Biology subjects

Bentsink, L.

Publications and source records attributed to Bentsink, L..

6 recordsLinked to original sources

bioRxiv2026

Drying kinetics govern transcriptional and post-transcriptional reprogramming during seed maturation

Desiccation tolerance (DT) serves as a cornerstone for seed survival and for long-term persistence in the natural environment. DT is acquired during seed development, as seeds undergo a drastic change in internal water content during maturation drying. Although the physiological effects of drying on the acquisition of DT and other seed traits have been described, the molecular mechanisms underlying these effects have not yet been fully understood. Here, we addressed this gap by submitting maturing seeds of Arabidopsis thaliana L. to three different drying regimes - fast drying (FD), slow drying (SD), and a combination of both (SDFD) and studying physiological, transcriptional, and post-transcriptional responses. We found that SD not only accelerated DT acquisition but also seed maturation. Each drying regime showed a distinct transcriptional signature, with SD and SDFD showing greater global gene downregulation compared to FD. This downregulation appeared to be crucial for establishing DT in developing seeds. Interestingly, FD triggered a specific defense-related transcriptional response that was detrimental to seed longevity. Using an abscisic acid deficient mutant, we found that most of the drying-mediated transcriptional changes were largely independent of the wild-type ABA levels. On a post-transcriptional level, SD led to a major turnover of mRNA populations undergoing co-translational mRNA decay (CTRD) and promoted CTRD of stress-related genes. Overall, our study provides fundamental insights into the mechanisms by which seeds perceive and respond to drying, advancing our basic understanding of the molecular regulation of DT and seed maturation. Significance StatementSeed maturation is a critical phase of the plant life cycle when seeds acquire desiccation tolerance (DT) required for long-term storage. Drying rate, together with abscisic acid (ABA), has been implicated in this process, but whether seed development actively responds to different drying rates and how such responses are regulated has remained unclear. Here, we show that maturing seeds sense and respond to different drying regimes through distinct molecular programs, with slow drying triggering coordinated transcriptional and post-transcriptional reprogramming associated with enhanced DT. This response occurs partly independent of wild-type ABA levels, revealing drying rate as a developmental signal acting alongside hormonal regulation to direct seed maturation. These findings provide a framework for improving drying strategies and identifying molecular markers of seed quality.

plant biology↗

bioRxiv2025

Translational landscape during Seed Germination at Sub-Codon resolution

Seed germination is crucial for agricultural reproduction. A deep understanding of this process can secure healthy growth at the early phases of plant development and therefore the yield. Recent research indicates that germination is a complex process involving translational regulation. A large group of seed stored mRNAs together with newly synthesized transcripts are regulated by post-transcriptional mechanisms and selectively translated at different stages to support the germination process. To investigate the mechanism of translational control, we performed ribosome profiling on mRNAs of distinct physiological stages during Arabidopsis thaliana seed germination. The 3-nucleotide periodicity of the ribosome association on mRNAs identified indicates their translational potential. Dry seeds, in which translation is on hold are characterized by a unique ribosome association landscape with high association at the 5 and 3 UTR, compared to physiological stages that show active translation. Start codon specific stalling of ribosomes in dry seeds is associated with an adenine enriched sequence motif. Throughout germination codons encoding glycine, aspartate, tyrosine and proline are the most frequent ribosome pausing sites. Moreover, the non-coding RNAs which we identified as associated to ribosomes are indeed translated as was revealed by investigating total seed proteome data. Seed specific upstream Open Reading Frames (uORFs) are identified which may be associated to translational control of adaptative response during early seed germination. Altogether, we present a first ribosome profiling analysis across seed germination that illuminates various regulatory mechanisms that potentially contribute to the seeds survival strategy.

