Biology subjects

Hilhorst, H. W. M.

Publications and source records attributed to Hilhorst, H. W. M..

4 recordsLinked to original sources

bioRxiv2023

Modulation of quantitative trait loci for Arabidopsis thaliana seed performance by the maternal and germination environment.

The quality of seeds contributes to plant performance, especially during germination and in the young seedling stage, and hence affects the economic value of seed crops. A seeds innate quality is determined during seed development and the following seed maturation phase. It is tightly controlled by the genetic make-up of the mother plant and further shaped by the environmental conditions of the mother plant. The interaction between genotype and environment can result in substantial quantitative variation in seed traits like dormancy and viability. Making use of naturally occurring variation within the Arabidopsis thaliana germplasm, we studied the interaction between seed production environments and the genetic architecture of mother plants on diverse seed quality traits. An Arabidopsis Bayreuth-0 x Shahdara recombinant inbred line (RIL) population was grown in four different seed production environments: high temperature, high light, low phosphate, and control conditions. The seeds harvested from the mother plants that were exposed to these environments from flowering until seed harvest were subsequently subjected to germination assays under standard and mild stress conditions (cold, heat, osmotic stress and added phytohormone ABA). Quantitative trait locus (QTL) analysis identified many environmental-sensitive QTLs (QTL x E) as well as several interactions between the maternal and germination environments. Variation in the number and position of the QTLs was largely determined by the germination conditions, however effects of the maternal environment were clearly present regarding the genomic location as well as significance of the individual QTLs. Together, our findings uncover the extensive environmental modulation of the genetic influence on seed performance and how this is shaped by the genetic make-up of the mother plant. Our data provides a systems-view of the complex genetic basis of genotype-by-environment interactions determining seed quality.

plant biology↗

bioRxiv2021

Plasticity of maternal environment dependent expression-QTLs of tomato seeds

Seeds are essential for plant reproduction, survival, and dispersal. Germination ability and successful establishment of young seedlings strongly depends on seed quality and on environmental factors such as nutrient availability. In tomato (Solanum lycopersicum) and many other species, seed quality and seedling establishment characteristics are determined by genetic variation, as well as the maternal environment in which the seeds develop and mature. The genetic contribution to variation in seed and seedling quality traits and environmental responsiveness can be estimated at transcriptome level in the dry seed by mapping genomic loci that affect gene expression (expression QTLs) in contrasting maternal environments. In this study, we applied RNA-sequencing to measure gene expression of seeds of a tomato RIL population derived from a cross between S. lycopersicum (cv. Moneymaker) and S. pimpinellifolium (G1.1554). The seeds matured on plants cultivated under different nutritional environments; i.e. on high phosphorus or low nitrogen. The obtained SNPs were subsequently used to construct a high-density genetic map. We show how the genetic landscape of plasticity in gene regulation in dry seeds is affected by the maternal nutrient environment. The combined information on natural genetic variation mediating (variation in) responsiveness to the environment may contribute to knowledge-based breeding programs aiming to develop crop cultivars that are resilient to stressful environments.

plant biology↗

bioRxiv2020

Network analysis prioritizes DEWAX and ICE1 as the candidate genes for two major eQTL hotspots in seed germination

Seed germination is characterized by a constant change of gene expression across different time points. These changes are related to specific processes, which eventually determine the onset of seed germination. To get a better understanding on the regulation of gene expression during seed germination, we performed a quantitative trait locus mapping of gene expression (eQTL) at four important seed germination stages (primary dormant, after-ripened, six-hour after imbibition, and radicle protrusion stage) using Arabidopsis thaliana Bay x Sha recombinant inbred lines (RILs). The mapping displayed the distinctness of the eQTL landscape for each stage. We found several eQTL hotspots across stages associated with the regulation of expression of a large number of genes. Interestingly, an eQTL hotspot on chromosome five collocates with hotspots for phenotypic and metabolic QTLs in the same population. Finally, we constructed a gene co-expression network to prioritize the regulatory genes for two major eQTL hotspots. The network analysis prioritizes transcription factors DEWAX and ICE1 as the most likely regulatory genes for the hotspot. Together, we have revealed that the genetic regulation of gene expression is dynamic along the course of seed germination. One-sentence summaryTwo transcription factors, DEWAX and ICE1, may be important regulators of gene expression during seed germination, based on network analysis of eQTL hotspots.

plant biology↗

bioRxiv2019

Intertwined signatures of desiccation and drought tolerance in grasses

Grasses are among the most resilient plants and some can survive prolonged desiccation in semi-arid regions with seasonal rainfall. This vegetative desiccation tolerance has arisen independently multiple times within the grass family, but the genetic elements that differentiate desiccation tolerant and sensitive grasses are largely unknown. Here we leveraged comparative genomic approaches with the resurrection grass Eragrostis nindensis and the closely related desiccation sensitive cereal Eragrostis tef to identify changes underlying desiccation tolerance. We extended the analyses to include the grasses maize, sorghum, rice, and the model desiccation tolerant grass Oropetium thomaeum to identify broader evolutionary conservation and divergence. We identified changes in chromatin architecture and expression dynamics related to desiccation in E. nindensis. It was previously hypothesized that transcriptional re-wiring of seed desiccation pathways confers vegetative desiccation tolerance. We demonstrate that the majority of seed dehydration related genes show similar expression patterns in leaves of desiccation tolerant and sensitive species during dehydration. However, we discovered a small set of orthologs with expression specific to leaves of desiccation tolerant species, and seeds of sensitive species. This supports a nuanced role of seed-related genes where many overlap with typical drought responses but some crucial genes are desiccation specific in resurrection plants.

plant biology↗