Biology subjects

Bayer, M.

Publications and source records attributed to Bayer, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Before auxin distribution matters: Prepatterning of the Arabidopsis embryo axis by MPK6-dependent AUX/IAA8 phosphorylation

In growth and development of plants, the signaling molecule auxin plays an instrumental role. Many patterning processes are controlled by auxin signaling in a self-organizing matter. After fertilization, such a patterning process needs to be started for the first time during plant life. Contrary to previous models, we show that the first differential auxin response that separates embryonic from extra-embryonic development in the two zygotic daughter cells happens independently of a detectable auxin gradient. Instead, differential phosphorylation of the transcriptional inhibitor Aux/IAA8 by MAP kinase signaling leads to differences in auxin sensitivity between the two daughter cells, initiating embryonic development in the apical cell. IAA8 phosphorylation in the basal cell prevents proteasomal degradation, suppressing canonical auxin responses, which initiates extra-embryonic development. MAP kinase signaling therefore precedes auxin gradients and prepatterns the apical-basal axis independently of an auxin gradient.

plant biology↗

bioRxiv2026

Whole genome sequencing and variant discovery in 344 global grasspea (Lathyrus sativus L.) lines

The rapid expansion of genomic data resources for major crops is opening new options for crop improvement, while resources for most underutilised crops lag behind, risking a widening gap in crop improvement. One of these underutilised crops is grasspea (Lathyrus sativus), an ancient crop with modern cultivation centred on South Asia and Ethiopia. We conducted whole genome shotgun sequencing on a global collection of 344 grasspea lines, producing over 152 billion reads. Following variant discovery and filtering we created a single nucleotide polymorphism (SNP) marker set of over 1.5 million SNPs. This is a resource of major significance for this crop which can help unlock its breeding potential through marker development and the identification of genes controlling agronomically important traits.

genomics↗

bioRxiv2026

EoRNA2: Autonomous Data Discovery and Processing for Databasing of Gene Expression Data

We describe a major new release of the EoRNA database, a gene expression database for barley based on public data, first published in 20211. EoRNA v.2 (https://ics.hutton.ac.uk/eorna2/index.html) features an order of magnitude more samples and is based on a new automated workflow of sample discovery and processing which has enabled a dramatic scale-up the original database. EoRNA v.2 also features a major rebuild of the web user interface with rich new functionality. All infrastructure-related code and database schemas and web components are now species agnostic and publicly available for reuse with other taxa. A dedicated new reference transcript dataset has been created for EoRNA v.2 which is largely based on the recently published barley pan-transcriptome and represents the most comprehensive dataset of its kind to date.

bioinformatics↗

bioRxiv2025

Environmental DNA Reveals Reykjavik's Human and Ecological History

Iceland was among the last large islands settled by humans, with colonization (Landnam) in the late 9th century CE (Common Era) and is often portrayed as an ecological disaster driven by the Norse settlers. Here, we revisit this narrative through environmental DNA (eDNA) and multiproxy analyses of sediment cores from Lake Tjornin in central Reykjavik, one of Icelands earliest and longest-occupied settlements. Originally a marine embayment, Tjornin became a freshwater lake around 660 CE. Our record reveals a human presence decades before the long-accepted arrival date of 877 CE, marked by the Landnam volcanic tephra. Early settlement brought livestock, barley cultivation, and other introduced taxa that enhanced nutrient cycling and unexpectedly increased local biodiversity. Contrary to the conventional view of rapid deforestation, eDNA shows that birch and willow expanded during the settlement period, likely supported by deliberate management. Pronounced ecological and land use shifts occurred after 1200 CE, but these were coeval with the Little Ice Age cooling, compounded by volcanic eruptions, storm surges, and plague, rather than anthropogenic degradation. Crop cultivation ceased, arboreal taxa retracted, and grazing pressure maintained open landscapes. Even more profound ecological changes came after c. 1750 CE with urbanization and industrialization, as wastewater discharge, heavy-metal pollution, and fossil fuel use reshaped Tjornins ecosystem. These findings challenge the prevailing model of Norse-induced environmental collapse, revealing instead a dynamic human-environment relationship shaped by both cultural practices and external stressors. By applying eDNA to a long-occupied urban catchment, we demonstrate the power of genomic methods to refine settlement chronologies, reassess ecological baselines and changes, and integrate natural and cultural histories. This approach offers a model for revisiting human-environment interactions in urban centers worldwide.

genomics↗

bioRxiv2025

Phased Potato Genome Assembly and Association Genetics Enable Characterisation of the Elusive H1 Resistance Locus Against Potato Cyst Nematodes

