ORCID Profile
0000-0001-6483-7473
Current Organisations
Universiteit Utrecht
,
Utrecht University
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Publisher: Bio-Protocol, LLC
Date: 2020
Publisher: Springer Science and Business Media LLC
Date: 20-09-2023
Publisher: American Association for the Advancement of Science (AAAS)
Date: 20-09-2019
Abstract: Some plants tolerate flooding better than others. Reynoso et al. compared gene regulatory networks activated by flooding in rice, which is adapted to flooding, with those in species less adapted to flooding. Flood-related gene regulation was characterized according to chromatin accessibility as well as transcription. Although flood response circuitry is evident in dryland species as well, its activation is greater in wetland rice. Science , this issue p. 1291
Publisher: Oxford University Press (OUP)
Date: 13-05-2014
DOI: 10.1093/AOB/MCU065
Publisher: Cold Spring Harbor Laboratory
Date: 26-05-2021
DOI: 10.1101/2021.05.25.445664
Abstract: Rice feeds more than half of the world's human population. In modern rice farming, a major constraint for productivity is weed proliferation and the ecological impact of herbicide application. Increased weed competitiveness of commercial rice varieties requires enhanced shade casting to limit growth of shade-sensitive weeds and the need for herbicide. We aimed to identify traits that enhance rice shading capacity based on the canopy architecture and the underlying genetic components. We performed a phenotypic screen of a rice ersity panel comprised of 344 varieties, examining 13 canopy architecture traits linked with shading capacity in 4-week-old plants. The analysis revealed a vast range of phenotypic variation across the ersity panel. We used trait correlation and clustering to identify core traits that define shading capacity to be shoot area, number of leaves, culm and solidity (the compactness of the shoot). To simplify the complex canopy architecture, these traits were combined into a Shading Rank metric that is indicative of a plant's ability to cast shade. Genome wide association study (GWAS) revealed genetic loci underlying canopy architecture traits, out of which five loci were substantially contributing to shading potential. Subsequent haplotype analysis further explored allelic variation and identified seven haplotypes associated with increased shading. Identification of traits contributing to shading capacity and underlying allelic variation presented in this study will serve future genomic assisted breeding programmes. The investigated ersity panel, including widely grown varieties, shows that there is big potential and genetic resources for improvement of elite breeding lines. Implementing increased shading in rice breeding will make its farming less dependent on herbicides and contribute towards more environmentally sustainable agriculture.
Publisher: Oxford University Press (OUP)
Date: 12-2018
Abstract: Regulation of plant root angle is critical for obtaining nutrients and water and is an important trait for plant breeding. A plant’s final, long-term root angle is the net result of a complex series of decisions made by a root tip in response to changes in nutrient availability, impediments, the gravity vector and other stimuli. When a root tip is displaced from the gravity vector, the short-term process of gravitropism results in rapid reorientation of the root toward the vertical. Here, we explore both short- and long-term regulation of root growth angle, using natural variation in tomato to identify shared and separate genetic features of the two responses. Mapping of expression quantitative trait loci mapping and leveraging natural variation between and within species including Arabidopsis suggest a role for PURPLE ACID PHOSPHATASE 27 and CELL DIVISION CYCLE 73 in determining root angle.
Publisher: Authorea, Inc.
Date: 21-09-2023
Publisher: Oxford University Press (OUP)
Date: 18-02-2011
DOI: 10.1093/JXB/ERR022
Abstract: Every day almost one billion people suffer from chronic hunger, and the situation is expected to deteriorate with a projected population growth to 9 billion worldwide by 2050. In order to provide adequate nutrition into the future, rice yields in Asia need to increase by 60%, a change that may be achieved by introduction of the C(4) photosynthetic cycle into rice. The international C(4) Rice Consortium was founded in order to test the feasibility of installing the C(4) engine into rice. This review provides an update on two of the many approaches employed by the C(4) Rice Consortium: namely, metabolic C(4) engineering and identification of determinants of leaf anatomy by mutant screens. The aim of the metabolic C(4) engineering approach is to generate a two-celled C(4) shuttle in rice by expressing the classical enzymes of the NADP-ME C(4) cycle in a cell-appropriate manner. The aim is also to restrict RuBisCO and glycine decarboxylase expression to the bundle sheath (BS) cells of rice in a C(4)-like fashion by specifically down-regulating their expression in rice mesophyll (M) cells. In addition to the changes in biochemistry, two-celled C(4) species show a convergence in leaf anatomy that include increased vein density and reduced numbers of M cells between veins. By screening rice activation-tagged lines and loss-of-function sorghum mutants we endeavour to identify genes controlling these key traits.
