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Results for “Plant Biology”

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bioRxiv2018

Organ-wide and ploidy-dependent regulations both contribute to cell size determination: evidence from a computational model of tomato fruit

The development of a new organ is the result of coordinated events of cell division and expansion, in strong interaction with each other. This paper presents a dynamic model of tomato fruit development that includes cells division, endoreduplication and expansion processes. The model is used to investigate the interaction among these developmental processes, in the perspective of a neo-cellular theory. In particular, different control schemes (either cell-autonomous or organ-controlled) are tested and results compared to observed data from two contrasted genotypes. The model shows that a pure cell-autonomous control fails to reproduce the observed cell size distribution, and an organ-wide control is required in order to get realistic cell sizes. The model also supports the role of endoreduplication as an important determinant of the final cell size and suggests a possible interaction through carbon allocation and metabolism.

plant biology↗

bioRxiv2018

Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation

Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell - vegetative cell (VC) - of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation.

plant biology↗

bioRxiv2018

Glycerol phosphate acyltransferase 6 controls filamentous pathogen interactions and cell wall properties of the tomato and Nicotiana benthamiana leaf epidermis

The leaf epidermal wall is covered by a cuticle, composed of cutin and waxes, which protects against dehydration and constitutes a barrier against pathogen attack. Cutin monomers are formed by the transfer of 16- or 18-carbon fatty acids to glycerol by glycerol-3-phosphate acyltransferase (GPAT) enzymes, which facilitates their transport to the plant surface. Here we address the dual functionality of pathogen-inducible Glycerol phosphate acyltransferase 6 (GPAT6) in controlling pathogen entry and dehydration in leaves. Silencing of Nicotiana benthamiana NbGPAT6a increased leaf susceptibility to the oomycetes Phytophthora infestans and P. palmivora, whereas stable overexpression of NbGPAT6a-GFP rendered leaves more resistant to infection. A loss-of-function mutation of the orthologous gene in tomato (Solanum lycopersicum), SlGPAT6, similarly resulted in increased susceptibility of leaves to Phytophthora infection concomitant with altered intracellular infection structure morphology. Conversely, Botrytis cinerea disease symptoms were reduced. Modulation of GPAT6 expression predominantly altered the outer cell wall of leaf epidermal cells. The impaired cell wall-cuticle continuum of tomato gpat6-a mutants resulted in increased water loss and these plants had fewer stomata. Our work highlights a hitherto unknown role for GPAT6-generated cutin monomers in controlling epidermal cell properties that are integral to leaf-microbe interactions and limit dehydration.

plant biology↗

bioRxiv2018

Pinnularia baetica sp. nov. (Bacillarophyceae): a new diatom species found in an alkaline mountain lagoon in the south of Europe (Granada, Spain)

A new benthic freshwater diatom species belonging to the genus Pinnularia was found in Laguna Seca of Sierra Seca in the north of the province of Granada, Spain. Pinnularia baetica sp.nov. is proposed as a new species based on observations under light (LM) and scanning electron microscopy (SEM) and its special ecology typical of a calcareous lagoon. The most similar taxa to P. baetica is P. atlasii and with more differences P. infirma and the last two were studied through material obtained in lagoons of northern Morocco. Although there are similarities in the morphological characters of the frustule, it was possible to verify through LM and SEM micrographs, evident differences between P. baetica and the other two taxa; on the one end, P. baetica has a panduriform shape more pronounced than P. infirma and bigger size. On the other hand, the absence of spines in P. baetica and the more convergent striation at the poles are the main differences with P. atlasi.\n\nPhylum Ochrophyta Caval.-Sm. (Cavalier-Smith 1995)\n\nClass Bacillariophyceae Haeckel emend. Medlin & Kaczmarska (Medlin & Kaczmarska 2004)\n\nSubclass Bacillariophycidae Round (Round et al. 1990)\n\nOrder Naviculales (Bessey 1907 sensu emend)\n\nFamily Pinnulariaceae D.G. Mann, 1990, Genus Pinnularia C.G. Ehrenberg, 1843\n\nPinnularia baetica Fernandez Moreno & Sanchez Castillo sp. nov

plant biology↗

bioRxiv2018

Ethnobotanical and nutritional study of quelites sold in two traditional markets of Oaxaca, Mexico