The complexity of potato genetics, characterised by tetrasomic inheritance, has contributed to slower genetic gain in potato compared to other major crops. Disease resistance genes, often found in large clusters of highly similar paralogs and alleles, further complicate genetic studies. The H1 resistance locus, introgressed into potato cultivars from Solanum tuberosum spp. andigena, has been successfully used for over 60 years to control Globodera rostochiensis in Europe. Although previous genetic studies mapped this resistance to chromosome 5, the complete structure of the locus remained elusive. To reduce genomic complexity, we generated a dihaploid of the cultivar Athlete, DH4_Athlete, carrying the H1 resistance locus, and produced a phased haplotype representation of the H1 interval using Oxford Nanopore sequencing. Combined with RenSeq-based association genetics, this approach allowed us to reconstruct the entire H1 locus, including recombination points at both the 5' and 3' ends of the interval.

plant biology↗

bioRxiv2025

Post-Domestication selection of MKK3 Shaped Seed Dormancy and End-Use Traits in Barley

Anthropogenic selection of grain traits such as dormancy has shaped the developmental trajectories of crop plants (1). In cereals, shortening dormancy provides rapid and even post-harvest germination, but increases the risk of weather-induced pre-harvest sprouting (PHS) with harvest losses estimated at beyond 1 billion USD a year (2, 3, 4). Our understanding of how, why, when and where diversification of cereal dormancy arose is fragmentary. Here, we show in the founder cereal crop barley (Hordeum vulgare) that the Mitogen-Activated Protein Kinase (MAPK) pathway regulates dormancy primarily through a mosaic of locus haplotypes comprising copy-number variation and inherent kinase activity of Mitogen-activated protein kinase kinase 3 (MKK3). We provide evidence supporting the historical selection of specific MKK3 haplotypes that shape dormancy levels according to changing climatic pressures. Understanding the regulatory landscape of MKK3 provides a genetic framework to balance short grain dormancy and PHS-avoidance during a period of rapid climate change.

plant biology↗

bioRxiv2024

Phosphorylation-Dependent Activation of the bHLH Transcription Factor ICE1/SCRM Promotes Polarization of the Arabidopsis Zygote

Asymmetric cell divisions are a key mechanism for breaking symmetry and orchestrating different cell identities in multicellular organisms. In Arabidopsis thaliana, as in most flowering plants, the first zygotic cell division is asymmetric, giving rise to the embryo proper and an extraembryonic suspensor. Zygotic polarization and differential cell identities in the daughter cells are controlled by the ERECTA-YODA pathway, a prototype receptor kinase-MAP kinase signaling pathway. This pathway also controls asymmetric cell divisions in the epidermis during stomatal development. In this context, the bHLH transcription factor ICE1/SCRM is a direct target of MPK3/6, and phosphorylation negatively controls SCRM activity by targeting the protein for proteasomal degradation. This raises the question if this regulatory module is also involved in the asymmetric division of the zygote. Our results show that SCRM has a critical function in zygote polarization and acts in parallel with the known MPK3/6 target WRKY2 in activating the homeobox transcription factor gene WOX8. Our work further demonstrates that SCRM activity in the early embryo is positively controlled by MPK3/6-mediated phosphorylation. Therefore, the mode of MAP kinase regulation of the same target protein fundamentally differs between the embryo and the epidermis, shedding light on cell type-specific, differential gene regulation by common signaling pathways.

plant biology↗

bioRxiv2024

An AINTEGUMENTA phospho-switch controls bilateral stem cell activity during secondary growth

Plant stem cells have the remarkable ability to give rise to distinct tissues and organs throughout development. Two concentric cylinders of actively dividing stem cells are the main drivers of radial thickening during secondary growth, each producing distinct vascular cell types towards the inside and the outside. While the molecular mechanisms underlying their initiation have been well studied, it remains unclear how these stem cell layers determine which cell type is generated. Here, we demonstrate that the cross-talk between the ERECTA (ER) receptor pathway and auxin signalling controls the amount and choice of output tissue in these two stem cell regions. Mechanistically, we show that the ER pathway phosphorylates the transcription factor AINTEGUMENTA, thereby modulating bilateral stem cell activity and favouring the differentiation of only one type of cell. Our results thus show that the phosphorylation status of ANT regulates root girth and biomass accumulation by influencing bilateral stem cell production. This highlights the critical role of post-translational modifications in plant growth and development. SignificanceThis study uncovers a critical regulatory mechanism governing bilateral stem cell activity during plant radial growth. Stem cells in the cambia proliferate and differentiate into specialized tissues like wood and cork, key sites of biomass accumulation. By exploring the interplay between the ERECTA (ER) receptor and auxin signalling, we reveal how these pathways modulate stem cell differentiation and radial thickening through the phosphorylation of the transcription factor AINTEGUMENTA (ANT). Phosphorylation status of ANT modulates stem cell activity, dictating the production of specific vascular cell types like wood thus controlling root girth. This research underscores the importance of post-translational modifications in plant development and provides a novel regulation underpinning stem cell differentiation, with significant implications for enhancing biomass accumulation as wood.

