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.

     

Special issue “Deepen knowledge in plant pathology for innovative agroecology”

This study aimed to determine the genetic variability of isolates of rotting of pineapple fruitlet core in Brazil on the states of Paraiba, Pernambuco and Rio Grande do Norte, based on phylogenetic analysis of the RPB2 gene, morphocultural markers and aggressiveness of the isolates. The phylogenetic reconstruction of maximum parsimony and bayesian inference of the isolates were performed. Twenty-seven phylogenetic lineages were characterized with morphocultural markers on potato dextrose agar and synthetic nutrient-poor agar. The aggressiveness of these lineages were characterized in leaves and fruits of pineapple ‘Pérola’ cultivar. The Phylogenetic reconstruction showed close relationship between isolates of this study and phylogenetic lineages of F. guttiforme, F. ananatum and F. oxysporum by analysis of RPB2 gene. Phylogenetic lineages of this study shared significant morphocultural markers similar to those described for this species. Overall, the lineages related with Fusarium oxysporum Species Complex were more aggressive to the fruits of the Fusarium lineages related with Fusarium fujikuroi Species Complex. It is possible that F. ananatum and F. guttiforme or other lineages closely related to these species or F. oxysporum are present in the fields causing pineapple rotting fruitlet core in fruits of pineapple ‘Pérola’ in Brazil. The used markers determined high genetic variability in isolates analyzed in leaves and pineapple fruit ‘Pérola’ in the states of Paraíba, Pernambuco and Rio Grande do Norte of Brazil and the pathogenic lineages analyzed were better adapted to the fruits than to the detached leaves in pineapple ‘Pérola’ analyzed.     

The Content of Dietary Fibre and Polyphenols in Morphological Parts of Buckwheat (<Emphasis Type="Italic">Fagopyrum tataricum</Emphasis>)

In this report, we presented the profile of polyphenolic substances in flowers, leaves, stalk and roots of Fagopyrum tataricum estimated by using RP–UHPLC–ESI-MS equipment (reversed-phase ultra-high-performance liquid chromatography electrospray ionisation mass spectrometry). The neutral detergent fibre, acid detergent fibre, acid detergent lignin, cellulose and hemicellulose were also determined. Flowers, leaves, stalk and roots showed varying levels of dietary fibre and polyphenols. The highest content of neutral and acid detergent fibre were found in the roots (63.92 and 45.45% d.m., respectively) while the most rich in phenolic compounds were flowers (4.8 mg/1 g d.m.). Root and stalk contained the highest level of cellulose, 38.70 and 25.57% d.m., respectively. Among the investigated polyphenolic substances such as: 2,6-dihydroxybenzoic acid, 3,4-dihydroxybenzoic acid, 3,5-dihydroxybenzoic acid, 4-hydrobenzoic acid, caffeic acid, catechin, chlorogenic acid, fagopyrin, ferulic acid, myricetin, gallic acid, isovanilic acid, isovitexin, kaempferol, luteolin, p-coumaric acid, procyanidin B2, quercetin, quercetin 3-D galactoside, rutin, syringic acid and vitexin, we observed that the contents of rutin and chlorogenic acid were the highest. We found some correlation between dietary fibre fractions and individual phenolic substances. The levels of acid detergent fibre (ADF), cellulose and hemicellulose were negatively correlated with isovitexin, kaempferol, vitexin, fagopyrin, caffeic acid and procyanidin B2 content. In this investigation, two solvents (water and methanol) were estimated regarding their extraction efficiency of phenolic compounds. Taking these results into consideration, we recommend using methanol as the extractor to isolate chlorogenic acid, fagopyrin, kaempferol, procyanidin B2, quercetin, quercetin 3-D-galactoside, rutin, vitexin, and water for other investigated polyphenolic substances obtained from Fagopyrum tataricum.     