Publisher: Wiley
Date: 04-2019
DOI: 10.1002/PLD3.131
Publisher: Oxford University Press (OUP)
Date: 27-09-2017
DOI: 10.1104/PP.17.00688
Publisher: Wiley
Date: 16-08-2023
DOI: 10.1002/PPP3.10419
Abstract: Rice farming is transitioning from transplanting rice seedlings towards the less labour‐intensive and less water‐demanding method of directly seeding rice. This, however, is accompanied by increased weed proliferation. To tackle this issue, this study seeks to identify how the crop itself can better suppress weeds, with a focus on light competition via shading. Using a rice ersity panel, traits were identified that contribute to enhanced shading capacity, and these traits were encapsulated into a single shading capacity metric. This was followed by the identification of the genetic loci underpinning variation in the core traits. The identified haplotypes can be used in breeding programmes to improve weed suppression by rice, thus contributing to sustainable agriculture. In modern rice farming, one of the major constraints is weed proliferation and the entailed ecological impact of herbicide application. This requires increased weed competitiveness in current rice varieties, achieved via enhanced shade casting to limit the growth of shade‐sensitive weeds. To identify traits that increase rice shading capacity, we exhaustively phenotyped a rice ersity panel of 344 varieties at an early vegetative stage. A genome‐wide association study (GWAS) revealed genetic loci underlying variation in canopy architecture traits linked with shading capacity. The screen shows considerable natural variation in shoot architecture for 13 examined traits, of which shading potential is mostly determined by projected shoot area, number of leaves, culm height and canopy solidity. The shading rank, a metric based on these core traits, identifies varieties with the highest shading potential. Five genetic loci were found to be associated with canopy architecture, shading potential and early vigour. Identification of traits contributing to shading capacity and underlying allelic variation will serve future genomic‐assisted breeding programmes. Implementing the presented genetic resources for increased shading and weed competitiveness in rice breeding will make its farming less dependent on herbicides and contribute towards more environmentally sustainable agriculture.
Publisher: Oxford University Press (OUP)
Date: 27-05-2014
Publisher: Cold Spring Harbor Laboratory
Date: 11-10-2022
DOI: 10.1101/2022.10.10.511665
Abstract: Plant roots integrate environmental signals and developmental programs using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates the entry and exit of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation, but we find that it is absent in the tomato endodermis during normal development. Instead, suberin is present in the exodermis, a cell type that is absent in the model organism Arabidopsis thaliana . Here, we uncover genes driving exodermal suberization and describe its effects on drought responses in tomato, unravelling the similarities and differences with the paradigmatic Arabidopsis endodermis. Cellular resolution imaging, gene expression, and mutant analyses reveal loss of this program from the endodermis, and its co-option in the exodermis. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response. Controlling the degree of exodermal suberization could be a new strategy for breeding climate-resilient plants.
Publisher: Bio-Protocol, LLC
Date: 2018
Publisher: eLife Sciences Publications, Ltd
Date: 20-06-2023
DOI: 10.7554/ELIFE.83361
Abstract: Intercellular signalling is an indispensable part of multicellular life. Understanding the commonalities and differences in how signalling molecules function in two remote branches of the tree of life may shed light on the reasons these molecules were originally recruited for intercellular signalling. Here we review the plant function of three highly studied animal intercellular signalling molecules, namely glutamate, γ-aminobutyric acid (GABA), and melatonin. By considering both their signalling function in plants and their broader physiological function, we suggest that molecules with an original function as key metabolites or active participants in reactive ion species scavenging have a high chance of becoming intercellular signalling molecules. Naturally, the evolution of machinery to transduce a message across the plasma membrane is necessary. This fact is demonstrated by three other well-studied animal intercellular signalling molecules, namely serotonin, dopamine, and acetylcholine, for which there is currently no evidence that they act as intercellular signalling molecules in plants.
