Application of unmanned aerial systems for high throughput phenotyping of large wheat breeding nurseries

Background

Low cost unmanned aerial systems (UAS) have great potential for rapid proximal measurements of plants in agriculture. In the context of plant breeding and genetics, current approaches for phenotyping a large number of breeding lines under field conditions require substantial investments in time, cost, and labor. For field-based high-throughput phenotyping (HTP), UAS platforms can provide high-resolution measurements for small plot research, while enabling the rapid assessment of tens-of-thousands of field plots. The objective of this study was to complete a baseline assessment of the utility of UAS in assessment field trials as commonly implemented in wheat breeding programs. We developed a semi-automated image-processing pipeline to extract plot level data from UAS imagery. The image dataset was processed using a photogrammetric pipeline based on image orientation and radiometric calibration to produce orthomosaic images. We also examined the relationships between vegetation indices (VIs) extracted from high spatial resolution multispectral imagery collected with two different UAS systems (eBee Ag carrying MultiSpec 4C camera, and IRIS+ quadcopter carrying modified NIR Canon S100) and ground truth spectral data from hand-held spectroradiometer.

Results

We found good correlation between the VIs obtained from UAS platforms and ground-truth measurements and observed high broad-sense heritability for VIs. We determined radiometric calibration methods developed for satellite imagery significantly improved the precision of VIs from the UAS. We observed VIs extracted from calibrated images of Canon S100 had a significantly higher correlation to the spectroradiometer (r = 0.76) than VIs from the MultiSpec 4C camera (r = 0.64). Their correlation to spectroradiometer readings was as high as or higher than repeated measurements with the spectroradiometer per se.

Conclusion

The approaches described here for UAS imaging and extraction of proximal sensing data enable collection of HTP measurements on the scale and with the precision needed for powerful selection tools in plant breeding. Low-cost UAS platforms have great potential for use as a selection tool in plant breeding programs. In the scope of tools development, the pipeline developed in this study can be effectively employed for other UAS and also other crops planted in breeding nurseries.

     

Protected wading bird species threaten relict centenarian cork oaks in a Mediterranean Biosphere Reserve: A conservation management conflict

Conservation management conflicts frequently arise when an overpopulation of a protected organism has negative effects on other valuable elements in the same ecosystem. We studied the interactions between a colony of protected tree-nesting wading birds and a remnant population of centenarian cork oaks that was part of the formerly dominant forests in the Doñana Biological Reserve (SW Spain). A significant increase in the tree mortality rates has been recorded in areas that are yearly influenced by the bird colony.We analysed a cohort of surviving trees using a gradient of nesting bird influence. Tree-nesting history, bird isotopic signature (δ¹⁵N), tree health-related parameters (defoliation, δ¹³C and leaf surface coverage by faeces) and several soil variables were evaluated. Bird influence was related to increased soil salinity. This increase correlated to increased water-use efficiency for the leaves and to crown defoliation, suggesting that the heavily occupied trees are under higher stress and in poorer health condition than the unoccupied ones. We tested structural equations models (SEM) that were based on hypothesised bird effects on the health of the trees. Soil-mediated effects of the nesting birds best explained the symptoms of the declining health of the trees, whereas the percent of leaves’ surface that was covered by faeces did not improve the fitted SEM model.For the reserve’s managers, a challenging trade-off exists between preserving the relict trees, which have a high genetic diversity and a key ecological role in these savannah-like ecosystems, and maintaining the current nesting area for these protected, but expanding, wading birds.     

Fermentation as a bio-process to obtain functional soybean flours

The effect of fermentation on the antioxidant compounds [vitamins C and E, total phenolic compounds (TPC), and reduced glutathione (GSH)], and antioxidant capacity [superoxide anion scavenging activity (SOD-like activity), peroxyl radical-trapping capacity (PRTC), inhibition of phosphatidylcholine (PC) peroxidation, and Trolox equivalent antioxidant capacity (TEAC)] of soybean (Glycine max cv. Merit) was studied. Fermentation was carried out in solid state in cracked seeds inoculated with Aspergillus oryzae, Rhizopus oryzae, Bacillus subtilis, and Lactobacillus plantarum and in liquid state either in cracked seeds or milled soybean flours fermented naturally by only the microorganisms present in the seeds or by inoculation with L. plantarum. Vitamin C was not detected in the studied samples. Fermentation caused a decrease in vitamin E activity, except when cracked seed was fermented with A. oryzae, R. oryzae, or B. subtilis that increased 31, 30, and 89%, respectively. Fermentation produced an increase in TPC content and did not affect or reduce the GSH content. Fermentation decreased SOD-like activity drastically, while PRTC increased except when it was carried out naturally in cracked seed. TEAC values rose sharply when soybeans were fermented with B. subtilis. Processed soybean extracts inhibited PC peroxidation in comparison with the control assay. On the basis of the results obtained, the relative contributions of vitamin E, TPC, and GSH to antioxidant capacity were calculated and results showed a very high TPC contribution and a low contribution of GSH and vitamin E activity. Optimum results for functional soybean flours were achieved when fermentation was carried out with B. subtilis inoculum.     