Background.In Mexico, it is called quelites to certain edible vegetables (young plants, germ, shoots or flowers). Since pre-Hispanic times, quelites have been eaten as a source of vitamins, minerals and proteins. Now, its traditional and healthy consumption has decreased. We studied the quelites of two traditional markets in the Valles Centrales of Oaxaca state, Mexico using an ethnobotanical and nutritional approach.\n\nMethodsFrom July 2017 to July 2018, weekly ethnobotanical interviews were conducted with 26 collectors-sellers of the Zimatlan market and 36 in the Zaachila market. The vegetal supply was acquired, herborized and identified by through dichotomous keys. There were determined the proximal composition, phenolic compounds, flavonoids, antioxidant capacity and mineral content of the floral structures of two quelites types. The statistical analysis was performed through a one-way analysis of variance (ANOVA) of Tukey HSD.\n\nResultsIn two sampled markets, 23 species belonging to 11 botanical families were registered, from which leaves, branches, stems, flowers and fruits are eaten. The flowers of the species Diphysa americana (Q1) and Phaseolus coccineus (Q2) are the most used for human consumption of the communities involved in the sale of the sampled quelites. Both flowers had important amounts of proteins (2.66-3.29%) and fiber (1.66-2.43%). Q1 had higher content of phenols and flavonoids and therefore higher antioxidant capacity than Q2 (p <0.05). When we talk about Q2 minerals, it presented a greater amount of Zn, Ca and Mg in comparison to Q1 (p> 0.05).\n\nConclusionsIn local markets of the state of Oaxaca, a wide variety of quelites are usually found, where their botanical structures, such as flowers, are widely eaten. The flowers of Q1 and Q2 proved to be a rich source of proteins and bioactive compounds, as well as minerals. Showing thus to be a food alternative to enrich the human diet.

plant biology↗

bioRxiv2018

N-terminal β-strand underpins biochemical specialization of an ATG8 isoform

ATG8 is a highly-conserved ubiquitin-like protein that modulates autophagy pathways by binding autophagic membranes and numerous proteins, including cargo receptors and core autophagy components. Throughout plant evolution, ATG8 has expanded from a single protein in algae to multiple isoforms in higher plants. However, the degree to which ATG8 isoforms have functionally specialized to bind distinct proteins remains unclear. Here, we describe a comprehensive protein-protein interaction resource, obtained using in planta immunoprecipitation followed by mass spectrometry, to define the potato ATG8 interactome. We discovered that ATG8 isoforms bind distinct sets of plant proteins with varying degrees of overlap. This prompted us to define the biochemical basis of ATG8 specialization by comparing two potato ATG8 isoforms using both in vivo protein interaction assays and in vitro quantitative binding affinity analyses. These experiments revealed that the N-terminal {beta}-strand--and, in particular, a single amino acid polymorphism--underpins binding specificity to the substrate PexRD54 by shaping the hydrophobic pocket that accommodates this proteins ATG8 interacting motif. Additional proteomics experiments indicated that the N-terminal {beta}-strand shapes the ATG8 interactor profiles, defining interaction specificity with about 80 plant proteins. Our findings are consistent with the view that ATG8 isoforms comprise a layer of specificity in the regulation of selective autophagy pathways in plants.

plant biology↗

bioRxiv2018

Hypermorphic SERK1 mutations function via a SOBIR1 pathway to activate floral abscission signaling

