Biology subjects

Dreyer, F.

Publications and source records attributed to Dreyer, F..

3 recordsLinked to original sources

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

Mapping-by-sequencing reveals genomic regions associated with seed quality parameters in Brassica napus

Rapeseed (Brassica napus L.) is an important oil crop and harbours the potential to serve as a highly productive source of protein. This protein exhibits an excellent amino acid composition and has a high nutritional value for humans. Seed protein content (SPC) and seed oil content (SOC) are two complex quantitative and polygenic traits which are negatively correlated and assumed to be controlled by additive and epistatic effects. A reduction of seed glucosinolate (GSL) content is desired as GSLs cause a stringent and bitter taste. The goal here was the identification of genomic intervals relevant for seed GSL content and SPC/SOC. Mapping-by-sequencing (MBS) revealed 30 and 15 new and known genomic intervals associated with seed GSL content and SPC/SOC, respectively. Within these intervals we identified known but also so far unknown putatively causal genes and sequence variants. A 4 bp insertion in the MYB28 homolog on C09 shows a significant correlation with a reduction in seed GSL content. This study provides insights into the genetic architecture and potential mechanisms underlying seed quality traits, which will enhance future breeding approaches in B. napus.

genomics↗

bioRxiv2021

Investigating brain mechanisms underlying natural reading by co-registering eye tracking with combined EEG and MEG

Linking brain and behavior is one of the great challenges in cognitive neuroscience. Ultimately, we want to understand how the brain processes information to guide every-day behavior. However, most neuroscientific studies employ very simplistic experimental paradigms whose ecological validity is doubtful. Reading is a case in point, since most neuroscientific studies to date have used unnatural word-by-word stimulus presentation and have often focused on single word processing. Previous research has therefore actively avoided factors that are important for natural reading, such as rapid self-paced voluntary saccadic eye movements. Recent methodological developments have made it possible to deal with associated problems such as eye movement artefacts and the overlap of brain responses to successive stimuli, using a combination of eye-tracking and neuroimaging. A growing number of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) are successfully using this methodology. Here, we provide a proof-of-concept that this methodology can be applied to combined EEG and magnetoencephalography (MEG) data. Our participants naturally read 4-word sentences that could end in a plausible or implausible word while eye-tracking, EEG and MEG were being simultaneously recorded. Eye-movement artefacts were removed using independent-component analysis. Fixation-related potentials and fields for sentence-final words were subjected to minimum-norm source estimation. We detected an N400-type brain response in our EEG data starting around 200 ms after fixation of the sentence-final word. The brain sources of this effect, estimated from combined EEG and MEG data, were mostly located in left temporal lobe areas. We discuss the possible use of this method for future neuroscientific research on language and cognition.

neuroscience↗