Summary
We report on a whole‐genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in ...Central and Eastern Europe. Through whole‐genome shotgun sequencing of the 7.9‐Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low‐copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high‐density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high‐density genetic map and establishing a synteny‐based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome‐wide map of selection signals differentiating the divergent gene pools. This rye whole‐genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome‐based breeding in rye.
Significance statement
Rye is a diploid Triticeae species closely related to wheat and barley. Here we present a draft genome and a high‐density genotyping array that will facilitate genome‐based research in rye and comparative genomics in Triticeae.
Key message
Hyperspectral data is a promising complement to genomic data to predict biomass under scenarios of low genetic relatedness. Sufficient environmental connectivity between data used for ...model training and validation is required.
The demand for sustainable sources of biomass is increasing worldwide. The early prediction of biomass via indirect selection of dry matter yield (DMY) based on hyperspectral and/or genomic prediction is crucial to affordably untap the potential of winter rye (
Secale cereale
L.) as a dual-purpose crop. However, this estimation involves multiple genetic backgrounds and genetic relatedness is a crucial factor in genomic selection (GS). To assess the prospect of prediction using reflectance data as a suitable complement to GS for biomass breeding, the influence of trait heritability (
H
2
) and genetic relatedness were compared. Models were based on genomic (GBLUP) and hyperspectral reflectance-derived (HBLUP) relationship matrices to predict DMY and other biomass-related traits such as dry matter content (DMC) and fresh matter yield (FMY). For this, 270 elite rye lines from nine interconnected bi-parental families were genotyped using a 10 k-SNP array and phenotyped as testcrosses at four locations in two years (eight environments). From 400 discrete narrow bands (410 nm–993 nm) collected by an uncrewed aerial vehicle (UAV) on two dates in each environment, 32 hyperspectral bands previously selected by Lasso were incorporated into a prediction model. HBLUP showed higher prediction abilities (0.41 – 0.61) than GBLUP (0.14 – 0.28) under a decreased genetic relationship, especially for mid-heritable traits (FMY and DMY), suggesting that HBLUP is much less affected by relatedness and
H
2
. However, the predictive power of both models was largely affected by environmental variances. Prediction abilities for DMY were further enhanced (up to 20%) by integrating both matrices and plant height into a bivariate model. Thus, data derived from high-throughput phenotyping emerges as a suitable strategy to efficiently leverage selection gains in biomass rye breeding; however, sufficient environmental connectivity is needed.
The use of small rotors has increased due their applications in drones and UAVs. In order to improve the global performance of these aerial vehicles, it is necessary to understand the aerodynamics of ...small rotors, since this is related to the global energy consumption of such vehicles. Most of the computational fluid dynamics (CFD) studies found in the literature that are related to the analysis of small rotors employ fully turbulent models, despite the low-to-moderate Reynolds numbers of these applications. This paper presents CFD simulations for a small rotor at hover at different Reynolds numbers using fully turbulent and transitional SST k−ω turbulence models. Numerical results show that thrust and torque are close to experimental measurements, showing differences of less than 5% for both fully turbulent and transitional models. However, significant differences were observed between the fully turbulent and the transitional models when studying the boundary-layer development and separation. As the Reynolds number was increased, it was observed that at the tip of the blade, these differences were reduced, but at mid-span, the differences were more obvious.
ABSTRACT
Doubled haploid (DH) lines produced via in vivo haploid induction have become an indispensable tool in maize (Zea mays L.) breeding and research. To determine the predictive value of the per ...se performance of haploid and DH lines in population and hybrid breeding, genetically balanced sets of haploid and DH lines along with testcrosses of the DH lines were evaluated in field trials across four locations over 2 yr in Germany. Suitable material sets were provided by three collaborating breeders. Each set comprised 54 to 58 DH lines developed from a proprietary elite dent single cross. These DH lines were crossed with one or two flint testers and subjected to haploid induction for production of corresponding haploid versions. Haploid lines, DH lines, and testcrosses were grown in separate but adjacent blocks. Haploid lines were surrounded by a mixture of inbred lines functioning as pollen source. Most haploid plants were male sterile but showed a certain degree of female fertility. Highly significant genetic variation reflected by high heritability coefficients existed in all material sets for all traits. Genetic correlations between haploid and DH lines were moderate to strong (0.5 < genetic correlation coefficient rg < 0.9) for early vigor, silking date, plant height, and stover weight per plant. Correlations between DH lines and testcrosses varied from nonsignificant to moderately strong for grain yield but were strong for silking date, plant height, stover yield, and grain moisture content. Silking date, early vigor, and plant height of haploid lines were moderately but significantly associated with grain yield of testcrosses. Somewhat higher estimates were obtained for the corresponding correlations between DH lines and testcrosses. In conclusion, selection for silking date, early vigor, plant height, and stover weight at the haploid level is expected to result in positive correlated genetic gain for various traits not only at the DH but also at the testcross level. Likewise, selection at the DH level may substantially speed up progress in combining ability.
