Prospects for Knockout of MYB60, a Transcriptional Repressor of Anthocyanin Biosynthesis, in Brassicaceae Plants by Genome Editing

The Brassicaceae plant family contains many economically important crops such as Brassica napus L., Brassica rapa L., Brassica oleracea L., Brassica juncea L., Eruca sativa Mill., Camelina sativa L. and Raphanus sativus L. Insufficient data on the genetic regulation of agronomic traits in these species complicates the editing of their genomes. In recent years, the attention of the academic community has been drawn to anthocyanin hyperaccumulation. This trait is not only beneficial for human health, but can also increase plant resistance to stress. MYB transcription factors are the main regulators of flavonoid biosynthesis in plants. Some of them are well studied in Arabidopsis thaliana. The AtMYB60 gene is a transcriptional repressor of anthocyanin biosynthesis, and it also negatively impacts plant responses to drought stress. Myb60 is one of the least studied transcription factors with similar functions in Brassicaceae. There is a high degree of homology between predicted MYB60 genes of A. thaliana and related plant species. However, functions of these homologous genes have never been studied. Gene knockout by CRISPR/Cas technology remains the easiest way to perform genome editing in order to discover the role of individual plant genes. Disruption of genes acting as negative regulators of anthocyanin biosynthesis could result in color staining of plant tissues and an increase in stress tolerance. In the present study, we investigated the AtMYB60 gene and its homologs in Brassicaceae plants and suggested universal gRNAs to knockout these genes. Keywords: CRISPR, Brassicaceae, MYB60, knockout, anthocyanin

Evaluation of Individual Plant Growth Estimation in an Intercropping Field with UAV Imagery

Agriculture practices in monocropping need to become more sustainable and one of the ways to achieve this is to reintroduce intercropping. However, quantitative data to evaluate plant growth in intercropping systems are still lacking. Unmanned aerial vehicles (UAV) have the potential to become a state-of-the-art technique for the automatic estimation of plant growth. Individual plant height is an important trait attribute for field investigation as it can be used to derive information on crop growth throughout the growing season. This study aimed to investigate the applicability of UAV-based RGB imagery combined with the structure from motion (SfM) method for estimating the individual plants height of cabbage, pumpkin, barley, and wheat in an intercropping field during a complete growing season under varying conditions. Additionally, the effect of different percentiles and buffer sizes on the relationship between UAV-estimated plant height and ground truth plant height was examined. A crop height model (CHM) was calculated as the difference between the digital surface model (DSM) and the digital terrain model (DTM). The results showed that the overall correlation coefficient (R2) values of UAV-estimated and ground truth individual plant heights for cabbage, pumpkin, barley, and wheat were 0.86, 0.94, 0.36, and 0.49, respectively, with overall root mean square error (RMSE) values of 6.75 cm, 6.99 cm, 14.16 cm, and 22.04 cm, respectively. More detailed analysis was performed up to the individual plant level. This study suggests that UAV imagery can provide a reliable and automatic assessment of individual plant heights for cabbage and pumpkin plants in intercropping but cannot be considered yet as an alternative approach for barley and wheat.

Inter- and intra-event rainfall partitioning dynamics of two typical xerophytic shrubs in the Loess Plateau of China

