Biology subjects

Haupt, M.

Publications and source records attributed to Haupt, M..

9 recordsLinked to original sources

bioRxiv2024

k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance

BackgroundWheat landraces and cultivars stored in gene banks worldwide represent a valuable source of genetic diversity for discovering genes critical for agriculture, which is increasingly constrained by climate change and inputs reduction. We assembled and genotyped, using DArTseq technology, a panel of 461 accessions representative of the genetic diversity of Swiss wheat material. The collection was evaluated for powdery mildew resistance under field conditions for two consecutive years and at the seedling stage with 10 different wheat powdery mildew isolates. ResultsTo identify the genetic basis of mildew resistance in wheat, we developed a k-mer-based GWAS approach using multiple fully-assembled genomes including Triticum aestivum as well as four progenitor genomes. Compared to approaches based on single reference genomes, we unambiguously mapped an additional 25% resistance-associated k-mers. Our approach outperformed SNP-based GWAS in terms of number of loci identified and precision of mapping. In total, we detected 34 (Pm) powdery mildew resistance loci, including seven previously-described and more importantly 27 novel loci active at the seedling stage. Furthermore, we identified a region associated with adult plant resistance, which was not detected with SNP-based approaches. ConclusionsThe described non-reference-based approach highlights the potential of integrating multiple wheat reference genomes with k-mer GWAS to harness the untapped genetic diversity present in germplasm collections.

genomics↗

bioRxiv2024

Healthy aging delays and dedifferentiates high-level visual representations

1.Healthy aging impacts visual information processing with consequences for subsequent high-level cognition and everyday behavior, but the underlying neural changes in visual representations remain unknown. Here, we investigate the nature of representations underlying object recognition in older compared to younger adults by tracking them in time using EEG, across space using fMRI, and by probing their behavioral relevance using similarity judgements. Applying a multivariate analysis framework to combine experimental assessments, four key findings about how brain aging impacts object recognition emerge. First, aging selectively delays the formation of object representations, profoundly changing the chronometry of visual processing. Second, the delay in the formation of object representations emerges in high-level rather than low- and mid-level ventral visual cortex, supporting the theory that brain areas developing last deteriorate first. Third, aging reduces content selectivity in high-level ventral visual cortex, indicating age-related neural dedifferentiation as the mechanism of representational change. Finally, we demonstrate that the identified representations of the aging brain are behaviorally relevant, ascertaining ecological relevance. Together, our results reveal the impact of healthy aging on the visual brain.

neuroscience↗

bioRxiv2024

The transformation of sensory to perceptual braille letter representations in the visually deprived brain

1.Experience-based plasticity of the human cortex mediates the influence of individual experience on cognition and behavior. The complete loss of a sensory modality is among the most extreme such experiences. Investigating such a selective, yet extreme change in experience allows for the characterization of experience-based plasticity at its boundaries. Here, we investigated information processing in individuals who lost vision at birth or early in life by probing the processing of braille letter information. We characterized the transformation of braille letter information from sensory representations depending on the reading hand to perceptual representations that are independent of the reading hand. Using a multivariate analysis framework in combination with fMRI, EEG and behavioral assessment, we tracked cortical braille representations in space and time, and probed their behavioral relevance. We located sensory representations in tactile processing areas and perceptual representations in sighted reading areas, with the lateral occipital complex as a connecting "hinge" region. This elucidates the plasticity of the visually deprived brain in terms of information processing. Regarding information processing in time, we found that sensory representations emerge before perceptual representations. This indicates that even extreme cases of brain plasticity adhere to a common temporal scheme in the progression from sensory to perceptual transformations. Ascertaining behavioral relevance through perceived similarity ratings, we found that perceptual representations in sighted reading areas, but not sensory representations in tactile processing areas are suitably formatted to guide behavior. Together, our results reveal a nuanced picture of both the potentials and limits of experience-dependent plasticity in the visually deprived brain.

neuroscience↗

bioRxiv2023

Highly pathogenic avian influenza causes mass mortality in Sandwich tern (Thalasseus sandvicensis) breeding colonies across northwestern Europe