Publisher: Cold Spring Harbor Laboratory
Date: 25-08-2017
DOI: 10.1101/180992
Abstract: Isolated nuclei provide access to early steps in gene regulation involving chromatin as well as transcript production and processing. Here we describe transfer of the Isolation of N uclei from TA gged specific C ell T ypes (INTACT) to the monocot rice ( Oryza sativa L.). The purification of biotinylated nuclei was redesigned by replacing the outer nuclear envelope-targeting domain of the Nuclear Tagging Fusion (NTF) protein with an outer nuclear envelope-anchored domain. This modified NTF was combined with codon optimized E. coli BirA in a single T-DNA construct. We also developed inexpensive methods for INTACT, T-DNA insertion mapping and profiling of the complete nuclear transcriptome, including a rRNA degradation procedure that minimizes pre-rRNA transcripts. A high-resolution comparison of nuclear and steady-state poly (A) + transcript populations of seedling root tips confirmed the capture of pre-mRNA and exposed distinctions in ersity and abundance of the nuclear and total transcriptomes. This retooled INTACT can enable high-resolution monitoring of the nuclear transcriptome and chromatin in specific cell-types of rice and other species. Improved technology and methodology for affinity purification of nuclei and analysis of nuclear transcriptomes, chromatin and other nuclear components.
Publisher: Cold Spring Harbor Laboratory
Date: 28-05-2020
DOI: 10.1101/2020.05.25.114439
Abstract: Plants lacking phytochrome photoreceptors display elevated soluble sugar levels in leaves. Although pathogens principally feed on sugars supplied by the plant, the link between increased plant sugar levels upon phytochrome inactivation and disease development has not been considered. Tomato plants were exposed to control white LED (WL) or a combination of white and far-red LED (WL+FR) light, to inactivate phytochrome signaling and modulate soluble sugar levels. We also experimentally manipulated internal sugar levels by either supplementing glucose or inhibiting photosynthesis in tomato leaflets prior to performing soluble sugar quantifications or bioassays with pathogens. Tomato plants exposed to WL+FR or lacking phytochrome B ( phyB1phyB2 double mutants) show enhanced levels of soluble sugars, especially glucose and fructose, in their leaves. The jasmonic acid biosynthesis mutant def1 also has elevated soluble sugar levels, which could be rescued by exogenous methyl-jasmonate application. This indicates an interplay between JA signaling and primary metabolism. The increase in soluble sugar levels in tomato leaves upon phytochrome inactivation is regulated in a JA-dependent manner. Our data stress the importance of primary metabolism in the FR-induced susceptibility in tomato that could contribute to promote plant resistance when grown at high density.
Publisher: Wiley
Date: 16-01-2020
DOI: 10.1111/TPJ.14632
Publisher: Wiley
Date: 12-07-2021
DOI: 10.1111/PCE.14143
Abstract: Plants transitioned from an aquatic to a terrestrial lifestyle during their evolution. On land, fluctuations on water availability in the environment became one of the major problems they encountered. The appearance of morpho‐physiological adaptations to cope with and tolerate water loss from the cells was undeniably useful to survive on dry land. Some of these adaptations, such as carbon concentrating mechanisms (CCMs), desiccation tolerance (DT) and root impermeabilization, appeared in multiple plant lineages. Despite being crucial for evolution on land, it has been unclear how these adaptations convergently evolved in the various plant lineages. Recent advances on whole genome and transcriptome sequencing are revealing that co‐option of genes and gene regulatory networks (GRNs) is a common feature underlying the convergent evolution of these adaptations. In this review, we address how the study of CCMs and DT has provided insight into convergent evolution of GRNs underlying plant adaptation to dry environments, and how these insights could be applied to currently emerging understanding of evolution of root impermeabilization through different barrier cell types. We discuss ex les of co‐option, conservation and innovation of genes and GRNs at the cell, tissue and organ levels revealed by recent phylogenomic (comparative genomic) and comparative transcriptomic studies.
