Biology subjects

Mayer, K.

Publications and source records attributed to Mayer, K..

9 recordsLinked to original sources

bioRxiv2025

Genomic Analysis of Date Palm Fruit Size Trait and Identification of Candidate Genes through GWAS

The commercial value of economically significant fruits, including date palm fruit (dates), is influenced by various factors, such as biochemical composition and morphological features like size, shape, and visual appearance, which are key determinants of their quality and market value. Dates are typically consumed at the dry stage (Tamar), during which they exhibit a wide range of physical characteristics, such as color, length, weight, and skin appearance. Understanding the genetic basis of these traits is crucial for improving crop quality and breeding new cultivars. In this study, we integrated a genome dataset from highly diverse date cultivars with phenotypes of dry fruit such as length, width, area, and weight, identifying multiple significant genetic loci (SNPs) associated with these traits. We also identified candidate genes located near the associated SNPs that are involved in biological processes such as cell differentiation, proliferation, growth, and the regulation of signalling pathways for growth regulators like auxin and abscisic acid, as observed in other plants. Gene expression analysis reveals that many of these genes are highly expressed in the early stage of fruit development when the fruit attains its maximum size and weight. These findings will enhance our understanding of genetic determinants of fruit size particularly at the commercially important Tamar stage.

genomics↗

bioRxiv2024

The genetics of fruit skin separation in date palm

The physical appearance of date palm (Phoenix dactylifera) fruit (dates) is important for its market value. Many date-producing countries experience significant financial losses due to the poor appearance of the fruit, skin separation or puffiness being a major reason. Previous research showed evidence linking the skin separation phenotype to environmental conditions. In this study, we show that there is both an environmental and genetic contribution to the fruit skin separation phenotype. We show that beyond environmental factors, genetics is a strong contributor to the most extreme skin separation in some cultivars. A genome-wide association study was conducted using genome data of 199 samples collected from 14 countries that identified nine genetic loci associated with this phenotype and investigated genes in these regions that may contribute to the phenotype overall. Identifying the genetic factors may help better understand the biology and pathways that lead to the environmental effects on skin separation and improve commercial date production. In conclusion, our key finding is that both environmental and genetic factors contribute to skin separation variation, and improvements in environmental factors alone cannot overcome the extreme level of variation observed in some cultivars.

bioinformatics↗

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

Barley shows reduced Fusarium Head Blight under drought and modular expression of differential expressed genes under combined stress

Plants often face simultaneous abiotic and biotic stress conditions. However, physiological and transcriptional responses of plants under combined stress situations are little understood. Spring barley is susceptible to Fusarium Head Blight (FHB), which is strongly affected by weather conditions. We therefore studied the potential influence of drought on FHB severity and responses in three differently susceptible spring barley varieties and found strongly reduced FHB severity in susceptible varieties under drought. Quantity of differentially expressed genes (DEGs) and strength of transcriptomic regulation reflected the concentration of physiological stress markers such as abscisic acid or fungal DNA contents. Infection-related gene expression associated rather with susceptibility than resistance. Weighted gene correlation network analysis uncovered 18 modules of co-expressed genes, which reflect the pathogen or drought response in the used varieties. A generally infection-related module contained co-expressed genes for defence, programmed cell death and mycotoxin-detoxification indicating that diverse genotypes use a similar defence strategy towards FHB albeit with different success. Further DEGs showed co-expression in drought or genotype-associated modules correlating with measured phytohormones or the osmolyte proline. The combination of drought stress with infection lead to highest numbers of DEGs and provoked a modular composition of single stress responses rather than a specific transcriptional readout. HighlightCo-expression network analysis reveals association of physiological stress markers and gene expression modules under biotic and abiotic stress

plant biology↗

bioRxiv2022

Evaluating microbial contaminations of alternative heating oils

Since 2008, legislative initiatives for climate protection and reduced dependency on fossil resource imports led to the introduction of biofuels as CO2-reduced alternatives in the heating oil sector. In the case of biodiesel, the oil industry or its customers were confronted with accelerated and escalating microbial contaminations during heating oil storage. Since then, other fuel alternatives, like hydrogenated vegetable oils, gas-to-liquid products (GtL), or Oxymethylenether (OME) have been or will be developed and potentially introduced to the market. In this study, we use online monitoring of microbial CO2 production and the simulation of onset of microbial contamination to investigate the contamination potential of fuel alternatives during storage. As reference and blends, fossil heating oils of various refineries, in the course of this from various crude oils, and refinery processes reveal considerable variation in potential microbial activity. Oxymethylene ethers have an antimicrobial effect, while various forms of biodiesel confirm the promotion of microbial activity and diversity. The paraffinic Fischer-Tropsch products and biogenic hydrogenation products demonstrate high resistance to microbial contamination despite allowing microbial diversity. Through an array of analytics, including advanced chromatography coupled mass spectrometry, elemental analysis, and microbial sequencing, we can discuss critical fuel properties that promote or inhibit microbial contaminations. In summary, novel, non-fossil heating oils show different strengths and weaknesses for long-term storage. Designing blends for microbial activity reduced long-term storage might be an option. While being niche products, these fuels will contribute to the rapid reduction of fossil resource use.