plant biology↗

bioRxiv2024

Adaptive diversification through structural variation in barley

Pangenomes are collections of annotated genome sequences of multiple individuals of a species. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants. Here, we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that have become hot spots of gene copy number variation in evolutionarily recent times. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release, and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that rapid evolution at structurally complex loci may have helped crop plants adapt to new selective regimes in agricultural ecosystems.

plant biology↗

bioRxiv2023

The human cytomegalovirus-encoded pUS28 antagonizes CD4+ T-cell recognition by targeting CIITA

Human cytomegalovirus (HCMV) is a relevant pathogen especially for individuals with impaired immunity. Harnessing potent immune antagonists, HCMV circumvents sterile immunity. Given that HCMV prevents the upregulation of human leukocyte antigen (HLA)-DP and HLA-DR, we screened a library of HCMV genes by co-expression with the HLA class II (HLA-II)-inducing transcription coordinator class II transactivator (CIITA). We identified the latency regulator pUS28 as interaction factor and potent viral antagonist of CIITA-driven expression of CD74, HLA-DR, HLA-DM, HLA-DQ, and HLA-DP. Both wt-pUS28 and a mutant incapable to induce G-protein-coupled signaling (R129A), but not a mutant lacking the C-terminus, drastically reduced the CIITA protein abundance post-transcriptionally. While control CD4+ T cells from HCMV-seropositive individuals vigorously responded to CIITA-expressing cells decorated with HCMV antigens, pUS28 expression was sufficient to inhibit HLA-II induction and immune recognition by HCMV-specific CD4+ T cells. Our data uncover a mechanism employed by HCMV to evade HLA-II-mediated recognition by CD4+ T cells.

immunology↗

bioRxiv2023

Temperature-dependent regulation of Arabidopsis thaliana growth and development by LSM7

Temperature affects plant growth by modulating the expression of genes and subsequent processing of RNAs that govern essential physiological processes. Here, we show that Arabidopsis thaliana Sm-like7 (LSM7), a core component of the splicing and decapping machinery, is indispensable for embryogenesis and development. Hypomorphic lsm7-2 mutants display severe developmental defects that are exacerbated by high temperatures. Transcriptome analysis verified LSM7s extensive role in gene regulation. In particular, we found that the key regulator of thermomorphogenesis, PHYTOCHROME INTERACTING FACTOR 4 (PIF4), and auxin-related genes, including SMALL AUXIN UP-REGULATED (SAUR) genes, are misregulated in lsm7-2. Auxin metabolic profiling confirmed that auxin homeostasis was disturbed in lsm7-2. Importantly, overexpression of the auxin-responsive SAUR19 gene partially restored thermomorphogenesis defects in lsm7-2 under high ambient temperature. Taken together, our research provides mechanistic insights into the interplay between RNA processing, hormone homeostasis, and the response to temperature regulation in plants and elucidates LSM7s essential function in plant temperature acclimation and resilience. Significance StatementGiven their sessile nature, plants cannot escape adverse environmental conditions such as cold or heat. Instead, they continuously adjust their gene expression and RNA processing to regulate growth and physiology in response to their surroundings. In this study, we investigated the role of the core RNA processing factor LSM7 in temperature acclimation in Arabidopsis thaliana. We found that LSM7 knockdown mutants were impaired in thermomorphogenesis and, as a result, were hypersensitive to elevated temperatures. At the molecular level, we demonstrated that this temperature sensitivity was caused by the misregulation of key regulators of thermomorphogenesis, including PIF4, auxin homeostasis and signaling, and SAUR genes. Our findings provide valuable insights into the role of RNA processing in plant temperature acclimation.

plant biology↗

bioRxiv2022

SMRT-AgRenSeq-d in potato (Solanum tuberosum) identifies candidates for the nematode resistance Gpa5