AO_SCPLOWBSTRACTC_SCPLOWIn 2022, highly pathogenic avian influenza (HPAI) A(H5N1) virus clade 2.3.4.4b became enzootic and caused mass mortality in Sandwich terns and other seabird species across northwestern Europe. We present data on characteristics of the spread of the virus between breeding colonies and the number of dead adult Sandwich terns recorded at breeding sites throughout northwestern Europe. Within two months after the first mortalities were reported, in total 20,531 adult Sandwich terns were found dead, which is >17% of the total northwestern European breeding population. Losses are likely higher, as we expect that many victims were not found (mortality rate might be up to 74% of the breeding population). Inside the colonies almost all chicks died. After the peak of the outbreak, in a colony established by late breeders, 25.7% of adults showed immunity against HPAI subtype H5. Removal of carcasses helped in reducing the spread of the disease and consequently total mortality. More research on the sources and modes of transmission, incubation times, effective containment and immunity is urgently needed to combat this major threat for colonial seabirds.

ecology↗

bioRxiv2022

Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions

Understanding how crops adapt to specific environmental conditions is becoming increasingly important in the face of accelerating climate change, but the genetics of local adaptation remain little understood for many crops. Landscape genomics can reveal patterns of genetic variation that indicate adaptive diversification during crop evolution and dispersal. Here, we examine genetic differentiation and association signatures with environmental gradients in soybean (Glycine max) germplasm groups from China that were inferred from the USDA Soybean Germplasm Collection (N = 17,019 accessions) based on population structure and passport information. We recover genes previously known to be involved in soybean environmental adaptation and report numerous new candidate genes in selection signatures implicated by genomic resources such as the genome annotation and gene expression datasets to function in flowering regulation, photoperiodism and stress reaction cascades. Linkage disequilibrium network analysis suggested functional relationships between genomic regions with selection signatures, consistent with the polygenic nature of environmental adaptation. We tested whether haplotypes associated with environmental adaptation in China were present in 843 North American and 160 European soybean cultivars and found that haplotypes in major genes for early maturity have been selected during breeding, but also that a large number of haplotypes exhibiting putative adaptive variation for cold regions at high latitudes are underrepresented in modern cultivars. Our results demonstrate the value of landscape genomics analysis in genebank germplasm as a starting point for the study of crop environmental adaptation and have the potential to inform future research efforts focused on improved soybean adaptation. Functional validation of candidate genes will support understanding of their adaptive roles and likely enable the transfer of beneficial adaptive variation into modern breeding germplasm.

plant biology↗

bioRxiv2019

Combining Focused Identification of Germplasm and Core Collection Strategies to Identify Genebank Accessions for Central European Soybean Breeding

Environmental adaptation of crops is essential for reliable agricultural production and an important breeding objectives. Genbanks provide genetic variation for the improvement of modern varieties, but the selection of suitable germplasm is frequently impeded by incomplete phenotypic data. We address this bottleneck by combining a Focused Identification of Germplasm Strategy (FIGS) with core collection methodology to select soybean (Glycine max) germplasm for Central European breeding from a collection of >17,000 accessions. By focussing on environmental adaptation to high-latitude cold regions, we selected an environmental precore of 3,663 accessions using environmental data and compared the Donor Population of Environments (DPE) in Asia and the Target Population of Environments (TPE) in Central Europe in the present and in 2070. Using SNP genotypes we reduced the precore into two diverse core collections of 183 and 366 of accessions as diversity panels for evaluation in high-latitude cold regions. Tests of genetic differentiation between precore and core collections revealed differentiation signatures in genomic regions that control maturity, and novel candidate loci for environmental adaptation demonstrating the potential of diversity panels for studying environmental adaptation. Objective-driven core collections increase germplasm utilization for abiotic adaptation by breeding for a rapidly changing climate, or de novo adaptation of crop species to expand cultivation ranges.