plant biology↗

bioRxiv2024

The angiosperm seed life cycle follows a developmental reverse hourglass

The seed life cycle is one of the most crucial stages in determining the ecological success of angiosperms. It broadly comprises three developmental phases - embryogenesis, maturation, and germination. Among these phases, seed maturation is particularly critical, serving as a bridge between embryo development and germination. During this phase, seeds accumulate nutrient reserves and acquire essential physiological traits, such as desiccation tolerance, vital for seed survival in diverse environments. Phylotranscriptomics in Arabidopsis thaliana has shown that embryogenesis and germination follow an hourglass-like development, with high expression of older and conserved genes at the mid-developmental stages. However, unlike embryogenesis and germination, a phylotranscriptomic study of seed maturation has not yet been performed and a comprehensive overview of the phylotranscriptomic landscape throughout the entire seed life cycle is still lacking. Here, we combined existing RNA-seq data covering all three phases of the Arabidopsis seed life cycle to construct a complete picture of the phylotranscriptomic pattern of the seed life cycle by generating transcriptome age index (TAI) and transcriptome divergence index (TDI) profiles. We found that the seed life cycle resembles a reverse hourglass-like pattern, with seed maturation exhibiting increased expression of younger genes with divergent expression patterns compared to embryogenesis and germination. Notably, this pattern of increased expression of younger genes during seed maturation is also conserved across both dicot and monocot species. Tissue-specific phylotranscriptomic analyses revealed that, in monocots, the increased expression of younger genes during maturation is largely driven by genes expressed in the endosperm. Overall, our findings highlight the major shifts in phylotranscriptomic patterns during the seed life cycle and establish seed maturation as a pivotal developmental phase enabling the expression of young and rapidly evolving genes critical for seeds adaptive capacity in their surrounding environment.

plant biology↗

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↗

bioRxiv2021

DELAY OF GERMINATION 6, encoding the ANAC060 transcription factor, inhibits seed dormancy

The timing of seed germination is regulated by seed dormancy. There is ample natural variation for seed dormancy among as well as within plant species. In Arabidopsis several DELAY OF GERMINATION quantitative trait loci have been identified, of which DOG1 is best studied. Here we report the identification of DOG6, a quantitative trait locus with a similar strong effect on seed dormancy as DOG1. DOG6 affects the timing of germination both in laboratory as well as in field conditions. Complementation cloning revealed that DOG6 encodes the membrane bound transcription factor ANAC060. The absence of the ANAC060 protein or its sequestration outside the nucleus results in increased seed dormancy levels. The different natural variants of ANAC060 differ for the presence of the membrane binding domain, either due to the fact that this domain is absent in the genomic sequence or because the cDNA is alternatively spliced. Our data indicates that ANAC060 regulates seed dormancy by among others binding to and regulating the expression of protein phosphatases 2C class A proteins including PROTEIN PHOSPHATASE 2CA (PP2CA), ABI FIVE BINDING PROTEIN 3 (AFP3) and HIGHLY ABA-INDUCED PP2C GENE 3 (HAI3). Significance StatementANAC transcription factors are known to effect plant development as well as the response of plants to their environment. Here, we present the identification of DELAY OF GERMINATION 6 (DOG6), a seed dormancy quantitative trait locus that encodes the ANAC060 transcription factor. We have identified different natural alleles of ANAC060 and show that these genetic variants determine the localization of the protein. ANAC060 alleles that lack the membrane binding domain end up in the nucleus. Hence they affect transcription and as such attenuate seed dormancy.

plant biology↗

bioRxiv2019

Transcriptome and translatome profiling and translational network analysis during seed maturation reveals conserved transcriptional and distinct translational regulatory patterns

Seed maturation is an important plant developmental process that follows embryo development. It is associated with a series of physiological changes such as the establishment of desiccation tolerance, seed longevity and seed dormancy. However, the translational dynamics associated with seed maturation, especially its connection with seed germination remains largely elusive. Here transcriptome and translatome profiling were performed during seed maturation. During seed maturation we observed a gradual disappearance of polysomes and a relative increase of monosomes, indicating a gradual reduction of global translation. Comparing the levels of polysomal associated mRNAs with total mRNA levels showed that thousands of genes are translationally regulated at early sates of maturation, as judged by dramatic changes in polysomal occupancy. By including previous published data from germination and seedling establishment, a translational regulatory network: SeedTransNet was constructed. Network analysis identified hundreds of gene modules with distinct functions and transcript sequence features indicating the existence of separate translational regulatory circuits possibly acting through specific regulatory elements. The regulatory potential of one such element was confirmed in vivo. The network identified several seed maturation associated genes as central nodes, and we could confirm the importance of many of these hub genes with a maturation associated seed phenotype by mutant analysis. One of the identified regulators an AWPM19 family protein PM19-Like1 (PM19L1) was shown to regulate seed dormancy and longevity. This putative RBP also affects the transitional regulation of one its, by the SeedTransNet identified, target mRNAs. Our data shows the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.

systems biology↗