Biology subjects

Hilhorst, H.

Publications and source records attributed to Hilhorst, H..

5 recordsLinked to original sources

bioRxiv2024

SeedMatExplorer: The transcriptome atlas of Arabidopsis seed maturation

BackgroundSeed maturation is a critical developmental phase during which seeds acquire traits essential for nutritional value, desiccation tolerance, and long-term survival. Abscisic acid (ABA) signalling is a key regulator of this process, coordinating gene expression programs underlying the acquisition of seed quality traits. However, the molecular regulation of many of these traits remains poorly understood. To address this, we performed a comprehensive analysis of seed maturation in Arabidopsis thaliana, combining physiological and transcriptomic approaches across wild-type plants and mutants affected in ABA biosynthesis, signalling, and catabolism. ResultsWe generated a high-resolution transcriptome dataset covering seed development from 12 days after pollination to the dry seed stage in wild-type and ten mutant lines. In parallel, we characterized the temporal acquisition of multiple seed traits, including germination capacity, dormancy, chlorophyll fluorescence, longevity and desiccation tolerance. Integration of these datasets using weighted gene co-expression network analysis (WGCNA) identified gene modules associated with specific trait acquisition patterns. This approach enabled the identification of coordinated transcriptional programs linked to distinct seed quality traits, extending beyond individual gene-level analyses. Notably, modules associated with desiccation tolerance and longevity were enriched for genes involved in stress responses and ABA-regulated pathways, highlighting the complex and multifactorial regulation of these traits. ConclusionsThis study provides a comprehensive physiological and transcriptomic framework for understanding seed maturation and the acquisition of key seed quality traits in Arabidopsis thaliana. By linking gene expression dynamics to trait development, our work offers new insights into the regulatory networks underlying seed resilience and storage capacity. The dataset is made accessible through SeedMatExplorer (https://www.bioinformatics.nl/SeedMatExplorer), an open-access web platform that enables interactive exploration and supports hypothesis generation. Together, this resource represents a valuable tool for advancing research on seed biology and improving seed performance in agricultural contexts.

plant biology↗

bioRxiv2023

A Horizontal View of Primary Metabolomes in Vegetative Desiccation Tolerance

Vegetative desiccation tolerance (VDT), the ability of such tissues to survive the near complete loss of cellular water, is a rare but polyphyletic phenotype. It is a complex multifactorial trait, typified by some near universal (core) factors but with many and varied adaptations due to plant architecture, biochemistry and biotic/abiotic dynamics of particular ecological niches. The ability to enter into a quiescent biophysically stable state is what ultimately determines desiccation tolerance. Thus, understanding of the metabolomic complement of plants with VDT gives insight into the nature of survival as well as evolutionary aspects of VDT. In this study we measured the soluble carbohydrate profiles and the polar, TMS-derivatisable metabolomes of 7 phylogenetically diverse species with VDT, in contrast with 3 desiccation sensitive (DS) species, under conditions of full hydration, severe water deficit stress, and desiccated. Our study confirmed the existence of core mechanisms of VDT systems relying on either constitutively abundant trehalose, or the accumulation of raffinose family oligosaccharides and sucrose, with threshold ratios conditioned by other features of the metabolome. DS systems did not meet these ratios. Considerable chemical variations among VDT species suggest that similar stresses, e.g. photosynthetic stress, are dealt with using different chemical regimes. Furthermore, differences in timing of metabolic shifts suggest there is not a single "desiccation programme", but that subprocesses are coordinated differently at different phases of drying. There is likely to be constraints on the composition of a viable dry state and how different adaptive strategies interact with the biophysical constraints of VDT.

plant biology↗

bioRxiv2020

Clues on an intraspecific communication system in early plant establishment: The seed-seedling transition from the point of view of a crosstalk between information theory and gene expression

