Soybean maturity is a trait of critical importance for the development of new soybean cultivars, nevertheless, its characterization based on visual ratings has many challenges. Unmanned aerial ...vehicles (UAVs) imagery-based high-throughput phenotyping methodologies have been proposed as an alternative to the traditional visual ratings of pod senescence. However, the lack of scalable and accurate methods to extract the desired information from the images remains a significant bottleneck in breeding programs. The objective of this study was to develop an image-based high-throughput phenotyping system for evaluating soybean maturity in breeding programs. Images were acquired twice a week, starting when the earlier lines began maturation until the latest ones were mature. Two complementary convolutional neural networks (CNN) were developed to predict the maturity date. The first using a single date and the second using the five best image dates identified by the first model. The proposed CNN architecture was validated using more than 15,000 ground truth observations from five trials, including data from three growing seasons and two countries. The trained model showed good generalization capability with a root mean squared error lower than two days in four out of five trials. Four methods of estimating prediction uncertainty showed potential at identifying different sources of errors in the maturity date predictions. The architecture developed solves limitations of previous research and can be used at scale in commercial breeding programs.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Advances in phenotyping technology are critical to ensure the genetic improvement of crops meet future global demands for food and fuel. Field-based phenotyping platforms are being evaluated for ...their ability to deliver the necessary throughput for large scale experiments and to provide an accurate depiction of trait performance in real-world environments. We developed a dual-camera high throughput phenotyping (HTP) platform on an unmanned aerial vehicle (UAV) and collected time course multispectral images for large scale soybean Glycine max (L.) Merr. breeding trials. We used a supervised machine learning model (Random Forest) to measure crop geometric features and obtained high correlations with final yield in breeding populations (r=0.82). The traditional yield estimation model was significantly improved by incorporating plot row length as covariate (p<0.01). We developed a binary prediction model from time-course multispectral HTP image data and achieved over 93% accuracy in classifying soybean maturity. This prediction model was validated in an independent breeding trial with a different plot type. These results show that multispectral data collected from the UAV-based HTP platform could improve yield estimation accuracy and maturity recording efficiency in a modern soybean breeding program.
•A budget friendly airborne high throughput phenotyping platform was developed.•Canopy geometric features measured at plot-level highly correlated with yield.•Plot row length assessed from image improved yield estimation accuracy.•Time course multispectral data predicted soybean plot maturity with high accuracy.•The UAV-based high throughput phenotyping platform improved breeding efficiency.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Novel modifications of styrene-butadiene rubber were studied using conventional curatives, sulfur curing packages or peroxides, to efficiently utilize supramolecular reinforcement strategies that ...improve the mechanical properties of rubber. Thiol-ene coupling proved to be an effective method for modifying styrene-butadiene rubber during peroxide curing, but it was inadequate when attempted during sulfur vulcanization. Supramolecular reinforcement was achieved by grafting mercapto-functionalized sodium phosphate esters to styrene-butadiene rubber during peroxide curing which electrostatically associate. The association strength between these ionic grafts played a critical role in determining the degree of reinforcement. Possible mechanisms by which reinforcement occurs were discussed and, at low grafting densities, at least one mechanism was determined not to play a major role. It was shown that substantial modification of cis-1,4-polyisoprene does not occur by thiol-ene coupling and that another chemical means must be used to modify this substrate. Reagents consisting of thioaldehydes derived from thiosulfinates were used in Alder-ene reactions to modify cis-1,4-polyisoprene. Based on this chemistry, new grafting and crosslinking agents were developed that react quickly and at relatively low temperatures. Important elements in the molecular design of these curatives were discussed and it was demonstrated that good mechanical properties are attainable.
Reinforcement of styrene–butadiene rubber/butadiene rubber is achieved by grafting mercapto-functionalized sodium phosphate esters to the rubber during peroxide curing. The size of the anionic ...phosphate ester moiety is varied by changing the alkyl substituent (ethyl vs octyl) with the intention of modulating the association strength between the grafted ionic dipoles. The concentration of the ionic graft is also varied. These lead to different degrees of reinforcement and dynamic mechanical properties of the vulcanized rubber. The morphologies of ionic aggregates are characterized by transmission electron microscopy (TEM) imaging and X-ray scattering experiments. TEM imaging revealed heterogeneities in the material, which sometimes included the formation of vesicular aggregates with diameters of approximately 20–30 nm. These features are consistent with the radius of gyration calculated from a knee observed in X-ray scattering at scattering vectors below 0.4 nm–1. Smaller aggregates were analyzed using the Kinning–Thomas liquid-like hard sphere model and were found to be similar in radius (∼1.2–1.3 nm), irrespective of the molar volume of the ionic grafts from which they were constituted. However, the number of aggregates per unit volume within the material and the aggregation number are both profoundly affected by such variations. The structural variations of the ionic graft give rise to substantial changes in the tensile properties of the rubber at room temperature. At high temperatures, the differences in the dynamic moduli substantially diminish among the ionically grafted vulcanizates but remain substantial between the vulcanizates with and without ionic grafts. The equilibrium moduli of all vulcanizates converge at 60 °C. Possible mechanisms responsible for reinforcement are discussed at various temperatures, time scales, and ionic graft concentrations.