Histopathological Changes in Third-Instar and Adult Anastrepha ludens (Diptera: Tephritidae) After in vitro Heat Treatment

The Mexican fruit fly, Anastrepha ludens Loew (Diptera: Tephritidae), is one of the most harmful pests of mango causing direct damage by oviposition on the fruit pulp. Mango for export is subjected to hydrothermal treatment as a quarantine method for the control of this pest, but exposure to heat for long periods of time reduces considerably the quality and shelf-life of treated fruit. The aim of this work was to study morphological changes of third-instar larvae and adults of A. ludens after in vitro exposure to high temperature at sublethal times. A heating block system was used to expose larvae at 46.1°C for 19.6 and 12.9 min, producing 94.6 and 70% mortality, respectively. Treated larvae were processed for optical microscopy. A fraction of surviving treated larvae was separated into containers with artificial diet to allow development into adults. Adult sexual organs were dissected and processed for transmission electron microscopy analysis. Results showed that 94.6% of the treated larvae died at 46.1°C for 19.6 min and none of the surviving larvae eclosed to adulthood, as they developed as malformed puparia. For the in vitro treatment at 46.1°C during 12.9 min, 70% of the treated larvae died and only 3.75% reached the adult stage, but ultrastructural damage in the male testes and in the female ovaries was observed. Additionally, 11.1% of the adult flies from the in vitro treatment also showed wing malformation and were incapable of flying. The analysis showed that surviving flies were unable to reproduce.     

Diurnal and seasonal water variations of temperature,pH, redox potential and conductivity in gnammas (weathering pits): Implications for chemical weathering

A gnamma or weathering pit is a small-sized cavity sculpted into solid rock which refills with rainwater. This study describes the main hydrological processes in gnammas and the underlying chemical interactions with the environment. Four gnammas developed in a granite tor from central Spain were chosen for monitoring and studying the dynamics of the gnamma–water system. Parameters monitored were air and water temperature, pH, ORP (redox potential), and conductivity. These measurements describe the system dynamics, without the need for special sampling or other potential interferences under low water volumes. Additionally, chemical analyses were carried out to contrast the chemical properties with the chemical composition. As a consequence of water volumes less than 100 L, daily fluctuations tended to cause the largest amplitude changes. Photosynthesis and respiration/putrefaction processes in the gnamma are responsible for daily pH fluctuations up to 4 units, with pH values often greater than 9. ORP generally alternates from positive to negative values as the solution oscillates diurnally between basic and acidic conditions. Conductivity values ∼ 10 μS/cm occur most of the year, with only minor daily oscillations. During dry periods, conductivity increases significantly with maximum values > 400 μS/cm. These high conductivity values reflect atmospheric inputs by summer rainstorms after prolonged dry periods. Therefore, conductivity does not relate directly with chemical species dissolved from the host rock. Silica was the main weathering product of granite dissolution during the year, with highest concentrations (> 200 ppm) in the rainy season. Low Si values measured during the dry season are in accordance with observed precipitation of amorphous silica within the gnamma. Seasonal variations in concentration are also present in Al and Fe as a response to ORP variations and evaporative dynamics, causing mineral dissolution and new mineral precipitation during the year. Relations among the measured parameters are influenced by several factors, including biological processes, temperature effects and water level variations. Factors such as large pH oscillations, basic pH values, acids from biological activity, and alkali cations all increase silicate solubility, thus favoring granite dissolution. Overflow of water during the winter, when the water is chemically enriched, is an effective mechanism to remove weathering products.     