In Arabidopsis, the abscission of floral organs is regulated by two related receptor-like protein kinases (RLKs), HAESA and HAESA-like 2 (HAE/HSL2). HAE/HSL2, in complex with members of the SERK family of coreceptor protein kinases, are activated by the binding of the proteolytically processed peptide ligand IDA. This leads to expression of genes encoding secreted cell wall remodeling and hydrolase enzymes. hae hsl2 mutants fail to induce expression of these genes and retain floral organs indefinitely. In this paper we report identification of an allelic series of hae hsl2 suppressor mutations in the SERK1 coreceptor protein kinase gene. Genetic and transcriptomic evidence indicates these alleles represent a novel class of gain of function mutations that activate signaling independent of HAE/HSL2. We show that the suppression effect surprisingly does not rely on protein kinase activity of SERK1, and that activation of signaling relies on the RLK gene SOBIR1. The effect of these mutations can be mimicked by loss of function of BIR1, a known negative regulator of SERK-SOBIR1 signaling. These results suggest BIR1 functions to negatively regulate SERK-SOBIR1 signaling during abscission, and that the identified SERK1 mutations likely interfere with this negative regulation.

plant biology↗

bioRxiv2018

Effects of the Salinity under Soilless Culture Systems on Gamma Linolenic Acid Levels in Borage Seed Oil

Borage is a well-known plant of great importance in human nutrition and health. Expanding knowledge of particular plants that have anti-cancer products is a global concern. There is substantial information regarding the benefits, presence and extraction of gamma linolenic acid (GLA) in different plants around the world, especially in borage seeds. However, there is little information concerning the effects of the salinity of the nutrient solution on the growth and presence of GLA in borage seeds. The objective of this work was to determine the optimal salinity of the nutrient solution for obtaining GLA in soilless cultivation systems. Borage plants were grown in coconut fibre and provided three treatments of nutrient solution of 2.20, 3.35 and 4.50 dS m-1, increasing solution salinity with the standard nutrient solution of concentrated macronutrients as a reference. Vegetative growth, seed production and GLA ratio were measured. The results of vegetative development and GLA production doubled and tripled with the increase in salinity of the nutrient solution, respectively.

plant biology↗

bioRxiv2018

Use of a visible reporter marker- myb-related gene in crop plants to minimize herbicide usage against weeds

Weeds, a main threat to agricultural productivity worldwide, are mostly controlled by herbicides. To minimize herbicide usage by targeting it to weedy areas, we developed a new image-based methodology for robust weed detection that relies on manipulating the crop plants leaf hue, without affecting crop fitness. We generated transgenic tobacco (Nicotiana tabacum Xanthi) lines overexpressing anthocyanin pigment as a traceable marker that differentiates transgenes from the surrounding weeds at an early stage. Transformation with the anthocyanin VlmybA1-2 gene produced purple-colored leaves. Subsequent gene silencing with vector pTRV2:VlmybA1-2 significantly reduced anthocyanin pigments in tobacco leaves 40 days after agroinfiltration, with a concomitant reduction in VlmybA1-2 transcript levels. Purple hue faded gradually, and there were no fitness costs in terms of plant height or leaf number in the silenced vs. non-silenced tobacco transgenes. These results could lead to a new sustainable weed-control method that will alleviate weed-related ecological, agricultural and economic issues.

plant biology↗

bioRxiv2018

Comparative transcriptome analysis reveals higher expression of stress and defense responsive genes in dwarf soybeans obtained from the crossing of G. max and G. soja

Plant height is an important component of plant architecture and significantly affects crop breeding practices and yield. We obtained a few segregated dwarf soybeans in the populations derived from the crossing of Glycine max var. Peking and Glycine soja var. IT182936 in an F5 RIL population. These dwarf soybeans may be useful genetic resources for plant breeders, geneticists and biologists. We attempted to find differentially expressed genes to classify and understand the regulation of genes related to plant growth in mutant dwarf soybeans, which appeared in the F5 generation. Using the Illumina high-throughput platform, transcriptomes were generated and compared among normal and dwarf soybeans in triplicate. We found complex relationship of the expressed genes to plant growth. There are highly significantly up-/downregulated genes according to the comparison of gene expression in normal and dwarf soybeans. The genes related to disease and stress responses were found to be upregulated in dwarf soybeans. Such over-expression of disease resistance and other immune response genes was targeted to understand how the immune genes regulate the response of plant growth. In addition, photosynthesis-related genes showed very low expression in dwarf lines. The transcriptome expression and genes classified as related to plant growth may be useful resources to researchers studying plant growth.

plant biology↗

bioRxiv2018

A curated list of genes that control elemental accumulation in plants.

