Biology subjects

van Zanten, M.

Publications and source records attributed to van Zanten, M..

5 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↗

bioRxiv2022

Arabidopsis latent virus 1, a comovirus widely spread in Arabidopsis thaliana collections

O_LITranscriptome studies of Illumina RNA-seq datasets of different Arabidopsis thaliana natural accessions and T-DNA mutants revealed the presence of two virus-like RNA sequences which showed the typical two segmented genome characteristics of a comovirus. C_LIO_LIThis comovirus did not induce any visible symptoms in infected Arabidopsis plants cultivated under standard laboratory conditions. Hence it was named Arabidopsis latent virus 1 (ArLV1). Virus infectivity in Arabidopsis plants was confirmed by RT-qPCR, transmission electron microscopy and mechanical inoculation. ArLV1 can also mechanically infect Nicotiana benthamiana, causing distinct mosaic symptoms. C_LIO_LIA bioinformatics investigation of Arabidopsis RNA-Seq repositories, including nearly 6500 Sequence Read Archives (SRAs) in the NCBI SRA database, revealed the presence of ArLV1 in 25% of all archived natural Arabidopsis accessions and in 8.5% of all analyzed SRAs. ArLV1 could also be detected in Arabidopsis plants collected from the wild. C_LIO_LIArLV1 is highly seed-transmissible with up to 40% incidence on the progeny derived from infected Arabidopsis plants. This has likely led to a worldwide distribution in the model plant Arabidopsis with yet unknown effects on plant performance in a substantial number of studies. C_LI Plain language summaryWe identified Arabidopsis latent virus 1 (ArLV1), a comovirus that infects the model plant Arabidopsis thaliana without causing any visible symptoms. It is efficiently spread by transmission via seeds to the plant progeny. ArLV1 is infectious to Arabidopsis plants and another model plant, Nicotiana benthamiana. By analyzing public sequencing data, we found that ArLV1 is widely spread in Arabidopsis laboratory collections worldwide. Moreover, it was also detected in wild Arabidopsis plants collected from different locations in the Netherlands and Spain, suggesting that it is a virus that naturally occurs in Arabidopsis.

plant biology↗

bioRxiv2021

Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana

Plant responses to abiotic stresses are complex and dynamic, and involve changes in different traits, either as the direct consequence of the stress, or as an active acclimatory response. Abiotic stresses frequently occur simultaneously or in succession, rather than in isolation. Despite this, most studies have focused on a single stress and single or few plant traits. To address this gap, our study comprehensively and categorically quantified the individual and combined effects of three major abiotic stresses associated with climate change (flooding, progressive drought and high temperature) on 12 phenotypic traits related to morphology, development, growth and fitness, at different developmental stages in four Arabidopsis thaliana accessions. Combined sub-lethal stresses were applied either simultaneously (high temperature and drought) or sequentially (flooding followed by drought). In total, we analyzed the phenotypic responses of 1782 individuals across these stresses and different developmental stages. Overall, abiotic stresses and their combinations resulted in distinct patterns of effects across the traits analyzed, with both quantitative and qualitative differences across accessions. Stress combinations had additive effects on some traits, whereas clear positive and negative interactions were observed for other traits: 9 out of 12 traits for high temperature and drought, 6 out of 12 traits for post-submergence and drought showed significant interactions. In many cases where the stresses interacted, the strength of interactions varied across accessions. Hence, our results indicated a general pattern of response in most phenotypic traits to the different stresses and stress combinations, but it also indicated a natural genetic variation in the strength of these responses. Overall, our study provides a rich characterization of trait responses of Arabidopsis plants to sub-lethal abiotic stresses at the phenotypic level and can serve as starting point for further in-depth physiological research and plant modelling efforts.

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↗

bioRxiv2017

POWERDRESS-mediated histone deacetylation is essential for thermomorphogenesis in Arabidopsis thaliana

Ambient temperature influences plant growth and development and minor changes can substantially impact crop yields. The underlying mechanisms for temperature perception and response are just beginning to emerge. Chromatin remodeling via the eviction of the histone variant H2A.Z in nucleosomes that alters gene expression is a critical component of thermal response in plants. However, whether chromatin-remodeling processes such as histone modifications play a global role in thermal response remains unknown. Using a combination of genetic analysis, chemical inhibition studies and RNA-seq analysis coupled with meta-analysis, here we identify POWERDRESS (PWR), a SANT-domain containing protein that is known to interact with HISTONE DEACETYLASE 9 (HDA9), as a novel key factor required for thermomorphogenesis in Arabidopsis thaliana. We identify that mutations in PWR impede thermomorphogenesis exemplified by severely attenuated temperature-induced hypocotyl/petiole elongation and early flowering. We show that inhibitors of histone deacetylases diminish temperature-induced hypocotyl elongation, which demonstrates for the first time a requirement for histone deacetylation in thermomorphogenesis. Genes that are misregulated in pwr mutants showed enrichment for GO terms associated with \"response\". Our expression studies coupled with meta-analysis revealed a significant overlap between genes misregulated in pwr mutants and genes that are enriched for H2A.Z in their gene bodies. Meta-analyses reveal that genes misregulated in pwr mutants in diverse conditions also overlap with genes that are differentially expressed in the mutants of the components of the SWR1 complex that mediates H2A.Z nucleosome dynamics. Our findings thus uncover a role for PWR in facilitating thermal response and suggest a potential link between histone deacetylation and H2A.Z nucleosome dynamics in regulation of gene expression in plants.\n\nAuthor summaryPlant growth and development is influenced by a variety of external environmental cues. Ambient temperature affects almost all stages of plant development but the underlying molecular mechanisms remain largely unknown. In this paper, the authors show that histone deacetylation, one of the major chromatin remodeling processes, is essential for eliciting growth temperature-induced responses in plants. The authors identify POWERDRESS, a protein known to interact with HISTONE DEACETYLASE 9, as a novel key player essential for eliciting high temperature induced responses in Arabidopsis. Another chromatin remodeling mechanism that is known to play a role in thermal response is the eviction of histone variant H2A.Z from nucleosomes. Through transcriptome studies the authors demonstrate an overlap between gene regulations conferred through PWR-mediated histone H3 deacetylation and that conferred via histone H2A.Z eviction/incorporation dynamics. This study identifies a key novel gene that is essential for plants to elicit high temperature responses and reveals close links between two seemingly distinct chromatin-remodeling processes in regulating gene expression in plants.

genetics↗