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.

     

Molecular genetic structure and relationship of Chinese and Hungarian common carp (Cyprinus carpio L.) strains based on mitochondrial sequence

China and Hungary are major providers of the common carp (Cyprinus carpio L.) in East Asia and Europe respectively. However, the genetic variation and relationship of this species in the two countries have been poorly understood. In this study, mitochondrial COII‐tRNA^Lys and D‐loop sequences were analysed to investigate the genetic structure and relationships of the representative wild and domesticated common carps distributed in China and Hungary. The results indicated that the genetic diversities of the Chinese common carps are higher than those of Hungarian common carps, and the diversities of the wild common carps are higher than those of domesticated common carps in both the countries. Analysis of molecular variance and pairwise F_ST demonstrated a significant genetic divergence between the Chinese and the Hungarian common carps, and between the wild and the domesticated common carps. Bayesian phylogenetic analysis and statistical parsimony network showed an obvious genetic differentiation between the Chinese and the Hungarian common carps, between the wild and the domesticated common carps. However, a few specimens and haplotypes from the Chinese wild common carps appeared in the Hungarian common carps, demonstrating that there was no absolutely isolated and possible genetic linker between the Chinese and the Hungarian common carps.     

Technical note: isolation and characterization of sheep ruminal epithelial cells

A system for the isolation and characterization of sheep ruminal epithelial cells has been developed. Ruminal papillae from the ventral cranial sac of 12- to 24-wk-old Dorset ram lambs were subjected to serial tryptic digestions. Initial digestions (two 15-min periods) in the series were used to remove keratinized cells of the stratum corneum, which were able to produce only small amounts of beta-hydroxybutyrate from butyrate (5.37 +/- .72 nmol/120 min/per milligram of dry cell weight). Later digest fractions, containing primarily cells from the stratum basale, exhibited high viabilities (75 to 95%) and proved capable of converting butyrate to beta-hydroxybutyrate at relatively high rates (33.6 +/- 6.7 nmol/120 min per milligram of dry cell weight). Neither acetate nor propionate underwent significant conversion to beta-hydroxybutyrate. However, addition of acetate inhibited (77.4% of control) and addition of propionate stimulated (200% of control) beta-hydroxybutyrate production. Acetate addition reduced the propionate-induced stimulation of beta-hydroxybutyrate production from butyrate (136% of control). These results are similar to those obtained from in vitro incubations of ruminal papillae and suggest that an isolated cell system may prove useful in the further study of ruminal epithelial metabolism.     

The relationship between the occurrence of undifferentiated bovine respiratory disease and titer changes to bovine coronavirus and bovine viral diarrhea virus in 3 Ontario feedlots.

Serological evidence of previous viral exposure (titer at arrival) and current viral exposure (titer increase) during a 28-day study period, was used to determine if bovine coronavirus (BCV) or bovine viral diarrhea virus (BVDV) was associated with the occurrence of undifferentiated bovine respiratory disease (UBRD) in feedlot calves. Neutralizing antibody titers to BCV and BVDV were determined for 852 animals from 3 Ontario feedlots. Calves at 2 of the 3 feedlots (n = 753) received a modified live 4-way viral vaccine containing BVDV. On arrival at the feedlots, 90% of animals were seropositive for BCV, while 39% of animals were seropositive for BVDV. This evidence of previous exposure to both viruses was associated with reduced subsequent UBRD risk. Evidence of exposure to BCV during the study period was common, as 50% of animals showed a 16-fold or greater titer increase; however, treatment for UBRD was not associated with titer change. Although the majority of animals were vaccinated for BVDV at arrival, within a feedlot, animals treated for UBRD had larger titer increases to BVDV than non-treated animals. Based on our findings we infer that BCV was not causally related to UBRD occurrence, however consistent with other literature, BVDV may be causally related to UBRD occurrence.     

Zusammenhang zwischen Fertilität und Kopfschwanzkoppelung bei Eberspermien

Abstract: Relationship between the implantation of the tails and the fertility in boars In this study ejaculates of 47 different breed and age boars were examined. The aim of this study was to determine the relationship between the implantation of the tails and the fertility in boars. From the evaluation of 115 ejaculates it was observed that the rate of abaxial implantation of the tails in ejaculates of boars was very fluctuating. The rate of axial and abaxial implantation of the tails was stable in the ejaculates of the same boars. Although some studies indicate that abaxial implantation can be the reason for infertility the present authors observed better fertilisation results with ejaculates having higher percentages of abaxial spermatozoa.     