microbiology↗

bioRxiv2022

3D (x-y-t) Raman imaging of tomato fruit cuticle: microchemistry during development

The cuticle of tomato fruits was studied in-situ using Confocal Raman Microscopy. Microsections from cuticles isolated at different developmental stages were scanned to reveal the distribution of cuticle components with a spatial resolution of 342 nm by univariate and multivariate data analysis. From the three main components, cutin, polysaccharides and aromatics, the latter one exhibit the strongest Raman scattering intensity. Therefore, Raman imaging opened the view on phenolic acids and flavonoids within the cuticle and resulted in three schematic cuticle models depicting development. At the earliest stage of development, which corresponded to the procuticle layer, phenolic acids were found across the entire cuticle. Based on a mixture analysis with reference component spectra, the phenolic acids were identified as mainly esterified p-coumaric acid together with free p-hydroxybenzoic acid. Later in development, during the cell expansion period of growth, phenolic acids accumulated in an outermost layer of the cuticle and in the middle region of the pegs. In these stages of development cellulose and pectin were appeared towards the epidermal layer, where later during ripening the flavonoid impregnation started. In the first ripening stage chalconaringenin was observed, while methoxylated chalcones were chosen by the algorithm to fit the mature cuticle spectra. The co-location with carbohydrates and esterified p-coumaric acid and methoxylated chalconaringenin suggest that they link polysaccharide and cutin domains. Within the cutin matrix, aromatics confer mechanical and thermal functions, while the outermost phenolic acid layer displays UV-B protection of the plant tissue. One-sentence summaryNew insights into the distribution of cutin, carbohydrates and phenolics along cross sections of green and mature tomato fruit cuticles by Raman mapping and multivariate data analysis.

biophysics↗

bioRxiv2020

Looking for the needle in a downsized haystack: Whole-exome sequencing unravels how selection and gene flow have shaped climatic adaptation in Douglas-fir (Pseudotsuga menziesii)

The widespread Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) occurs along a steep gradient of diverse climates throughout its natural range, which is expected to result in spatially varying selection to local climate conditions. However, phenotypic signals of climatic adaptation can often be confounded, because unraveled clines covary with signals caused by neutral evolutionary processes such as gene flow and genetic drift. Here, we present phenotypic and genotypic data from a common garden experiment showing a putative signal of adaptation to climate after trees have been growing for 40 years in a common environment. Sixteen Douglas-fir provenances originating from a North-to-South gradient of approx. 1,000 km were analyzed and genomic information was obtained from exome capture, which resulted in an initial genomic dataset of >90,000 single nucleotide polymorphisms. We used a restrictive and conservative filtering approach which permitted us to include only SNPs and individuals in environmental association analysis (EAA) that were free of potentially confounding effects (LD, relatedness among trees, heterozygosity deficiency and deviations from Hardy-Weinberg proportions). We used four conceptually different genome scan methods based on FST outlier detection and gene-environment association in order to disentangle truly adaptive SNPs from neutral SNPs and found that a relatively small proportion of the exome showed a truely adaptive signal (0.01-0.17%) when population substructuring and multiple testing was accounted for. Nevertheless, the unraveled SNP candidates showed significant relationship with climate at provenance origins which strongly suggests that they have most likely featured adaption in Douglas-fir across a steep climatic gradient. Two SNPs were independently found by three of the employed algorithms and one could be assigned with high probability to a Picea abies homolog gene involved in circadian clock control as was also found in Populus balsamifera.

evolutionary biology↗

bioRxiv2019

TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We have developed TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluated the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and constructed an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.

genomics↗

bioRxiv2017

Epigenomic variation across a polyploid wheat diversity collection

Wheat has been domesticated into a large number of agricultural environments and has a remarkable ability to adapt to diverse environments. To understand this process, we survey genotype, repeat content and DNA methylation across a bread wheat landrace collection representing global genetic diversity. We identify independent variation in methylation, genotype and transposon copy number. We show that these, so far unexploited, sources of variation have had a massive impact on the wheat genome and that ancestral methylation states become preferentially hard coded as SNPs via 5-methylcytosine deamination. These mechanisms also drive local adaption, impacting important traits such as heading date and salt tolerance. Methylation and transposon diversity could therefore be used alongside single nucleotide polymorphism (SNP) based markers for breeding.

genomics↗