods, including jointing, bell-mouthed, heading, and maturity periods. Circadian rhythms were explored by using TLS data acquired around every 2 hours in a whole day under standard and cold stress conditions. Results showed that TLS can quantify the seasonal and circadian rhythm in structural traits at both plant and leaf levels. (1) Leaf inclination angle decreased significantly between the jointing stage and bell-mouthed stage. Leaf azimuth was stable after the jointing stage. (2) Some individual-level structural rhythms (e.g., azimuth and projected leaf area/PLA) were consistent with leaf-level structural rhythms. (3) The circadian rhythms of some traits (e.g., PLA) were not consistent under standard and cold stress conditions. (4) Environmental factors showed better correlations with leaf traits under cold stress than standard conditions. Temperature was the most important factor that significantly correlated with all leaf traits except leaf azimuth. This study highlights the potential of time-series TLS in studying outdoor agricultural chronobiology.

A Long-Term Terrestrial Laser Scanning Measurement Station to Continuously Monitor Structural and Phenological Dynamics of Boreal Forest Canopy

The terrestrial laser scanner (TLS) has become standard technology for vegetation dynamics monitoring. TLS time series have significant underlying application in investigating structural development and dynamics on a daily and seasonal scale. However, the high potential of TLS for the monitoring of long-term temporal phenomena in fully grown trees with high spatial and temporal resolution has not yet been fully explored. Automated TLS platforms for long-term data collection and monitoring of forest dynamics are rare; and long-term TLS time series data is not yet readily available to potential end-user, such as forestry researchers and plant biologists. This work presents an automated and permanent TLS measurement station that collects high frequency and high spatial resolution TLS time series, aiming to monitor short- and long-term phenological changes at a boreal forestry field station (0.006° angular resolution, one scan per hour). The measurement station is the first of its kind considering the scope, accuracy, and length of the time series it produces. The TLS measurement station provides a unique dataset to monitor the 3D physical structure of a boreal forest, enabling new insights into forest dynamics. For instance, the information collected by the TLS station can be used to accurately detect structural changes in tree crowns surrounding the station. These changes and their timing can be linked with the phenological state of plants, such as the start of leaf-out during spring growing season. As the first results of this novel station, we present time series data products collected with the station and what detailed information it provides about the phenological changes in the test site during the leaf sprout in spring.

Canopy Roughness: A New Phenotypic Trait to Estimate Aboveground Biomass from Unmanned Aerial System

Cost-effective phenotyping methods are urgently needed to advance crop genetics in order to meet the food, fuel, and fiber demands of the coming decades. Concretely, characterizing plot level traits in fields is of particular interest. Recent developments in high-resolution imaging sensors for UAS (unmanned aerial systems) focused on collecting detailed phenotypic measurements are a potential solution. We introduce canopy roughness as a new plant plot-level trait. We tested its usability with soybean by optical data collected from UAS to estimate biomass. We validate canopy roughness on a panel of 108 soybean [Glycine max (L.) Merr.] recombinant inbred lines in a multienvironment trial during the R2 growth stage. A senseFly eBee UAS platform obtained aerial images with a senseFly S.O.D.A. compact digital camera. Using a structure from motion (SfM) technique, we reconstructed 3D point clouds of the soybean experiment. A novel pipeline for feature extraction was developed to compute canopy roughness from point clouds. We used regression analysis to correlate canopy roughness with field-measured aboveground biomass (AGB) with a leave-one-out cross-validation. Overall, our models achieved a coefficient of determination (R ²) greater than 0.5 in all trials. Moreover, we found that canopy roughness has the ability to discern AGB variations among different genotypes. Our test trials demonstrate the potential of canopy roughness as a reliable trait for high-throughput phenotyping to estimate AGB. As such, canopy roughness provides practical information to breeders in order to select phenotypes on the basis of UAS data.