Effect of thinning on anatomical adaptations of Norway spruce needles

Conifers and other trees are constantly adapting to changes in light conditions, water/nutrient supply and temperatures by physiological and morphological modifications of their foliage. However, the relationship between physiological processes and anatomical characteristics of foliage has been little explored in trees. In this study we evaluated needle structure and function in Norway spruce families exposed to different light conditions and transpiration regimes. We compared needle characteristics of sun-exposed and shaded current-year needles in a control plot and a thinned plot with 50% reduction in stand density. Whole-tree transpiration rates remained similar across plots, but increased transpiration of lower branches after thinning implies that sun-exposed needles in the thinned plot were subjected to higher water stress than sun-exposed needles in the control plot. In general, morphological and anatomical needle parameters increased with increasing tree height and light intensity. Needle width, needle cross-section area, needle stele area and needle flatness (the ratio of needle thickness to needle width) differed most between the upper and lower canopy. The parameters that were most sensitive to the altered needle water status of the upper canopy after thinning were needle thickness, needle flatness and percentage of stele area in needle area. These results show that studies comparing needle structure or function between tree species should consider not only tree height and light gradients, but also needle water status. Unaccounted for differences in needle water status may have contributed to the variable relationship between needle structure and irradiance that has been observed among conifers.     

Locating and protecting critical reserve sites to minimize expected and worst-case losses

There has been much recent interest in the development of systematic reserve selection methods that are capable of incorporating uncertainty associated with site destruction. This paper makes a contribution to this line of research by presenting two different optimization models for minimizing species losses within a planning region. Given limited acquisition budgets, the first minimizes expected species losses over all possible site loss patterns outside the reserve network while the second minimizes maximum species losses following the worst-case loss of a restricted subset of nonreserve sites. By incorporating the uncertainty of site destruction directly into the decision planning process, these models allow a conservation planner to take a less defensive and more strategic view of reserve selection that seeks to minimize species losses through the targeted acquisition of high-value/high-risk sites. We compare both of these methods to a more standard approach, which simply maximizes within reserve representation without regard for the varied level of threat faced by different sites and species. Results on a realistic dataset show that significant reductions in species losses can be achieved using either of these more intelligent modeling frameworks.     

Allele mining and haplotype discovery in barley candidate genes for drought tolerance

In the present study, allele mining was conducted on a panel of drought related candidate genes in a set of 96 barley genotypes using EcoTILLING, which is a variant of the targeting induced local lesions in genomes (TILLING) technology. Analyzing approximately 1.5 million basepairs in barley a total number of 94 verified unique haplotypes were identified in 18 amplicons designed for 9 genes. Overall, 185 single nucleotide polymorphisms (SNPs) and 46 insertions/deletions (INDELs) were detected with a mean of 1SNP/92 bp and 1INDEL/372 bp genomic sequence. Based on overlapping haplotype sequences, markers were developed for four candidate genes (HvARH1, HvSRG6, HvDRF1, HVA1), which allows distinguishing between the main haplotypes showing either differences in amino acid sequence or which have larger INDELs in the promoter region. As “proof of concept”, the HvARH1 and HvSRG6 haplotypes were tested for the level of abscisic acid-induced gene expression in subsets of genotypes belonging to different haplotype categories. An integrated database was developed to contain information about the genes, genotypes, and haplotypes analyzed in this study. The database supplies profound information about the natural variation in the tested drought related candidate genes providing a significant asset for further mapping studies dealing with this highly polygenic trait.     

Alga-like forms in onverwacht series, South Africa: oldest recognized lifelike forms on Earth

Spheroidal and cupshaped, carbonaceous alga-like bodies, as well as filamentous structures and amorphous carbonaceous matter occur in sedimentary rocks of the Onverwacht Series (Swaziland System) in South Africa. The Onverwacht sediments are older than 3.2 eons, and they are probably the oldest, littlealtered sedimentary rocks on Earth. The basal Onverwacht sediments lie approximately 10,000 meters stratigraphically below the Fig Tree sedimentary rocks, from which similar organic microstructures have been interpreted as alga-like microfossils. The Onverwacht spheroids and filaments are best preserved in black, carbonrich cherts and siliceous argillites interlayered with thick sequences of lavas. These lifelike forms and the associated carbonaceous substances are probably biological in origin. If so, the origins of unicellular life on Earth are buried in older rocks now obliterated by igneous and metamorphic events.     

Productive infection and cell-free transmission of human T-cell leukemia virus in a nonlymphoid cell line

Human T-cell leukemia virus (HTLV), American PL isolate, was transmitted by cocultivation and by cell-free filtrates to a nonlymphoid human osteogenic sarcoma (HOS) cell line, designated HOS/PL, but not to nine other lines bearing receptors for HTLV. HOS and HOS/PL cells are not dependent on interleukin-2 and do not express interleukin-2 receptors that are recognized by anti-Tac monoclonal antibody. HTLV released by the Japanese MT2 cell line was also transmitted to HOS cells. The infected HOS cells release substantial titers of progeny HTLV which is antigenically indistinguishable from parental virus and is able to transform T cells.