Understanding the mechanisms underlying plants adaptation to their environment will require knowledge of the genes and alleles underlying elemental composition. Modern genetics is capable of quickly, and cheaply indicating which regions of DNA are associated with particular phenotypes in question, but most genes remain poorly annotated, hindering the identification of candidate genes. To help identify candidate genes underlying elemental accumulations, we have created the known ionome gene (KIG) list: a curated collection of genes experimentally shown to change uptake, accumulation, and distribution of elements. We have also created an automated computational pipeline to generate lists of KIG orthologs in other plant species using the PhytoMine database. The current version of KIG consists of 176 known genes covering 5 species, 23 elements and their 1588 orthologs in 10 species. Analysis of the known genes demonstrated that most were identified in the model plant Arabidopsis thaliana, and that transporter coding genes and genes altering the accumulation of iron and zinc are overrepresented in the current list.

plant biology↗

bioRxiv2018

Identification of transcription factors regulating senescence in wheat through gene regulatory network modelling

Senescence is a tightly regulated developmental programme which is coordinated by transcription factors. Identifying these transcription factors in crops will provide opportunities to tailor the senescence process to different environmental conditions and regulate the balance between yield and grain nutrient content. Here we use ten time points of gene expression data alongside gene network modelling to identify transcription factors regulating senescence in polyploid wheat. We observe two main phases of transcription changes during senescence: early downregulation of housekeeping and metabolic processes followed by upregulation of transport and hormone related genes. We have identified transcription factor families associated with these early and later waves of differential expression. Using gene regulatory network modelling alongside complementary publicly available datasets we identified candidate transcription factors for controlling senescence. We validated the function of one of these candidate transcription factors in senescence using wheat chemically-induced mutants. This study lays the ground work to understand the transcription factors which regulate senescence in polyploid wheat and exemplifies the integration of time-series data with publicly available expression atlases and networks to identify candidate regulatory genes.

plant biology↗

bioRxiv2018

CCA1 and ATAF2 differentially suppress cytochrome P450-mediated brassinosteroid inactivation in Arabidopsis

Brassinosteroids (BRs) are a group of steroid hormones regulating plant growth and development. Since BRs do not undergo transport among plant tissues, their metabolism is tightly regulated by transcription factors (TFs) and feedback loops. BAS1 (CYP734A1, formerly CYP72B1) and SOB7 (CYP72C1) are two BR-inactivating cytochrome P450s identified in Arabidopsis thaliana. We previously found that a TF ATAF2 (ANAC081) suppresses BAS1 and SOB7 expression by binding to the Evening Element (EE) and CCA1-binding sites (CBS) on their promoters. Both EE and CBS are known binding targets of the core circadian clock regulatory protein CCA1. Here, we confirm that CCA1 binds the EE and CBS motifs on BAS1 and SOB7 promoters, respectively. Elevated accumulations of BAS1 and SOB7 transcripts in the CCA1 null mutant cca1-1 indicate that CCA1 is a repressor of their expression. When compared to either cca1-1 or the ATAF2 null mutant ataf2-2, the cca1-1 ataf2-2 double mutant shows higher SOB7 transcript accumulations and stronger BR-insensitive phenotype of hypocotyl elongation in white light. CCA1 interacts with ATAF2 at both DNA-protein and protein-protein levels. ATAF2, BAS1 and SOB7 are all circadian-regulated with distinct expression patterns. These results demonstrate that CCA1 and ATAF2 differentially suppress BAS1- and SOB7-mediated BR inactivation.\n\nHighlightThe core circadian regulator CCA1 is a direct repressor of brassinosteroid inactivating genes BAS1 and SOB7, and interact with another repressor, ATAF2. Their differential suppressing effects are regulated by light.\n\nAbbreviations3-aminotriazole (3-AT), brassinolide (BL), brassinosteroid (BR), CCA1-binding site (CBS), cytochrome P450 (P450), Evening Element (EE), transcription factor (TF), yeast one-hybrid (Y1H), yeast two-hybrid (Y2H)