plant biology↗

bioRxiv2019

Right-lateralized fronto-parietal network and phasic alertness in healthy aging

Phasic alerting cues temporarily increase the brains arousal state. In younger and older participants, visual processing speed in a whole report task, estimated based on the theory of visual attention (TVA), is increased in cue compared to no-cue conditions. The present study assessed whether older participants ability to profit from warning cues is related to iFC in the cingulo-opercular and/or right fronto-parietal network. We obtained resting-state functional magnetic resonance imaging (rs-fMRI) data from 31 older participants. By combining an independent component analysis and dual regression, we investigated iFC in both networks. A voxel-wise multiple regression in older participants revealed that higher phasic alerting effects on visual processing speed were significantly associated with lower right fronto-parietal network iFC. We then compared healthy older participants to a previously reported sample of healthy younger participants to assess whether behaviour-iFC relationships are age group specific. The comparison revealed that the association between phasic alerting and cingulo-opercular network iFC is significantly lower in older than in younger adults. Additionally, it yielded a stronger association between phasic alerting and right fronto-parietal network iFC in older versus younger participants. The results support a particular role of the right fronto-parietal network in maintaining phasic alerting capabilities in aging.

neuroscience↗

bioRxiv2019

Structural requirements of the phytoplasma effector protein SAP54 for causing homeotic transformation of floral organs

Phytoplasmas are intracellular bacterial plant pathogens that cause devastating diseases in crops and ornamental plants by the secretion of effector proteins. One of these effector proteins, termed SECRETED ASTER YELLOWS-WITCHES BROOM PROTEIN 54 (SAP54), leads to the degradation of a specific subset of floral homeotic proteins of the MIKC-type MADS-domain family via the ubiquitin-proteasome pathway. In consequence, the developing flowers show the homeotic transformation of floral organs into vegetative leaf-like structures. The molecular mechanism of SAP54 action involves physical binding to the keratin-like K-domain of MIKC-type proteins, and to some RAD23 proteins, which translocate ubiquitylated substrates to the proteasome. The structural requirements and specificity of SAP54 function are poorly understood, however. Here we report, based on biophysical and molecular biological analyses, that SAP54 folds into -helical structures. We also show that the insertion of helix-breaking mutations disrupts correct folding of SAP54, which interferes with the ability of SAP54 to bind to its target proteins and to cause disease phenotypes in vivo. Surprisingly, dynamic light scattering data together with electrophoretic mobility shift assays suggest that SAP54 preferentially binds to multimeric complexes of MIKC-type proteins rather than to dimers or monomers of these proteins. Together with literature data this finding suggests that MIKC-type proteins and SAP54 constitute multimeric -helical coiled-coils, possibly also involving other partners such as RAD23 proteins. Our investigations clarify the structure-function relationship of an important phytoplasma effector protein and thus may ultimately help to develop treatments against some devastating plant diseases.\n\nSIGNIFICANCE STATEMENTPhytoplasmas are bacterial plant pathogens that cause devastating diseases in crops and ornamental plants by the secretion of effector proteins such as SAP54, which leads to the degradation of some floral homeotic proteins. Our study clarifies the structural requirements of SAP54 function and illuminates the molecular mode of interaction and thus may ultimately help to develop treatments against some devastating plant diseases.

plant biology↗

bioRxiv2019

Predictability of salient distractor increases top-down control in healthy younger and older adults

Younger adults are able to shield attentional selection against distractors when they have preknowledge about the upcoming distractor location. For older adults, who suffer from an overall decrease in attentional capacity and who are, in addition, particularly prone to attentional capture, such an adaptive shielding ability would be of particular importance. However, it is an open question whether healthy older adults can utilise the predictability of distractor locations to improve top-down controlled selection to the same degree as younger adults. The theory of visual attention (TVA) framework provides a systematic way to measure an individuals efficiency of top-down control. The present study combined a TVA-based partial-report paradigm with abrupt-onset cues rendering the indicated location highly salient in a bottom-up fashion. Experiment 1, in which (on cued trials) the cue was invariably followed by a distractor at the cued location, showed that the cueing increased the weight of the distractor in the competition for selection compared to uncued distractors (on trials without a cue). In Experiment 2, the probability with which the abrupt-onset cue indicated the upcoming distractor location (1/3 vs. 2/3 of trials) was manipulated between experimental blocks. Participants were able to learn these statistical contingencies and exert top-down control more efficiently in blocks with highly valid distractor location cues, as compared to low-validity blocks. This finding suggests that, even though abrupt-onset spatial cues increase the attentional weights of distractors, participants can acquire and use pre-knowledge about the likelihood that a distractor will appear at an indicated location to down-weight the bottom-up attentional-capture signal. This ability turned out to be comparable across age groups, suggesting that efficient use of predictive information to shield against distracting information is preserved in normal ageing.

neuroscience↗