Influence of stage of development in the efficiency of nitrogen fertilization on poplar

Poplar cuttings (Populus x euroamericana) were planted in pots and grown in a greenhouse for four months with drip irrigation. Two nitrogen (N) doses of 60 and 120 kg nitrate (N-NO₃^?) ha^?1 (labeling with ¹⁵N stable isotopes) were applied at one (time I), two (time II) and three months after of the plantation (time III). The aim of this study was to determine the N-fertilizer application method that resulted in optimal N-uptake by a short-rotation of poplar crop during first year of growth. Our data revealed that NUE (N use efficiency) was largest in the last part of the experiment. The larger development of those plants at this stage enabled the improved absorption and assimilation of N. Furthermore, ¹⁵N also revealed that supply of N at three months post-planting generated more biomass and increased the N reserves in the stem; a key factor for ensuring the optimum regrowth during the second year.     

Amorphous Aluminum Hydroxide Control on Sulfate and Phosphate in Sediment-Solution Systems

We experimentally determined the adsorption characteristics of natural, freshly precipitated Al(OH)₃ for SO₄ and PO₄. The fresh Al precipitate occurred in stream sediment of Jachymov Stream (Czech Republic). The Al-rich sediment strongly adsorbed added PO₄ prior to acidification experiment; this sorbed PO₄ was released only after substantial dissolution of the sediment, at pH?<?3.67. Sorption of P by Al(OH)₃ appears to be an important control on dissolved PO₄ concentration in surface waters, unless there is a large excess of PO₄. Acidification of the sediment-solution system caused protonation of the sediment surface, thereby increasing the adsorption capacity for SO₄. Maximum SO₄ adsorption occurred at pH 4.2, below which dissolution of the sediment offset the increasing anion adsorption capacity, and formation of AISO₄ ⁺ inhibited the increasing SO₄ adsorption capacity. This research demonstrates that there are important pH thresholds for anion adsorption in freshwaters below which dissolution of the Al(OH)₃ substrate reduces total capacity for anion adsorption. In freshwaters, with sufficient concentrations of suspended Al(OH)₃, or in Al(OH)₃-rich sediment, PO₄ mobility will be severely restricted. Suspended Al(OH)₃ in acidified surface waters cannot strongly influence SO₄ concentrations because of the considerably higher total SO₄ concentrations compared to the available surface area.     

Alkaline Comet Assay as a Potential Tool in the Assessment of DNA Integrity in Freshwater Zooplankton Affected by Pollutants from Water Treatment Facility

Water, Air, & Soil Pollution - In this pilot study, we evaluated the usefulness of the alkaline comet assay as a biomonitoring tool at the level of plankton communities affected by varying...     

Estimating nocturnal ecosystem respiration from the vertical turbulent flux and change in storage of CO2

Micrometeorological measurements of nighttime ecosystem respiration can be systematically biased when stable atmospheric conditions lead to drainage flows associated with decoupling of air flow above and within plant canopies. The associated horizontal and vertical advective fluxes cannot be measured using instrumentation on the single towers typically used at micrometeorological sites. A common approach to minimize bias is to use a threshold in friction velocity, u_*, to exclude periods when advection is assumed to be important, but this is problematic in situations when in-canopy flows are decoupled from the flow above. Using data from 25 flux stations in a wide variety of forest ecosystems globally, we examine the generality of a novel approach to estimating nocturnal respiration developed by van Gorsel et al. (van Gorsel, E., Leuning, R., Cleugh, H.A., Keith, H., Suni, T., 2007. Nocturnal carbon efflux: reconciliation of eddy covariance and chamber measurements using an alternative to the u_*-threshold filtering technique. Tellus 59B, 397–403, Tellus, 59B, 307-403). The approach is based on the assumption that advection is small relative to the vertical turbulent flux (F_C) and change in storage (F_S) of CO₂ in the few hours after sundown. The sum of F_C and F_S reach a maximum during this period which is used to derive a temperature response function for ecosystem respiration. Measured hourly soil temperatures are then used with this function to estimate respiration R_Rmax. The new approach yielded excellent agreement with (1) independent measurements using respiration chambers, (2) with estimates using ecosystem light-response curves of F_c + F_s extrapolated to zero light, R_LRC, and (3) with a detailed process-based forest ecosystem model, R_cast. At most sites respiration rates estimated using the u_*-filter, R_ust, were smaller than R_Rmax and R_LRC. Agreement of our approach with independent measurements indicates that R_Rmax provides an excellent estimate of nighttime ecosystem respiration.