Publisher: Wiley
Date: 04-09-2020
DOI: 10.1111/PCE.13870
Publisher: American Society for Microbiology
Date: 30-10-2014
Abstract: Here, we present the draft genome of Rhizobium rhizogenes strain ATCC 15834. The genome contains 7,070,307 bp in 43 scaffolds. R. rhizogenes , also known as Agrobacterium rhizogenes , is a plant pathogen that causes hairy root disease. This hairy root induction has been used in biotechnology for the generation of transgenic root cultures.
Publisher: Wiley
Date: 2010
Publisher: Cold Spring Harbor Laboratory
Date: 28-01-2022
DOI: 10.1101/2022.01.28.478192
Abstract: Plants detect their neighbors via various cues, including reflected light and touching of leaf tips, which elicit in upward leaf movement (hyponasty). It is currently unknown how touch is sensed and how the signal is transferred from the leaf tip to the petiole base that drives hyponasty. Here, we show that touch-induced hyponasty involves a signal transduction pathway that is distinct from light-mediated hyponasty. We found that mechanostimulation of the leaf tip upon touching causes cytosolic calcium ([Ca 2+ ] cyt induction in leaf tip trichomes that spreads towards the petiole. Both perturbation of the calcium response and the absence of trichomes inhibit touch-induced hyponasty. Finally, using plant competition assays, we show that touch-induced hyponasty is adaptive in dense stands of Arabidopsis. We thus establish a novel, adaptive mechanism regulating hyponastic leaf movement in response to mechanostimulation by neighbors in dense vegetation.
Publisher: Elsevier BV
Date: 06-2021
DOI: 10.1016/J.CELL.2021.04.024
Abstract: Plant species have evolved myriads of solutions, including complex cell type development and regulation, to adapt to dynamic environments. To understand this cellular ersity, we profiled tomato root cell type translatomes. Using xylem differentiation in tomato, ex les of functional innovation, repurposing, and conservation of transcription factors are described, relative to the model plant Arabidopsis. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Comparative translatome analyses of rice, tomato, and Arabidopsis cell populations suggest increased expression conservation of root meristems compared with other homologous populations. In addition, the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher order properties of cell type and pan-cell type regulation are evolutionarily conserved between plants and animals.
Publisher: Oxford University Press (OUP)
Date: 11-06-2010
Abstract: C4 photosynthesis involves alterations to the biochemistry, cell biology, and development of leaves. Together, these modifications increase the efficiency of photosynthesis, and despite the apparent complexity of the pathway, it has evolved at least 45 times independently within the angiosperms. To provide insight into the extent to which gene expression is altered between C3 and C4 leaves, and to identify candidates associated with the C4 pathway, we used massively parallel mRNA sequencing of closely related C3 (Cleome spinosa) and C4 (Cleome gynandra) species. Gene annotation was facilitated by the phylogenetic proximity of Cleome and Arabidopsis (Arabidopsis thaliana). Up to 603 transcripts differ in abundance between these C3 and C4 leaves. These include 17 transcription factors, putative transport proteins, as well as genes that in Arabidopsis are implicated in chloroplast movement and expansion, plasmodesmatal connectivity, and cell wall modification. These are all characteristics known to alter in a C4 leaf but that previously had remained undefined at the molecular level. We also document large shifts in overall transcription profiles for selected functional classes. Our approach defines the extent to which transcript abundance in these C3 and C4 leaves differs, provides a blueprint for the NAD-malic enzyme C4 pathway operating in a dicotyledon, and furthermore identifies potential regulators. We anticipate that comparative transcriptomics of closely related species will provide deep insight into the evolution of other complex traits.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 18-03-2011
Abstract: Recurrent evolution of C 4 photosynthesis is due to conserved regulatory sequences that localize photosynthetic enzymes.
Publisher: Cold Spring Harbor Laboratory
Date: 10-04-2020
DOI: 10.1101/2020.04.09.017285
Abstract: Plant species have evolved myriads of solutions to adapt to dynamic environments, including complex cell type development and regulation. To understand this ersity, we profiled tomato root cell type translatomes and chromatin accessibility. Using xylem differentiation in tomato, relative to Arabidopsis, ex les of functional innovation, repurposing and conservation of transcription factors are described. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Translatome analyses of rice, tomato and Arabidopsis tissues suggest that root meristems are more conserved, and that the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher-order properties of cell type and pan-cell type regulation are conserved between plants and animals. Pan-species cell type translatome and chromatin accessibility data reveal novelty, conservation and repurposing of gene function.
