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.

     

Getting a grip on strangles: recent progress towards improved diagnostics and vaccines

'Strangles', caused by infection with the bacterium Streptococcus equi, remains one of the most commonly diagnosed and important infectious diseases of horses world-wide. This review discusses the diagnosis and pathogenesis of strangles with particular attention to the significance of persistent infections in disease transmission and the rapid progress now being made towards the development of effective preventative vaccines. It is now possible combine recent sequence data from the N-terminal region of the SeM protein and reassign the SeM alleles using the on-line database http://pubmlst.org/szooepidemicus/seM/. Hypotheses concerning the origin of this variation and the potential for its exploitation for the epidemiological analysis of outbreaks are proposed. Advances in understanding of the molecular evolution of S. equi highlight the role played by phage-mediated acquisition of virulence factors and suggest new avenues for prophylactic intervention.     

Substitution of fish meal by soybean meal in diets for juvenile marbled spinefoot,Siganus rivulatus

The present work was performed to assess whether soybean meal (SBM) could replace fish meal (FM) as a source of dietary protein in diets of the marine herbivore Siganus rivulatus. Five iso-nitrogenous (40% protein) and iso-energetic (14 MJ/Kg) diets were prepared with SBM replacing fish meal at 0%, 25%, 50%, 75%, and 100% dietary protein. A 60-day feeding trial was conducted with 240 juvenile S. rivulatus (initial body mass 1.74 ± 0.03 g). Survival, growth, feed, and protein efficiency and hematological parameters were assessed. Growth correlated negatively with increase in dietary SBM. All production parameters measured were negatively affected at all levels of SBM inclusion. There were no effects on total or differential blood counts, hemoglobin, or plasma protein, but hematocrit values were negatively correlated with SBM addition. Results suggest that total replacement of FM by SBM without adding other supplements is not recommended, even for an herbivorous marine fish such as S. rivulatus.     

Osmoregulatory and immunological status of the pond-raised striped catfish (<Emphasis Type="Italic">Pangasianodon hypophthalmus</Emphasis> S.) as affected by seasonal runoff and salinity changes in the Mekong Delta,Vietnam

In Vietnam, the production of striped catfish Pangasianodon hypophthalmus S. reached more than 1.2 millions of tons in 2014 and is mainly gathered in the Mekong Delta (South Vietnam). A survey was carried out during the dry season 2013 (March–April) and rainy season 2014 (July–August) in 12 fish farms of the lower (Tra Vinh Province) and higher (Can Tho Province) Mekong River Delta. This study allowed drawing up current key osmoregulatory and innate immune parameters of striped catfish in aquaculture depending on the geographical location, particularly the proximity to the River Mekong Estuary and the seasonal surface runoff. In the dry season, plasma osmolality was positively correlated with salinity. Gill Na⁺K⁺ ATPase dropped in the rainy season, while kidney Na⁺K⁺ ATPase remained stable. Abundance of immune blood cells, especially thrombocytes and monocytes, tended to increase in farms located in tidal area. Production of reactive oxygen species in the spleen, kidney lysozyme activity and plasma complement activity did not vary whatever the season or the proximity to the estuary. Plasma lysozyme activity was 50-fold higher than in kidney and increased in the rainy season as well as in tidal sites. Kidney complement activity decreased in the dry season, especially in tidal sites. In conclusion, regarding key osmoregulatory and immune factors, striped catfish farms located in the Mekong Delta may be affected by seasonal and regional salinity and runoff fluctuations.     

Survival and respiration of marbled rabbitfish (Siganus rivulatus) fingerlings at various oxygen tensions

Marbled rabbitfish, Siganus rivulatus, is an economically valuable herbivorous fish and a potential candidate for warmwater aquaculture. This study was carried out to: (1) assess the effect of various oxygen concentrations on survival and behaviour of S. rivulatus fingerlings and (2) investigate the response of S. rivulatus to hypoxia and determine its critical oxygen tension (P_crit). In the first experiment, groups of rabbitfish (15 fish per group) were maintained for 1 h in waters of various oxygen concentrations. They were then transferred to well‐aerated tanks and observed for 72 h. Survival was recorded, fish behaviour at low oxygen concentrations observed, and LC₅₀ after 1‐h hypoxia and 72‐h recovery evaluated. In the second experiment, a series of stop‐flow respirometry experiments were performed during which dissolved oxygen was allowed to drop to 0.5 mg L^?1 and respiration rate recorded at various oxygen concentrations. In the first experiment, all fish survived for 1 h at oxygen concentration of 1.44 mg L^?1 and greater, but started dying at oxygen concentrations below 0.65 mg L^?1 (16% survival). The LC₅₀ of S. rivulatus fingerlings was 0.6 mg L^?1. Results of the second experiment showed that S. rivulatus is an oxyregulator until P_crit (1.7 mg L^?1 O₂) is reached, becoming an oxyconformer below this concentration. Findings allow for a better understanding of environmental oxygen tolerances and minimum acceptable oxygen concentration in rabbitfish aquaculture.     

Bonamia in Ostrea angasi: Diagnostic performance,field prevalence and intensity

Bonamia spp. parasites threaten flat oyster (Ostrea spp.) farming worldwide. Understanding test performance is important for designing surveillance and interpreting diagnostic results. Following a pilot survey which found low Bonamia sp. intensity in farmed Ostrea angasi, we tested further oysters (n = 100–150) from each of three farms for Bonamia sp. using heart smear, histology and qPCR. We used a Bayesian Latent Class Model to assess diagnostic sensitivity (DSe) and specificity (DSp) of these tests individually or in combination, and to assess prevalence. Histology was the best individual test (DSe 0.76, DSp 0.93) compared to quantitative polymerase chain reaction (qPCR) (DSe 0.69, DSp 0.93) and heart smear (DSe 0.61, DSp 0.60). Histology combined with qPCR and defining a positive from either test as an infected case maximized test performance (DSe 0.91, DSp 0.88). Prevalence was higher at two farms in a high‐density oyster growing region than at a farm cultivating oysters at lower density. Parasite intensities were lower than in New Zealand and European studies, and this is probably contributed to differences in the performance of test when compared to other studies. Understanding diagnostic test performance in different populations can support the development of improved Bonamia surveillance programs.     

Energy dynamics of subyearling Chinook salmon reveal the importance of piscivory to short‐term growth during early marine residence

Variation in prey quantity and quality can influence growth and survival of marine predators, including anadromous fish that migrate from freshwater systems. The objective of this study was to examine the energy dynamics of subyearling Chinook salmon (Oncorhynchus tshawytscha) following freshwater emigration. To address this objective, a population of Chinook salmon and their marine prey were repeatedly sampled from June to September over 2 years in coastal waters off Oregon and Washington. Subyearlings from the same population were also reared under laboratory conditions. Using a bioenergetics model evaluated in the laboratory, we found that growth rate variability in the field was associated more with differences in northern anchovy (Engraulis mordax) consumption and less with variation in diet energy density or ocean temperature. Highest growth rates (2.43–3.22% body weight/day) occurred in months when anchovy biomass peaked, and the timing of peak anchovy biomass varied by year. Our results support a general pattern among subyearling Chinook salmon occurring from Alaska to California that feeding rates contribute most to growth rate variability during early marine residence, although dominant prey types can differ seasonally, annually, or by ecosystem. In the northern California Current, faster growth appears to be associated with the availability of age‐0 anchovy. Identifying factors that influence the seasonal development of the prey field and regulate prey quantity and quality will improve understanding of salmon growth and survival during early marine residence.