Rainfall is known as the main water replenishment in dryland ecosystem, and rainfall partitioning by vegetation reshapes the spatial and temporal distribution patterns of rainwater entry into the soil. The dynamics of rainfall partitioning have been extensively studied at the inter-event scale, yet very few studies have explored its finer intra-event dynamics and the relating driving factors for shrubs. Here, we conducted a concurrent in-depth investigation of rainfall partitioning at inter- and intra-event scales for two typical xerophytic shrubs (Caragana korshinskii and Salix psammophila) in the Liudaogou catchment of the Loess Plateau, China. The event throughfall (TF), stemflow (SF), and interception loss (IC) and their temporal variations within the rainfall event as well as the meteorological factors and vegetation characteristics were systematically measured during the 2014–2015 rainy seasons. The C. korshinskii had significantly higher SF percentage (9.2 %) and lower IC percentage (21.4 %) compared to S. psammophila (3.8 % and 29.5 %, respectively) (p < 0.05), but their TF percentages were not significantly different (69.4 % vs. 66.7 %). At the intra-event scale, TF and SF of S. psammophila was initiated (0.1 vs. 0.3 h and 0.7 vs. 0.8 h) and peaked (1.8 vs. 2.0 h and 2.1 vs. 2.2 h) more quickly, and TF of S. psammophila lasted longer (5.2 vs. 4.8 h), delivered more intensely (4.3 vs. 3.8 mm∙h−1), whereas SF of C. korshinskii lasted longer (4.6 vs. 4.1 h), delivered more intensely (753.8 vs. 471.2 mm∙h−1). For both shrubs, rainfall amount was the most significant factor influencing inter-event rainfall partitioning, and rainfall intensity and duration controlled the intra-event TF and SF variables. The C. korshinskii with larger branch angle, more small branches and smaller canopy area, has an advantage to produce stemflow more efficiently over S. psammophila. The S. psammophila has lower canopy water storage capacity to generate and peak throughfall and stemflow earlier, and it has larger aboveground biomass and total canopy water storage of individual plant to produce higher interception loss compared to C. korshinskii. These findings contribute to the fine characterization of shrub-dominated eco-hydrological processes, and improve the accuracy of water balance estimation in dryland ecosystem.

Exploring the 4D scales of eco-geomorphic interactions along a river corridor using repeat UAV Laser Scanning (UAV-LS), multispectral imagery, and a functional traits framework

Vegetation plays a critical role in the modulation of fluvial process and morphological evolution. However, adequately capturing the spatial variability and complexity of vegetation characteristics remains a challenge. Currently, most of the research seeking to address these issues takes place at either the individual plant scale or via larger scale bulk classifications, with the former seeking to characterise vegetation-flow interactions and the latter identifying spatial variation in vegetation types. Herein, we devise a method which extracts functional vegetation traits using UAV laser scanning and multispectral imagery, and upscale these to reach scale guild classifications. Simultaneous monitoring of morphological change is undertaken to identify eco-geomorphic links between different guilds and the geomorphic response of the system in the context of long-term decadal changes. Identification of four guilds from quantitative structural modelling based on analysis of terrestrial and UAV based laser scanning and two further guilds from image analysis was achieved. These were upscaled to reach-scale guild classifications with an overall accuracy of 80 % and links to magnitudes of geomorphic activity explored. We show that different vegetation guilds have a role in influencing morphological change through the stabilisation of banks, but that limits on this influence are evident in the prior long-term analysis. This research reveals that remote sensing offers a solution to the difficulty of scaling traits-based approaches for eco-geomorphic research, and that these methods may be applied to larger areas using airborne laser scanning and satellite imagery datasets.

Bioavailability of selected trace and rare earth elements to Juncus effusus L.: the potential role of de-icing chlorides in the roadside environment

Background and aim The presence of chlorides in soils, e.g., from de-icing salts may change metal availability to plants. Methods To assess the role of de-icing chlorides on bioavailability of metals, the samples of the rhizosphere soils, roots and shoots of Juncus effusus L. were collected monthly from April to June of 2019 in the vicinity of roads and analyzed for trace (Ag, Cd, Co, Cu, Pb, Zn) and rare earth elements (from La to Lu). Results Concentrations of Cl− were distinctly higher in the shoots than in the roots. Apart from Cd, the concentration sequence of the other metals was as follows: rhizosphere soils>roots>shoots. The bioaccumulation and translocation factors indicated that Cd was the most preferably transported to the shoots as opposed to Ag, Co, Pb and REEs that showed a very low translocation potential. Negative correlations, which were noted between Cu and Co in the shoots and Cl− in soils, revealed their role in salinity stress alleviation. All soil samples showed a positive anomaly of Ce and a negative anomaly of Eu, whereas the shoots showed in turn a negative anomaly of Ce and a distinct positive anomaly of Eu. The lowest salinity factors (K/Na, Ca/Na) of the shoots resulted from an increase of salinity in J. effusus by higher sodium concentrations derived from de-icing NaCl. Conclusions De-icing agents may change the uptake of other elements. In natural habitats, the factors affecting this process include: type of element, soil metal concentrations and interactions, and individual plant features.

