Biology subjects

Obermeier, C.

Publications and source records attributed to Obermeier, C..

5 recordsLinked to original sources

bioRxiv2024

VC2 regulates baseline vicine content in faba bean

Faba bean (Vicia faba) is a valuable legume crop desired globally for its high nutritional composition. However, the seed vicine and convicine (v-c) content reduces the nutritional quality of faba bean protein and can induce favism in individuals with glucose-6-phosphate dehydrogenase deficiency. Recently, VC1 gene, encoding a bi-functional riboflavin protein, was reported to be responsible for initiating the biosynthetic pathway in V. faba. In low v-c cultivars, a 2 bp insertion in this gene results in a loss of function, but the mutation only partially eliminates v-c biosynthesis, indicating the involvement of other genes. Here, we demonstrate that a novel V. faba riboflavin gene, VC2, is responsible for the residual v-c contents in faba bean. VC2 shares nearly identical functional domains with VC1 and has GTP cyclohydrolase II activity, catalyzing the conversion of GTP into an intermediate molecule in the biosynthetic pathway. Gene expression analysis reveals that VC2 contributes a minor effect to the trait, accounting for approximately 5-10% of total riboflavin gene transcripts which significantly correlates with the baseline contents in low v-c cultivars. Our results illustrate that cultivars carrying the 2 bp inactivating insertion in VC1 still have residual v-c levels due to VC2 activity. Furthermore, we find that VC1 has multiple alleles and exhibits copy number variations, complicating molecular marker development. Conversely, single nucleotide polymorphisms within VC2 provide a reliable alternative for marker-assisted selection in faba bean breeding. In conclusion, our study elucidates the complex genetic regulation of v-c biosynthesis and provides valuable insights to facilitate its elimination in faba bean.

genetics↗

bioRxiv2022

Benchmarking Oxford Nanopore Read Alignment-Based Structural Variant Detection Tools in Crop Plant Genomes

Structural variations (SVs) are larger polymorphisms (>50 bp in length), which consist of insertions, deletions, inversions, duplications, and translocations. They can have a strong impact on agronomical traits and play an important role in environmental adaptation. The development of long-read sequencing technologies, including Oxford Nanopore, allows for comprehensive SV discovery and characterization even in complex polyploid crop genomes. However, many of the SV discovery pipeline benchmarks do not include complex plant genome datasets. In this study, we benchmarked popular long-read alignment-based SV detection tools for crop plant genomes. We used real and simulated Oxford Nanopore reads for two crops, allotetraploid Brassica napus (oilseed rape) and diploid Solanum lycopersicum (tomato), and evaluated several read aligners and SV callers across 5x, 10x, and 20x coverages typically used in re-sequencing studies. Our benchmarks provide a useful guide for designing Oxford Nanopore re-sequencing projects and SV discovery pipelines for crop plants.

bioinformatics↗

bioRxiv2022

Direct access to millions of mutations by Whole Genome Sequencing of an oilseed rape mutant population

Induced mutations are an essential source of genetic variation in plant breeding. EMS mutagenesis has been frequently applied, and mutants have been detected by phenotypic or genotypic screening of large populations. In this study, a rapeseed M2 population was derived from M1 parent cultivar "Express" treated with EMS. Whole genomes were sequenced from fourfold (4x) pools of 1,988 M2 plants representing 497 M2 families. Detected mutations were not evenly distributed and displayed distinct patterns across the 19 chromosomes with lower mutation rates towards the ends. Mutation frequencies ranged from 32/Mb to 48/Mb. On average, 284,442 single nucleotide polymorphisms per M2 DNA pool were found resulting from EMS mutagenesis. 55% were C[->]T and G[->]A transitions, characteristic for EMS induced ( canonical) mutations, whereas the remaining SNPs were non-canonical transitions (15%) or transversions (30%). Additionally, we detected 88,725 high confidence insertions and deletions (InDels) per pool. On average, each M2 plant carried 39,120 canonical mutations, corresponding to a frequency of one mutation per 23.6 kb. Roughly 82% of such mutations were located either 5 kb upstream or downstream (~56%) of gene coding regions or within intergenic regions (26%). The remaining 18% were located within regions coding for genes. All mutations detected by whole-genome sequencing could be verified by comparison with known mutations. Furthermore, all sequences are accessible via the online tool "EMS Brassica" (http://www.emsbrassica.plantbreeding.uni-kiel.de/), which enables direct identification of mutations in any target sequence. The sequence resource described here will further add value for functional gene studies in rapeseed breeding.