Potato is the third most important food crop in the world. Diverse pathogens threaten sustainable crop production but can be controlled, in many cases, through the deployment of disease resistance genes belonging to the family of nucleotide-binding, leucine-rich-repeat (NLR) genes. To identify functional NLRs in established varieties, we have successfully established SMRT-AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMRT-AgRenSeq-d. The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible potatoes that is translated into an F1 score. Using a SMRT-RenSeq based sequence representation of the NLRome from the cultivar Innovator, SMRT-AgRenSeq-d analyses reliably identified the late blight resistance benchmark genes R1, R2-like, R3a and R3b in a panel of 117 varieties with variable phenotype penetrations. All benchmark genes were identified with an F1 score of 1 which indicates absolute linkage in the panel. When applied to the elusive nematode disease resistance gene Gpa5 that controls the Potato Cyst Nematode (PCN) species Globodera pallida (pathotypes Pa2/3), SMRT-AgRenSeq-d identified nine strong candidates. These map to the previously established position on potato chromosome 5 and are potential homologs of the late blight resistance gene R1. Assuming that NLRs are involved in controlling many types of resistances, SMRT-AgRenSeq-d can readily be applied to diverse crops and pathogen systems. In potato, SMRT-AgRenSeq-d lends itself, for example, to further study the elusive PCN resistances H1 or H3 for which phenotypic data exist.

plant biology↗

bioRxiv2021

BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification

Accurate characterization of splice junctions as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA-seq data and enable detailed investigations of transcriptional and post-transcriptional regulation. Using novel computational methods and a combination of PacBio Iso-seq and Illumina short read sequences from 20 diverse tissues and conditions, we generated a comprehensive and highly resolved barley reference transcript dataset (RTD) from the European 2-row spring barley cultivar Barke (BaRTv2.18). Stringent and thorough filtering was carried out to maintain the quality and accuracy of the splice junctions and transcript start and end sites. BaRTv2.18 shows increased transcript diversity and completeness compared to an earlier version, BaRTv1.0. The accuracy of transcript level quantification, splice junctions and transcript start and end sites has been validated extensively using parallel technologies and analysis, including high resolution RT PCR and 5 RACE. BaRTv2.18 contains 39,434 genes and 148,260 transcripts, representing the most comprehensive and resolved reference transcriptome in barley to date. It provides an important and high-quality resource for advanced transcriptomic analyses, including both transcriptional and post-transcriptional regulation, with exceptional resolution and precision.

plant biology↗

bioRxiv2021

Vibrio cholerae biofilm dispersal regulator causes cell release from matrix through type IV pilus retraction

The extracellular matrix is a defining feature of bacterial biofilms and provides structural stability to the community by binding cells to the surface and to each other. Transitions between bacterial biofilm initiation, growth, and dispersion require different regulatory programs, all of which result in modifications to the extracellular matrix composition, abundance, or functionality. However, the mechanisms by which individual cells in biofilms disengage from the matrix to enable their departure during biofilm dispersal are unclear. Here, we investigated active biofilm dispersal of Vibrio cholerae during nutrient starvation, resulting in the discovery of the conserved Vibrio biofilm dispersal regulator VbdR. We show that VbdR triggers biofilm dispersal by controlling cellular release from the biofilm matrix, which is achieved by inducing the retraction of the mannose-sensitive hemagglutinin (MSHA) type IV pili and the expression of a matrix protease IvaP. We further show that MSHA pili have numerous binding partners in the matrix and that the joint effect of MSHA pilus retraction and IvaP activity is necessary and sufficient for causing biofilm dispersal. These results highlight the crucial role of type IV pilus dynamics during biofilm dispersal and provide a new target for controlling V. cholerae biofilm abundance through the induction and manipulation of biofilm dispersal.

microbiology↗

bioRxiv2020

Independent parental contributions initiate zygote polarization in Arabidopsis thaliana

Embryogenesis of flowering plants is initiated by polarization of the zygote, a prerequisite for correct axis formation in the embryo. Zygote polarity and the decision between embryonic and non-embryonic development in the daughter cells is controlled by a MITOGEN-ACTIVATING PROTEIN (MAP) kinase signaling pathway including the MAPKK kinase YODA (YDA). Upstream of YDA act two members of the BRASINOSTEROID SIGNALING KINASE (BSK) family, BSK1 and BSK2. These membrane-associated proteins serve as signaling relay linking receptor kinase complexes with intracellular signaling cascades. The receptor kinases acting upstream of BSK1 and BSK2 in the zygote, however, have so far not been identified. Instead, YDA can in part be activated by the non-canonical BSK family member SHORT SUSPENSOR (SSP) that is contributed by the sperm cell during fertilization. Here, we show that the receptor kinase ERECTA plays a crucial role in zygote polarization as maternally contributed part of the embryonic YDA pathway. SSP on the other hand provides an independent, paternal input to YDA activation, outlining a Y-shaped pathway. We conclude that two independent parental contributions initiate zygote polarization and control suspensor formation and embryonic development.

plant biology↗

bioRxiv2020

EoRNA, a barley gene and transcript abundance database.