Globalization has led to an increase in the use of small copters for different activities such as geo-referencing, agricultural fields monitoring, survillance, among others. This is the main reason ...why there is a strong interest in the performance of small-scale propellers used in unmanned aerial vehicles. The flow developed by rotors is complex and the estimation of its aerodynamic performance is not a trivial process. In addition, viscous effects, when the rotor operates at low Reynolds, affect its performance. In the present paper, two different computational methods, Computational Fluid Dynamics (CFD) and the Unsteady Vortex Lattice Method (UVLM) with a viscous correction, were used to study the performance of an isolated rotor of a quadcopter flying at hover. The Multi Reference Frame model and transition S S T κ − ω turbulence model were used in the CFD simulations. The tip vortex core growth was used to account for the viscous effects in the UVLM. The wake structure, pressure coefficient, thrust and torque predictions from both methods are compared. Thrust and torque results from simulations were validated by means of experimental results of a characterization of a single rotor. Finally, figure of merit of the rotor is evaluated showing that UVLM overestimates the efficiency of the rotor; meanwhile, CFD predictions are close to experimental values.
Claviceps purpurea
causing ergot maintains to be a problem in commercial cytoplasmic male sterile (CMS)-based hybrid rye growing. The fungal spores compete with pollen during flowering and ergot ...incidence is reduced in highly pollen-shedding stands. This study was carried out to identify maternal differences in ergot infection in the absence of pollen. Ten male-sterile single crosses were tested by needle and spray inoculation and kept unfertilized in up to four field sites (Germany, Austria) and three greenhouse experiments, respectively, in two years. A medium to high correlation was observed between field (needle inoculation) and greenhouse (spray inoculation) experiments. The environments (=location × year combinations) differed in their ergot severity and ergot incidence. Significant (
P
≤ 0.05) genotypic and genotype × environment interaction variances were detected for the unfertilized male-sterile single crosses in both test systems for both traits. The single cross K_4 showed a significantly lower ergot severity averaged across all environments, thus being more resilient to ergot than the other genotypes. In conclusion, spray and needle inoculation are suitable for testing unfertilized male-sterile rye materials, testing across several environments (locations, years) is definitely necessary. Selection of specific females might give the potential for further reducing ergot contamination in hybrid rye in future. The frequency of such genotypes within larger breeding populations needs to be analyzed.
Stem rust (SR) and leaf rust (LR) are currently the two most important rust diseases of cultivated rye in Central Europe and resistant cultivars promise to prevent yield losses caused by those ...pathogens. To secure long-lasting resistance, ideally pyramided monogenic resistances and race-nonspecific resistances are applied. To find respective genes, we screened six breeding populations and one testcross population for resistance to artificially inoculated SR and naturally occurring LR in multi-environmental field trials. Five populations were genotyped with a 10K SNP marker chip and one with DArTseq
. In total, ten SR-QTLs were found that caused a reduction of 5-17 percentage points in stem coverage with urediniospores. Four QTLs thereof were mapped to positions of already known SR QTLs. An additional gene at the distal end of chromosome 2R,
, that caused a reduction of 40 percentage points SR infection, was validated. One SR-QTL on chromosome 3R, QTL-SR4, was found in three populations linked with the same marker. Further QTLs at similar positions, but from different populations, were also found on chromosomes 1R, 4R, and 6R. For SR, additionally seedling tests were used to separate between adult-plant and all-stage resistances and a statistical method accounting for the ordinal-scaled seedling test data was used to map seedling resistances. However, only
could be detected based on seedling test data, even though genetic variance was observed in another population, too. For LR, in three of the populations, two new large-effect loci (
and
) on chromosomes 1R and 2R were mapped that caused 34 and 21 percentage points reduction in leaf area covered with urediniospores and one new QTL on chromosome 1R causing 9 percentage points reduction.