genomics↗

bioRxiv2022

Individual neurophysiological signatures of spontaneous rhythm processing

When sensory input conveys rhythmic regularity, we can form predictions about the timing of upcoming events. Although rhythm processing capacities differ considerably between individuals, these differences are often obscured by participant- and trial-level data averaging procedures in M/EEG research. Here, we systematically assessed the neurophysiological variability displayed by individuals listening to isochronous equitone sequences interspersed with unexpected deviant tones. We first focused on rhythm tracking and tested the anticipatory phase alignment of delta-band activity to expected tone onsets. These analyses confirmed that individuals encode temporal regularities and form temporal predictions, but highlight clear inter- and intra-participant variability. This observation may indicate individual and flexible tracking mechanisms, which show consistency at the single-trial level, but variability over trials. We then modelled single-trial time-locked neural responses in the beta-band to investigate individual tendencies to spontaneously employ binary grouping ("tic-toc effect"). This approach identified binary (strong-weak), ternary (strong-weak-weak), and mixed accentuation patterns, confirming the superimposition of a basic beat pattern. Furthermore, we characterized individual grouping preferences and tendencies to use binary, ternary, or combined patterns over trials. Importantly, the processing of standard and deviant tones was modulated by the employed pattern. The current approach supports individualized neurophysiological profiling as a sensitive strategy to identify dynamically evolving neural signatures of rhythm and beat processing. We further suggest that close examination of neurophysiological variability is critical to improve our understanding of the individual and flexible mechanisms underlying the capacities to rapidly evaluate and adapt to environmental rhythms. Significance statementFor decades, music, speech and rhythm research investigated how humans process, predict, and adapt to environmental rhythms. By adopting a single-trial and -participant approach, we avert the common pooling of EEG data in favor of individual time-varying neural signatures of rhythm tracking and beat processing. The results highlight large inter- and intra-individual differences in rhythm tracking, arguing against the typically documented phase-specificity for entrainment. On top of that, we characterize individual variability in beat processing, by showing that binary, ternary and other accentuation patterns are used over time, and ultimately affect the processing of (un-)expected auditory events. The approach aids individual neural profiling and may therefore allow identifying altered neural activity and its consequences in natural listening contexts.

neuroscience↗

bioRxiv2020

Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

Genome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single nucleotide polymorphism (SNP). In recent years there have been a number of studies associating large, chromosomal scale SV ranging from hundreds of kilobases all the way up to a few megabases to key agronomic traits in plant genomes. However, there have been little or no efforts towards cataloging small (30 to 10,000 bp) to mid-scale (10,000 bp to 30,000 bp) SV and their impact on evolution and adaptation related traits in plants. This might be attributed to complex and highly-duplicated nature of plant genomes, which makes them difficult to assess using high-throughput genome screening methods. Here we describe how long-read sequencing technologies can overcome this problem, revealing a surprisingly high level of widespread, small to mid-scale SV in a major allopolyploid crop species, Brassica napus. We found that up to 10% of all genes were affected by small to mid-scale SV events. Nearly half of these SV events ranged between 100 bp to 1000 bp, which makes them challenging to detect using short read Illumina sequencing. Examples demonstrating the contribution of such SV towards eco-geographical adaptation and disease resistance in oilseed rape suggest that revisiting complex plant genomes using medium-coverage, long-read sequencing might reveal unexpected levels of functional gene variation, with major implications for trait regulation and crop improvement.

genomics↗