How much interactivity is there in a seed-seedling transition system? The answer for this question can reveal a key aspect for early plant establishment. Thus, we hypothesize that information entropy is correlated with early plant development because it is directly related to interactions between seed-seed, seed-seedling, and seedling-seedling. To test this hypothesis, we perform an overlapping of classical physiological measurements (embryo protrusion), gene expression in germination sensu stricto, water dynamics in germinating seeds and information theory. For a biological model, we used Solanum lycocarpum A. St.{square}Hil. seeds. This is a Neotropical species with high intra-specific variability in the seed sample. Our finds demonstrate that the dynamic and transient seed-seedling transition system is influenced by the number of individuals (seed or seedling) in the sample, especially at a same physiological stage. In addition, we also discuss that: (i) information entropy enables the quantification of system disturbance relative to individuals in the same physiological stage (seed-seed or seedling-seedling), which may be determinant for embryo growth during germination. (ii) there is possible intraspecific communication in seed-seedling transition systems formed by germinating seeds with the potential to alter the pattern of embryonic development of the sample. In view of this, we suggest the use of information entropy as a tool for studies of biological systems to clarify the phenomenon of mutual stimulation in the germination process.

plant biology↗

bioRxiv2019

A blueprint of seed desiccation sensitivity in the genome of Castanospermum australe

O_LIMost angiosperms produce seeds that are desiccated on dispersal with the ability to retain viability in storage facilities for prolonged periods. However, some species produce desiccation sensitive seeds which rapidly lose viability in storage, precluding ex situ conservation. Current consensus is that desiccation sensitive seeds either lack or do not express mechanisms necessary for the acquisition of desiccation tolerance.\nC_LIO_LIWe sequenced the genome of Castanospermum australe, a legume species producing desiccation sensitive seeds, and characterized its seed developmental physiology and - transcriptomes.\nC_LIO_LIC. australe has a low rate of evolution, likely due to its perennial life-cycle and long generation times. The genome is syntenic with itself, with several orthologs of genes from desiccation tolerant legume seeds, from gamma whole-genome duplication events being retained. Changes in gene expression during development of C. australe seeds, as compared to desiccation tolerant Medicago truncatula seeds, suggest they remain metabolically active, prepared for immediate germination.\nC_LIO_LIOur data indicates that the phenotype of C. australe seeds arose through few changes in specific signalling pathways, precluding or bypassing activation of mechanisms necessary for acquisition of desiccation tolerance. Such changes have been perpetuated as the habitat in which dispersal occurs is favourable for prompt germination.\nC_LI

plant biology↗

bioRxiv2018

The interaction between genotype and maternal nutritional environments affects tomato seed and seedling quality

Seed and seedling traits are affected by the conditions of the maternal environment, such as light, temperature and nutrient availability. In this study, we have investigated whether different maternally applied nitrate and phosphate concentrations affect the seed and seedling performance of two tomato genotypes: Solanum lycopersicum cv. Money maker and Solanum pimpinellifolium accession CGN14498. We observed large differences for seed and seedling traits between the two genotypes. Additionally, we have shown that for nitrate most of the seed and seedling traits were significantly affected by genotype by environment interactions (GxE). The effect of the maternal environment was clearly visible in the primary metabolites of the dry seeds. For example, we could show that the amount of {gamma}-aminobutyric acid (GABA) in Money maker seeds was affected by the differences in the maternal environments and was positively correlated with seed germination under high temperature. Overall, compared to phosphate, nitrate had a larger effect on seed and seedling performance in tomato. In general, the different responses to the maternal environments of the two tomato genotypes show a major role of genotype by environment interactions in shaping seed and seedling traits.\n\nHighlightThe presented data specifically provides knowledge towards understanding a multi-level effect of the maternal nutritional environment on seed and seedling characteristics in tomato. We show a clear genotype by environment interactions (GxE) especially for maternal growth on different nitrate concentrations. Additionally we identified metabolites with either positive or negative correlations with maternal environment affected phenotypical traits.

plant biology↗