Estimation of Genetic Parameters of Biomass Production and Composition Traits in Miscanthus Sinensis Using a Staggered-start Design

Traits for biomass production and composition make Miscanthus a promising bioenergy crop for different bioconversion routes. They need to be considered in miscanthus breeding programs as they are subjected to genetic and genetic x environment factors. The objective was to estimate the genetic parameters of an M. sinensis population grown during four years in two French locations. In each location, the experiment was established according to a staggered-start design in order to decompose the year effect into age and climate effects. Linear Mixed Models were used to estimate genetic variance, genotype x age, genotype x climate interaction variances and residual variances. Individual plant broad-sense heritability means ranged from 0.42 to 0.62 for biomass production traits, and were more heritable than biomass composition traits with means ranging from 0.26 to 0.47. Heritability increased through time for most of the biomass production and composition traits. Low genetic variance along with large genotype x age and genotype x climate interaction variances tended to decrease the heritability of biomass production traits for young plant ages. Most of the production traits showed large interaction variances for age and climate in both locations, while biomass composition traits highlighted large interaction variances due to climate in Orléans. The genetic and phenotypic correlations between biomass production and composition traits were moderate and positive, while hemicelluloses were negatively correlated with all traits. Efficient genetic progress is achievable for miscanthus breeding when plants get older. The joint improvement of biomass production and composition traits would help provide a better response of miscanthus to selection.

Evaluation of Antioxidant and Antidiabetic Potential of Polyherbal Drug Made with Three Herbs: An In vitro Cell Culture Model

In diabetes, the postprandial phase is characterized by a rapid and large increase in blood glucose levels, and the possibility that the postprandial “hyperglycemic spikes” may be relevant to the onset of cardiovascular complications has recently received much attention. Medicinal use of herbal medicine in the treatment and prevention of diseases including diabetes has a long history compared to conventional medicine. These plants have no side effects and many existing medicines are derived from the plants. Hence, the current investigation was planned to make a poly herbal drug (PHD) through Punica granatum (fruits), Illicium verum (flowers) and Nyctanthes arbor (leaves) and assess their antioxidant and antidiabetic activities in vitro and in HepG2 cell line. The respective plant methanolic extracts and PHD are exposed to phytochemical assessment and to discriminate the bioactive factors by Gas Chromatography–Mass Spectrometry. We evaluated the antioxidant properties 2, 2-diphenyl-1-picrylhydrazyl scavenging, hydrogen peroxide scavenging, thiobarbituric acid reactive substances and total antioxidant activity of individual plant extracts and the PHD. At the same time, In vitro and cell culture approaches were used to assess the anti-diabetic activity. The PHD has a higher concentration of secondary metabolites than individual plant extracts, according to our findings. On the other hand, we also notice that PHD demonstrated higher antioxidant capability and considerable in vitro glucose-lowering effects along with noteworthy inhibition of ɑ-amylase, glucosidase, lipase, dipeptidyl peptidase-IV, collagenase and protein glycation in HepG2 cell line. In conclusion, this study clearly demonstrated the significant antioxidant and antidiabetic activities of the PHD. Hence, PHD may be used as a potential source in the management of diabetes, hyperglycemia and the related state of oxidative stress.

Synanthropization and species diversityof floodplain ecosystems of the Ob-Irtysh basin, Russia