A high-quality, barley gene reference transcript dataset (BaRTv1.0), was used to quantify gene and transcript abundances from 22 RNA-seq experiments, covering 843 separate samples. Using the abundance data we developed a Barley Expression Database (EoRNA* - Expression of RNA) to underpin a visualisation tool that displays comparative gene and transcript abundance data on demand as transcripts per million (TPM) across all samples and all the genes. EoRNA provides gene and transcript models for all of the transcripts contained in BaRTV1.0, and these can be conveniently identified through either BaRT or HORVU gene names, or by direct BLAST of query sequences. Browsing the quantification data reveals cultivar, tissue and condition specific gene expression and shows changes in the proportions of individual transcripts that have arisen via alternative splicing. TPM values can be easily extracted to allow users to determine the statistical significance of observed transcript abundance variation among samples or perform meta analyses on multiple RNA-seq experiments. * Eorna is the Scottish Gaelic word for Barley

genomics↗

bioRxiv2020

AUXIN RESPONSE FACTOR 6 (ARF6) and ARF8 promote Gibberellin-mediated hypocotyl xylem expansion and cambium homeostasis

During secondary growth, the thickening of plant organs, wood (xylem) and bast (phloem) are continuously produced by the vascular cambium. In Arabidopsis hypocotyl and root, we can distinguish two phases of secondary growth based on cell morphology and production rate. The first phase, in which xylem and phloem are equally produced, precedes the xylem expansion phase in which xylem formation is enhanced and xylem fibers differentiate. It is known that Gibberellins (GA) trigger this developmental transition via the degradation of DELLA proteins and that the cambium master regulator BREVIPEDICELLUS/KNAT1 (BP/KNAT1) and the receptor like kinases ERECTA and ERL1 regulate this process downstream of GA. However, our understandings on the regulatory network underlying GA-mediated secondary growth, are still limited. Here, we demonstrate that DELLA-mediated xylem expansion is mainly achieved through RGA and GAI and that RGA and GAI promote cambium senescence. We further show that AUXIN RESPONSE FACTOR (ARF6) and ARF8, which physically interact with DELLAs, specifically repress phloem proliferation and induce cambium senescence during the xylem expansion phase. Moreover, the inactivation of BP in arf6 arf8 background revealed an essential role for ARF6 and ARF8 in cambium establishment and maintenance. Overall, our results shed light on a pivotal hormone cross-talk between GA and auxin in the context of plant secondary growth.

plant biology↗

bioRxiv2020

Constitutive activation of leucine-rich repeat receptor kinase signaling pathways by BAK1-interacting receptor-like kinase 3 chimera

Receptor kinases with extracellular leucine-rich repeat domains (LRR-RKs) form the largest group of membrane signaling proteins in plants. LRR-RKs can sense small molecule, peptide or protein ligands, and may be activated by ligand-induced interaction with a shape complementary SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK) co-receptor kinase. We have previously shown that SERKs can also form constitutive, ligand-independent complexes with the LRR ectodomains of BAK1-interacting receptor-like kinase 3 (BIR3) receptor pseudokinases, negative regulators of LRR-RK signaling. Here we report that receptor chimaera in which the extracellular LRR domain of BIR3 is fused to the cytoplasmic kinase domains of the SERK-dependent LRR-RKs BRASSINOSTEROID INSENSITIVE1, HAESA and ERECTA form tight complexes with endogenous SERK co-receptors in the absence of ligand stimulus. Expression of these chimaera under the control of the endogenous promoter of the respective LRR-RK leads to strong gain-of-function brassinosteroid, floral abscission and stomatal patterning phenotypes, respectively. Importantly, a BIR3-GSO1/SGN3 chimera can partially complement sgn3 Casparian strip formation phenotypes, suggesting that GSO1/SGN3 receptor activation is also mediated by SERK proteins. Collectively, our protein engineering approach may be used to elucidate the physiological functions of orphan LRR-RKs and to identify their receptor activation mechanism in single transgenic lines.

plant biology↗