Winter rye (
Secale cereale
L.), a potential alternative biogas substrate, is traditionally bred for grain yield. Thus, our objective was to evaluate the possibility to predict dry matter yield ...combining vegetation indices derived from visible to NIR spectral data as a proxy for agronomic traits. A total of 404 elite rye hybrids were tested for grain yield, and a subset of this comprising 274 hybrids were also tested for dry matter yield over 2 years and at 4 locations in Germany bringing the total number of environments to 8. Spectral data were collected around solar noontime on mostly clear sky by an unmanned aerial vehicle (UAV) on two dates and measured in the wavelength range between 410 and 993 nm. Observed variation among tested hybrids ranged between 3.64–10.53 Mg ha
–1
for grain yield and 8.44–14.66 Mg ha
–1
for dry matter yield across different sites. The 23 vegetation indices and the agronomic traits, such as plant height, grain yield, and dry matter yield, showed mostly moderate to high heritability estimates (
h
2
> 0.50), and their genetic variances were significantly (
P
< 0.001) different from zero. Plant height was more informative than grain yield for indirect selection of high dry matter yield. An index combining hyperspectral and agronomic data developed by a multiple regression procedure showed a cross-validated prediction ability of 0.75, representing an improvement of about 6% to a model incorporating only agronomic traits. During earlier selection stages, the developed index could be a suitable tool for the cost-effective selection of superior candidates for biomass trials based on grain yield trials.
Ergot caused by
is a problem for food and feed security in rye due to the occurrence of toxic ergot alkaloids (EAs). For grain elevators and breeders, a quick, easy-to-handle, and cheap screening ...assay would have a high economic impact. The study was performed to reveal (1) the covariation of ergot severity (= percentage of sclerotia in harvested grain) and the content of 12 EAs determined by high performance liquid chromatography (HPLC) and (2) the covariation between these traits and results of one commercial enzyme linked immunosorbent assays (ELISA). In total, 372 winter rye samples consisting of a diverse set of genotypes, locations from Germany, Austria, and Poland over two years, and three isolates were analyzed. Ergocornine and α-ergocryptine were detected as major EAs. Ergocristinine occurred as a minor component.
isolates from different countries showed a similar EA spectrum, but different quantities of individual EAs. A moderate, positive covariation between ergot severity and EA content determined by HPLC was observed across two years (
= 0.53,
< 0.01), but large deviation from the regression was detected. ELISA values did neither correlate with the HPLC results nor with ergot severity. In conclusion, a reliable prediction of the EA content based on ergot severity is, at present, not possible.
Mitochondrial short and long-range movements are necessary to generate the energy needed for synaptic signaling and plasticity. Therefore, an effective mechanism to transport and anchor mitochondria ...to pre- and post-synaptic terminals is as important as functional mitochondria in neuronal firing. Mitochondrial movement range is regulated by phosphorylation of cytoskeletal and motor proteins in addition to changes in mitochondrial membrane potential. Movement direction is regulated by serotonin and dopamine levels. However, data on mitochondrial movement defects and their involvement in defective signaling and neuroplasticity in relationship with mood disorders is scarce. We have previously reported the effects of lithium, valproate and a new antipsychotic, paliperidone on protein expression levels at the synaptic level.
Mitochondrial function defects have recently been implicated in schizophrenia and bipolar disorder. We postulate that mood stabilizer treatment has a profound effect on mitochondrial function, synaptic plasticity, mitochondrial migration and direction of movement.
Synaptoneurosomal preparations from rat pre-frontal cortex were obtained after 28 daily intraperitoneal injections of lithium, valproate and paliperidone. Phosphorylated proteins were identified using 2D-DIGE and nano LC-ESI tandem mass spectrometry.
Lithium, valproate and paliperidone had a substantial and common effect on the phosphorylation state of specific actin, tubulin and myosin isoforms as well as other proteins associated with neurofilaments. Furthermore, different subunits from complex III and V of the electron transfer chain were heavily phosphorylated by treatment with these drugs indicating selective phosphorylation.
Mood stabilizers have an effect on mitochondrial function, mitochondrial movement and the direction of this movement. The implications of these findings will contribute to novel insights regarding clinical treatment and the mode of action of these drugs.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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