plant biology↗

bioRxiv2018

The complete plastid genomes of four species from Brassicales

Brassicales is a diverse angiosperm order with about 4,700 recognized species. Here, we assembled and described the complete plastid genomes from four species of Brassicales: Capparis urophylla F.Chun (Capparaceae), Carica papaya L. (Caricaceae), Cleome rutidosperma DC. (Cleomaceae), and Moringa oleifera Lam. (Moringaceae), including two plastid genomes newly assembled for two families (Capparaceae and Moringaceae). The four plastid genomes are 159,680 base pairs on average in length and encode 78 protein-coding genes. The genomes each contains a typical structure of a Large Single-Copy (LSC) region and a Small Single-Copy (SSC) region separated by two Inverted Repeat (IR) regions. We performed the maximum-likelihood (ML) phylogenetic analysis using three different data sets of 66 protein-coding genes (ntAll, ntNo3rd and AA). Our phylogenetic results from different dataset are congruent, and are consistent with previous phylogenetic studies of Brassiales.

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↗

bioRxiv2018

Efficient reverse breeding by VIGS-mediated transient crossover reduction

F1 heterozygotes are traditionally generated by crossing homozygous parental lines. The opposite is achieved through reverse breeding, in which parental lines are generated from a heterozygote. Reverse breeding can be used to develop new F1 hybrid varieties without having prior access to homozygous breeding lines. For successful reverse breeding, the heterozygotes homologous chromosomes must be divided over two haploid complements, which is achieved by suppression of meiotic crossover (CO) recombination. We here show two innovations that facilitate efficient reverse breeding. Firstly, we demonstrate that downregulation of CO rates can be accomplished using virus-induced gene silencing (VIGS). We obtain transgene-free parental lines for a heterozygote in just two generations. Secondly, we show that incomplete CO suppression opens up several alternative strategies for the preservation of hybrid phenotypes through reverse breeding.

plant biology↗

bioRxiv2018

Taxonomy, ecology and distribution of Juniperus oxycedrus L. group in the Mediterranean Region using morphometric, phytochemical and bioclimatic approaches.

The ecology, taxonomy and distribution of the Juniperus oxycedrus L. group of taxa are studied. From an ecological aspect, this work proposes a new ombroedaphoxeric index to explain the presence of populations of Juniperus in ombrotypes that are not the optimum for these taxa. The controversy among various authors on the taxonomy of the oxycedrus group with regard to J. oxycedrus subsp. badia and J. oxycedrus subsp. lagunae is clarified. The phytochemical differences in essential oils are addressed, and their similarities analysed; greater similarities are observed between oxycedrus and badia (H. Gay) Debeaux, and between navicularis Grand. and macrocarpa (Sm.) Ball. The phytochemical, molecular and distribution differences allow J. macrocarpa and J. navicularis to be maintained as species.

plant biology↗

bioRxiv2018

Convergent recruitment of life cycle regulators to direct sporophyte development in two eukaryotic supergroups

Three amino acid loop extension homeodomain transcription factors (TALE HD TFs) act as life cycle regulators in green algae and land plants. In mosses these regulators are required for the deployment of the sporophyte developmental program. We demonstrate that mutations in either of two TALE HD TF genes, OUROBOROS or SAMSARA, in the brown alga Ectocarpus result in conversion of the sporophyte generation into a gametophyte. The OUROBOROS and SAMSARA proteins heterodimerise in a similar manner to TALE HD TF life cycle regulators in the green lineage. These observations demonstrate that TALE-HD-TF-based life cycle regulation systems have an extremely ancient origin, and that these systems have been independently recruited to regulate sporophyte developmental programs in at least two different complex multicellular eukaryotic supergroups, Archaeplastida and Chromalveolata.

plant biology↗