Currently, the phytocenoses of the Irtysh floodplain are experiencing intense anthropogenic pressures due to the intensive development of the oil and gas industry, as well as the urbanization of the territory. This paper focuses on the structure and species composition of the 27 studied areas in the floodplain ecosystems of the Ob-Irtysh basin. As a result of the research, we found 111 species of vascular plants from 33 families in plant communities. The areas belong to meadows and forest vegetation are represented by (1) birch forests (33%), (2) pine forests (10%), (3) fir forests (8%), (4) aspen forests (4%) and (5) associations of meadows (45%). Furthermore, we conducted a comparative analysis of the studied phytocenoses according to the Drude scale. To determine the anthropogenic transformation of the flora and individual plant communities, we determined the synanthropization index (the ratio of synanthropic species to the total number of species). In the synanthropic flora fraction, we distinguished 45 species belonging to 12 families, with the most multispecies being Apiaceae, Scrophulariaceae, Compositeae, Ranunculaceae, Poaceae, Fabaceae, Plantaginaceae. The synanthropization index of the studied phytocenoses ranges from 6.6% to 81.2%. The largest number of synanthropic species occurs in meadow associations, the content of synanthropes is greater than 50%, the structure is becoming more superficial, and the productivity and stability of plant communities are changing. The study of the horizontal structure of grass stands of meadow phytocenoses makes it possible to find the variability of different years, the change of dominant species and the stability of the species composition. Currently, researchers are paying considerable attention to the analysis of the structure of the herbage, since its study is of great theoretical and practical importance in clarifying phytocenotic relations.

Mathematical modeling suggests cooperation of plant-infecting viruses

Viruses are major pathogens of agricultural crops. Viral infections often start after the virus enters the outer layer of a tissue or surface and many successful viruses, after local replication in the infected tissue, are able to spread systemically. Quantitative details of virus dynamics in plants, however, have been poorly understood, in part, because of the lack of experimental methods allowing to accurately measure the degree of infection in individual plant tissues. Recently, by using flow cytometry and two different flourescently-labeled strains of the Tobacco etch virus (TEV), Venus and BFP, kinetics of viral infection of individual cells in leaves of {\it Nicotiana tabacum} plants was followed over time \cite{Tromas.pg14}. A simple mathematical model, assuming that viral spread occurs from lower to upper leaves, was fitted to these data. While the the original model could accurately describe the kinetics of viral spread locally and systemically, we also found that many alternative versions of the model, for example, if viral spread starts at upper leaves and progresses to lower leaves or when virus dissemination is stopped due to an immune response, provided fits of the data with reasonable quality, and yet with different parameter estimates. These results strongly suggest that experimental measurements of the virus infection in individual leaves may not be sufficient to identify the pathways of viral dissemination between different leaves and reasons for viral control; we propose experiments that may allow discrimination between the alternatives. By analyzing the kinetics of coinfection of individual cells by Venus and BFP strains of TEV we found a strong deviation from the random infection model, suggesting cooperation between the two strains when infecting plant cells. Importantly, we showed that many mathematical models on the kinetics of coinfection of cells with two strains could not adequately describe the data, and the best fit model needed to assume i) different susceptibility of uninfected cells to infection by two viruses locally in the leaf vs. systemically from other leaves, and ii) decrease in the infection rate depending on the fraction of uninfected cells which could be due to a systemic immune response. Our results thus demonstrate the difficulty in reaching definite conclusions from extensive and yet limited experimental data and provide evidence of potential cooperation between different viral variants infecting individual cells in plants.

Development of a Low-Cost System for 3D Orchard Mapping Integrating UGV and LiDAR

Growing evaluation in the early stages of crop development can be critical to eventual yield. Point clouds have been used for this purpose in tasks such as detection, characterization, phenotyping, and prediction on different crops with terrestrial mapping platforms based on laser scanning. 3D model generation requires the use of specialized measurement equipment, which limits access to this technology because of their complex and high cost, both hardware elements and data processing software. An unmanned 3D reconstruction mapping system of orchards or small crops has been developed to support the determination of morphological indices, allowing the individual calculation of the height and radius of the canopy of the trees to monitor plant growth. This paper presents the details on each development stage of a low-cost mapping system which integrates an Unmanned Ground Vehicle UGV and a 2D LiDAR to generate 3D point clouds. The sensing system for the data collection was developed from the design in mechanical, electronic, control, and software layers. The validation test was carried out on a citrus crop section by a comparison of distance and canopy height values obtained from our generated point cloud concerning the reference values obtained with a photogrammetry method. A 3D crop map was generated to provide a graphical view of the density of tree canopies in different sections which led to the determination of individual plant characteristics using a Python-assisted tool. Field evaluation results showed plant individual tree height and crown diameter with a root mean square error of around 30.8 and 45.7 cm between point cloud data and reference values.