Effect of salicylic acid treatment on tomato plant physiology and tolerance to potato virus X infection

Salicylic acid (SA) is an inducer of systemic acquired resistance (SAR) and could be a potential candidate in the control of plant virus diseases. In this study we assayed under controlled conditions the potential effect of three doses of exogenous SA treatment on tomato plants infected with Potato virus X (PVX) and measured their effects on: different physiological parameters (gas exchange, stable isotopes, chlorophyll content), the activation of secondary metabolism, viral accumulation and induction of the expression of pathogenesis-related proteins (PRs) such as ß-1, 3-glucanase (PR2) and chitinase (PR3). SA treatment increased the expression of PR2, the activity of phenylalanine ammonia lyase (PAL) and the concentration of antioxidant compounds at 7 days post-treatment. Earlier expression of PR3 compared to PR2 was observed. SA treatment delayed the detection of PVX by ELISA in uninoculated leaves of mechanically infected tomato plants. Although the effect of PVX infection on physiological parameters was weak, moderate SA treatments showed enhanced photosynthesis, particularly for infected plants. The results obtained confirm that SA promotes major changes in the induction of resistance in tomato plants and suggest that treatment with exogenous SA could be considered to reduce the infections caused by PVX.     

A Syndrome Resembling Idiopathic Noncirrhotic Portal Hypertension in 4 Young Doberman Pinschers

We describe 4 young male Doberman Pinschers (3 littermates and 1 unrelated dog) with a syndrome resembling idiopathic or noncirrhotic portal hypertension of humans. Each dog was evaluated for a hepatopathy resulting in portal hypertension, development of portosystemic collateral vessels, and hepatic encephalopathy. These dogs differ from previous reports of young dogs with hepatic insufficiency associated with portal hypertension and acquired portal systemic shunting by their lack of intrahepatic arteriovenous fistulae, portal vein atresia, or intrahepatic fibrosis. Clinicopathologic features included erythrocyte microcytosis, normal to mildly increased liver enzyme activities, increased concentrations of serum bile acids, reduced plasma indocyanine green clearance, and normal total bilirubin concentration. Abdominal ultrasonography disclosed a small liver and portosystemic collateral vessels. Radiographic imaging studies confirmed hepatofugal portal circulation and discounted hepatic arteriovenous fistulae. Histopathologic features in liver tissue from each dog were similar and consistent in all sections examined. Common findings included increased cross-sectional views of hepatic arterioles; hepatic lobular atrophy; scanty increase in connective tissue around some large portal triads; and absence of inflammation, disturbed lobular architecture, bile duct proliferation, or intrahepatic cholestasis.     

Interindividual variability in plasma concentrations after systemic exposure of swine to dietary doxycycline supplied with and without paracetamol: a population pharmacokinetic approach

Anorexigenic substances released during infection may hinder the therapeutic efficacy of in-feed antibiotics. Paracetamol (acetaminophen; PARA) inhibits the anorexia of infection and seems to improve the clinical efficacy of doxycycline (DOX) against bacterial respiratory disease in swine herds. In order to verify whether PARA selectively stimulates intake of DOX-medicated feed in diseased pigs, we documented the pharmacokinetics (PK) of DOX when coadministered with PARA and examined the effect of in-feed PARA on the interindividual variability in plasma concentrations after systemic exposure to in-feed DOX in swine herds with respiratory disease. Systemic exposure to DOX was measured with the area under the curve (AUC) of its plasma concentrations over time. First, a rich-sampling PK study of in-feed and i.v. DOX (10 mg/kg of BW) and PARA (30 and 10 mg/kg of BW, respectively) was performed on 5 pigs. The PK profiles of in-feed DOX were used in mathematical simulations to determine 5 optimal sampling times for the farm-based population PK study. A randomized, blind, parallel PK study was performed in 2 herds with bacterial respiratory disease, where liquid feed was fortified with DOX alone (5 mg x kg of BW(-1) x meal(-1)) or combined with PARA (15 mg x kg of BW(-1) x meal(-1)). Medicated meals were given twice, 12 h apart, to group-housed growing pigs (n > 50 pigs x treatment(-1) x herd(-1), totaling 215 pigs). Plasma concentrations of DOX and PARA were measured with HPLC. At variance with our expectations, PARA decreased (P = 0.069) mean AUC of in-feed DOX and did not decrease its variability (P > 0.34). Mean AUC of DOX increased with feed intake and with initial exposure to DOX, and was greater in sick animals. Therefore, symptomatic PARA-induced improvement in bacterial respiratory disease control with DOX is more likely caused by its analgesic/antipyretic effects than by its orexigenic effect. Interindividual variation in the AUC of DOX was large in pigs given group medication, even when sufficient feeding space was allowed and the amount of feed offered was greater than their requirements. Therefore, future studies to improve the efficacy of group antibiotic therapy should focus on feeding behavior characteristics as well as biopharmaceutical properties of medicated feeds.