Publisher: Oxford University Press (OUP)
Date: 11-12-2017
DOI: 10.1105/TPC.17.00581
Publisher: Oxford University Press (OUP)
Date: 24-07-2021
Abstract: Plants detect neighboring competitors through a decrease in the ratio between red and far-red light (R:FR). This decreased R:FR is perceived by phytochrome photoreceptors and triggers shade avoidance responses such as shoot elongation and upward leaf movement (hyponasty). In addition to promoting elongation growth, low R:FR perception enhances plant susceptibility to pathogens: the growth–defense tradeoff. Although increased susceptibility in low R:FR has been studied for over a decade, the associated timing of molecular events is still unknown. Here, we studied the chronology of FR-induced susceptibility events in tomato (Solanum lycopersicum) plants pre-exposed to either white light (WL) or WL supplemented with FR light (WL+FR) prior to inoculation with the necrotrophic fungus Botrytis cinerea (B.c.). We monitored the leaf transcriptional changes over a 30-h time course upon infection and followed up with functional studies to identify mechanisms. We found that FR-induced susceptibility in tomato is linked to a general d ening of B.c.-responsive gene expression, and a delay in both pathogen recognition and jasmonic acid-mediated defense gene expression. In addition, we found that the supplemental FR-induced ethylene emissions affected plant immune responses under the WL+FR condition. This study improves our understanding of the growth–immunity tradeoff, while simultaneously providing leads to improve tomato resistance against pathogens in dense cropping systems.
Publisher: Cold Spring Harbor Laboratory
Date: 21-01-2021
DOI: 10.1101/2021.01.21.427668
Abstract: Plants detect neighboring competitors through a decrease in the ratio between red and far-red light (R:FR). This decreased R:FR is perceived by phytochrome photoreceptors and triggers shade avoidance responses such as shoot elongation and upward leaf movement (hyponasty). In addition to promoting elongation growth, low R:FR perception enhances plant susceptibility to pathogens: the growth-defense trade-off. Although increased susceptibility in low R:FR has been studied for over a decade, the associated timing of molecular events is still unknown. Here, we studied the chronology of FR-induced susceptibility events in tomato plants pre-exposed to either white light (WL) or WL supplemented with FR light (WL+FR) prior to inoculation with the necrotrophic fungus Botrytis cinerea ( B.c. ). We monitored the leaf transcriptional changes over a 30-hr time course upon infection and followed up with functional studies to identify mechanisms. We found that FR-induced susceptibility in tomato is linked to a general d ening of B.c.- responsive gene expression, and a delay in both pathogen recognition and jasmonic acid-mediated defense gene expression. In addition, we found that the supplemental FR-induced ethylene emissions affect plant immune responses under WL+FR conditions. This study increases our understanding of the growth-immunity trade-off, while simultaneously providing leads to improve tomato resistance against pathogens in dense cropping systems. Low Red:Far-red ratio enhances tomato susceptibility towards the necrotrophic fungus Botrytis cinerea via delayed early pathogen detection and d ening of jasmonic acid-mediated defense activation.
Publisher: Wiley
Date: 10-02-2017
DOI: 10.1111/NPH.14448
Abstract: Plant secondary cell walls constitute the majority of plant biomass. They are predominantly found in xylem cells, which are derived from vascular initials during vascularization. Little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well‐annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition. Here we generated tissue‐specific transcriptome and DNA methylome data from sorghum shoots, roots and developing root vascular and nonvascular tissues. Many genes associated with vascular development in other species show enriched expression in developing vasculature. However, several transcription factor families varied in vascular expression in sorghum compared with Arabidopsis and maize. Furthermore, differential expression of genes associated with DNA methylation were identified between vascular and nonvascular tissues, implying that changes in DNA methylation are a feature of sorghum root vascularization, which we confirmed using tissue‐specific DNA methylome data. Roots treated with a DNA methylation inhibitor also showed a significant decrease in root length. Tissues and organs can be discriminated based on their genomic methylation patterns and methylation context. Consequently, tissue‐specific changes in DNA methylation are part of the normal developmental process.
Publisher: Wiley
Date: 14-10-2011
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Kaisa Kajala.