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Plant breeding has traditionally relied on combining the genetic diversity present within a species to develop combinations of alleles that provide desired traits. Epigenetic diversity may provide ...additional sources of variation within a species that could be captured or created for crop improvement. It will be important to understand the sources of epigenetic variation and the stability of newly formed epigenetic variants over generations to fully use the potential of epigenetic variation to improve crops. The development and application of methods for widespread epigenome profiling and engineering may generate new avenues for using the full potential of epigenetics in crop improvement.
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DNA methylation and dimethylation of lysine 9 of histone H3 (H3K9me2) are two chromatin modifications that can be associated with gene expression or recombination rate. The maize genome provides a ...complex landscape of interspersed genes and transposons. The genome-wide distribution of DNA methylation and H3K9me2 were investigated in seedling tissue for the maize inbred B73 and compared to patterns of these modifications observed in Arabidopsis thaliana. Most maize transposons are highly enriched for DNA methylation in CG and CHG contexts and for H3K9me2. In contrast to findings in Arabidopsis, maize CHH levels in transposons are generally low but some sub-families of transposons are enriched for CHH methylation and these families exhibit low levels of H3K9me2. The profile of modifications over genes reveals that DNA methylation and H3K9me2 is quite low near the beginning and end of genes. Although elevated CG and CHG methylation are found within gene bodies, CHH and H3K9me2 remain low. Maize has much higher levels of CHG methylation within gene bodies than observed in Arabidopsis and this is partially attributable to the presence of transposons within introns for some maize genes. These transposons are associated with high levels of CHG methylation and H3K9me2 but do not appear to prevent transcriptional elongation. Although the general trend is for a strong depletion of H3K9me2 and CHG near the transcription start site there are some putative genes that have high levels of these chromatin modifications. This study provides a clear view of the relationship between DNA methylation and H3K9me2 in the maize genome and how the distribution of these modifications is shaped by the interplay of genes and transposons.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a ...species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species.
By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species.
These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.
Alzheimer's disease neurodegeneration is thought to spread across anatomically and functionally connected brain regions. However, the precise sequence of spread remains ambiguous. The prevailing ...model used to guide in vivo human neuroimaging and non-human animal research assumes that Alzheimer's degeneration starts in the entorhinal cortices, before spreading to the temporoparietal cortex. Challenging this model, we previously provided evidence that in vivo markers of neurodegeneration within the nucleus basalis of Meynert (NbM), a subregion of the basal forebrain heavily populated by cortically projecting cholinergic neurons, precedes and predicts entorhinal degeneration. There have been few systematic attempts at directly comparing staging models using in vivo longitudinal biomarker data, and none to our knowledge testing if comparative evidence generalizes across independent samples. Here we addressed the sequence of pathological staging in Alzheimer's disease using two independent samples of the Alzheimer's Disease Neuroimaging Initiative (n1 = 284; n2 = 553) with harmonized CSF assays of amyloid-β and hyperphosphorylated tau (pTau), and longitudinal structural MRI data over 2 years. We derived measures of grey matter degeneration in a priori NbM and the entorhinal cortical regions of interest. To examine the spreading of degeneration, we used a predictive modelling strategy that tests whether baseline grey matter volume in a seed region accounts for longitudinal change in a target region. We demonstrated that predictive spread favoured the NbM→entorhinal over the entorhinal→NbM model. This evidence generalized across the independent samples. We also showed that CSF concentrations of pTau/amyloid-β moderated the observed predictive relationship, consistent with evidence in rodent models of an underlying trans-synaptic mechanism of pathophysiological spread. The moderating effect of CSF was robust to additional factors, including clinical diagnosis. We then applied our predictive modelling strategy to an exploratory whole-brain voxel-wise analysis to examine the spatial specificity of the NbM→entorhinal model. We found that smaller baseline NbM volumes predicted greater degeneration in localized regions of the entorhinal and perirhinal cortices. By contrast, smaller baseline entorhinal volumes predicted degeneration in the medial temporal cortex, recapitulating a prior influential staging model. Our findings suggest that degeneration of the basal forebrain cholinergic projection system is a robust and reliable upstream event of entorhinal and neocortical degeneration, calling into question a prevailing view of Alzheimer's disease pathogenesis.
Chromatin modifications and epigenetics may play important roles in many plant processes, including developmental regulation, responses to environmental stimuli, and local adaptation. Chromatin ...modifications describe biochemical changes to chromatin state, such as alterations in the specific type or placement of histories, modifications of DNA or histories, or changes in the specific proteins or RNAs that associate with a genomic region. The term epigenetic is often used to describe a variety of unexpected patterns of gene regulation or inheritance. Here, we specifically define epigenetics to include the key aspects of heritability (stable transmission of gene expression states through mitotic or meiotic cell divisions) and independence from DNA sequence changes. We argue against genetically equating chromatin and epigenetics; although many examples of epigenetics involve chromatin changes, those chromatin changes are not always heritable or may be influenced by genetic changes. Careful use of the terms chromatin modifications and epigenetics can help separate the biochemical mechanisms of regulation from the inheritance patterns of altered chromatin states. Here, we also highlight examples in which chromatin modifications and epigenetics affect important plant processes.
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