Biology subjects

Bitz, O.

Publications and source records attributed to Bitz, O..

4 recordsLinked to original sources

bioRxiv2026

Early cadmium responses in developing oat caryopses indicate an unexpected regulatory network linked to low grain cadmium accumulation

Heavy-metal accumulation in cereal grains is becoming critical for European food safety, regulation and plant breeding. In the EU, Cd maximum levels in certain foodstuffs have been revised, including lowering or establishing limits for relevant food categories, while new maximum levels for nickel (Ni) have recently been introduced for several foodstuffs, including cereal categories, with limits for oats and selected cereals applying from 2026. Together, these developments create an urgent need to identify genetic and physiological mechanisms that reduce Cd and Ni accumulation in cereal grains while maintaining crop quality and productivity. Against this regulatory and food-safety background, our broader RNA-seq experiment investigates early transcriptional responses to Cd and Ni in oat F2 segregants contrasting for metal accumulation. The full dataset includes low- and high-accumulating segregants, roots and developing caryopses sampled at 3 h and 7 h after treatment. In the present pilot analysis, we focus on the Cd response in developing caryopses of the low-Cd accumulating segregant AS131 to identify candidate processes associated with reduced grain Cd accumulation. The strongest transcriptional responses were not dominated by canonical Cd-detoxification pathways. At 3 h after Cd exposure, differentially expressed transcripts were mainly associated with cell-wall functions, endosperm transfer-cell-specific PR60 proteins, DUF239-containing proteins and cysteine proteinase inhibitors, whereas several dehydration-, pathogen-, defence-, cell-wall-loosening- and ROS- related genes were repressed. By 7 h, the response suggested a shift towards homeostatic acclimation, with induction of TIP2 aquaporins, thiamine thiazole synthases, EF-Tu proteins, coatomer-related genes and carbohydrate metabolism-associated genes, together with repression of LEA/SMP/dehydrin genes, FRO7-like genes, EF-hand calcium-binding proteins and stress-regulatory transcription factors. Pathway-level analyses were broadly consistent with these transcript-level patterns, highlighting structural, nucleosome-associated, translation-related, metabolic and developmental processes. Several Cd-responsive transcripts were also associated with broader abiotic-stress responses, suggesting recruitment of shared stress-regulatory modules rather than Cd-specific detoxification pathways alone. Overall, these results support a working hypothesis in which low Cd accumulation in developing oat grain may involve regulation of solute-transfer interfaces, cellular protection, intracellular homeostasis, trafficking pathways and caryopsis developmental programmes. These findings provide candidate processes for future comparison with high-Cd accumulating segregants, root tissues and Ni responses in the broader dataset.

genomics↗

bioRxiv2026

Genetic Structure and Diversity of Amaranth Populations across Multi-Environmental Sites in Burkina Faso Revealed by Simple Sequence Repeats (SSRs) and Genotyping-by-Sequencing (GBS)

The genus Amaranthus L. (Amaranthaceae) comprises 70-80 species, including leafy vegetables, pseudocereals, ornamentals, and weedy forms, and is widely distributed across tropical and temperate regions. Despite its nutritional and agronomic importance, the taxonomy of Amaranthus remains challenging due to extensive phenotypic plasticity, sporadic hybridization, and limited diagnostic traits. In Burkina Faso, three species (A. cruentus, A. hypochondriacus, and A. dubius) are commonly cultivated, displaying considerable morphological variability and forming seven distinct morphotypes. To better understand the genetic diversity and population structure of West African Amaranthus, we analyzed accessions from multi-environmental sites in Burkina Faso using both simple sequence repeat (SSR) markers and genotyping-by-sequencing (GBS). SSR-based STRUCTURE analysis revealed a pronounced {Delta}K peak at K = 2, indicating two major genetic groups, with additional substructure at K = 4. Principal Coordinates Analysis confirmed species-level separation and morphotype-based clustering, while bar plots from STRUCTURE analysis highlighted admixture among several accessions. Complementary GBS analysis provided higher-resolution insights, partitioning species into multiple sub-clusters, detecting introgression, and linking genetic differentiation to morphological traits such as leaf shape, pigmentation, and inflorescence type. These findings are consistent with previous studies in Burkina Faso that reported both major genetic groups and significant morphological diversity. Together, SSR and GBS analyses underscore the multilayered nature of Amaranthus diversity, with SSRs capturing broad population subdivision and GBS refining fine-scale structure. This dual approach provides a robust framework for conservation of genetic resources and for genomics-assisted breeding aimed at exploiting heterosis, preserving unique alleles, and developing resilient varieties to enhance food and nutrition security in sub-Saharan Africa.

genetics↗

bioRxiv2024

A pangenome and pantranscriptome of hexaploid oat

Oat grain is a traditional human food rich in dietary fiber that contributes to improved human health. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogs. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here, we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oats along with an atlas of gene expression across six tissues of different developmental stages in 23 accessions. We describe the interplay of gene expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory up-regulation of the remaining homeologs, but this process is constrained by subgenome divergence. Chromosomal rearrangements have significantly impacted recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semidwarf mutant has risen to prominence in Australian elite varieties. The oat pangeome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.

genomics↗

bioRxiv2023

Fine-Tuning GBS Data with Comparison of Reference and Mock Genome Approaches for Advancing Genomic Selection in Less Studied Farmed Species

BackgroundDiversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack efficient genotyping solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data was used to automate the bioinformatic analysis. The application of the optimization was demonstrated on non-model European whitefish data. ResultsDdRAD data generation was designed for a reliable estimation of relatedness and is scalable to up to 384 samples. The GBS sequencing yielded approximately one million reads for each of the around 100 assessed samples. Optimizing various strategies to create a de-novo reference genome for variant calling (mock reference) showed that using three samples outperformed other building strategies with single or very large number of samples. Adjustments to most pipeline tuning parameters had limited impact on high-quality data, except for the identity criterion for merging mock reference genome clusters. For each species, over 15k GBS variants based on the mock reference were obtained and showed comparable results with the ones called using an existing reference genome. Repeatability analysis showed high concordance over replicates, particularly in bovine while in European whitefish data repeatability did not exceed earlier observations. ConclusionsThe proposed cost-effective ddRAD strategy, coupled with an efficient bioinformatics workflow, enables broad adoption of ddRAD GBS across diverse farmed species. While beneficial, a reference genome is not obligatory. The integration of Snakemake streamlines the pipeline usage on computer clusters and supports customization. This user-friendly solution facilitates genotyping for both model and non-model species.

bioinformatics↗