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bioRxiv2018

WUSCHEL acts as a rheostat on the auxin pathway to maintain apical stem cells in Arabidopsis

To maintain the balance between long-term stem cell self-renewal and differentiation, dynamic signals need to be translated into spatially precise and temporally stable gene expression states. In the apical plant stem cell system, local accumulation of the small, highly mobile phytohormone auxin triggers differentiation while at the same time, pluripotent stem cells are maintained throughout the entire life-cycle. We find that stem cells are resistant to auxin mediated differentiation, but require low levels of signaling for their maintenance. We demonstrate that the WUSCHEL transcription factor confers this behavior by rheostatically controlling the auxin signaling and response pathway. Finally, we show that WUSCHEL acts via regulation of histone acetylation at target loci, including those with functions in the auxin pathway. Our results reveal an important mechanism that allows cells to differentially translate a potent and highly dynamic developmental signal into stable cell behavior with high spatial precision and temporal robustness.

plant biology↗

bioRxiv2018

From spatio-temporal morphogenetic gradients to rhythmic patterning at the shoot apex

Rhythmic patterning is central to the development of eukaryotes, particularly in plant shoot post-embryonic development. The plant hormone auxin drives rhythmic patterning at the shoot apical meristem, but the spatio-temporal dynamics of the auxin gradients is unknown. We used quantitative imaging to demonstrate that auxin provides high-definition graded information not only in space but also in time. We provide evidence that developing organs are auxin-emitting centers that could self-organize spatio-temporal auxin gradients through a transport network converging on the meristem center. We further show that a memory of the exposition of cells to auxin allows to differentiate temporally sites of organ initiation, providing a remarkable example of how the dynamic redistribution of a morphogenetic regulator can be used to create rhythmicity.

plant biology↗

bioRxiv2018

A novel model plant to study the light control of seed germination

Timing of seed germination is crucial for seed plants and coordinated by internal and external cues, reflecting adaptations to different habitats. Physiological and molecular studies with lettuce and Arabidopsis thaliana have documented a strict requirement for light to initiate germination and identified many receptors, signalling cascades, and hormonal control elements. In contrast, seed germination of several other plants is inhibited by light, but the molecular basis of this converse response is unknown. We describe Aethionema arabicum (Brassicaceae) as a suitable model plant to investigate the mechanism of germination inhibition by light, as it comprises accessions with natural variation between light-sensitive and light-neutral responses. Inhibition is independent of light wavelength and increases with light intensity and duration. Gibberellins and abscisic acid are involved in the control of germination as in Arabidopsis, but transcriptome comparisons of light- and dark-exposed Aethionema arabicum seeds revealed that expression of genes for key regulators upon light exposure undergo converse changes, resulting in antipodal hormone regulation. This illustrates that similar modular components of a pathway in light-inhibited, light-neutral and light requiring germination among the Brassicaceae have been assembled by evolution to produce divergent pathways, likely as adaptive traits.\n\nHighlightIn contrast to light requirement for Arabidopsis seed germination, germination of several Aethionema arabicum accessions is inhibited by light, due to antipodal transcriptional regulation of hormone balance.

plant biology↗

bioRxiv2018

PERPETUAL FLOWERING2 coordinates the vernalization response and perennial flowering in Arabis alpina

The floral repressor APETALA2 (AP2) in Arabidopsis regulates flowering through the age pathway. The AP2 orthologue in the alpine perennial Arabis alpina, PERPETUAL FLOWERING 2 (PEP2), was previously reported to regulate flowering through the vernalization pathway by enhancing the expression of another floral repressor PERPETUAL FLOWERING 1 (PEP1), the orthologue of Arabidopsis FLOWERING LOCUS C (FLC). However, PEP2 also regulates flowering independently of PEP1. To characterize the function of PEP2 we analyzed the transcriptomes of pep2 and pep1 mutants. The majority of differentially expressed genes were detected between pep2 and the wild type or between pep2 and pep1, highlighting the importance of the PEP2 role that is independent of PEP1. Here we demonstrate that PEP2 prevents the upregulation of the A. alpina floral meristem identity genes FRUITFUL (AaFUL), LEAFY (AaLFY) and APETALA1 (AaAP1) which ensure floral commitment during vernalization. Young pep2 seedlings respond to vernalization, suggesting that PEP2 regulates the age-dependent response to vernalization independently of PEP1. The major role of PEP2 through the PEP1-dependent pathway takes place after vernalization, when it facilitates PEP1 activation both in the main shoot apex and in the axillary branches. These multiple roles of PEP2 in vernalization response contribute to the A. alpina life-cycle.\n\nHIGHLIGHTThe Arabis alpina APETALA2 orthologue, PERPETUAL FLOWERING2, regulates the age-dependent response to vernalization and it is required to facilitate the activation of the A. alpina FLOWERING LOCUS C after vernalization.

plant biology↗

bioRxiv2018

Effect of simulated microgravity on gene expression during embryogenesis of Arabidopsis thaliana

Gravitational force is one of environmental factors that influence growth and development of plants. Changes in this force, including microgravity, can be one of the stress factor which plants have to adapt to cope with. That kind of stress can lead to several abnormalities such as chromosomal breakage, morphological abnormalities or changes in gene expression. The aim of this study was to examine the influence of simulated microgravity on gene expression of Arabidopsis thaliana embryos by use Random Positioning Machine (RPM). RPM is laboratory facility that can generate conditions comparable to the true microgravity. This paper studies effect of simulated microgravity on expression of genes which are involved in plant embryogenesis (LEAFY COTYLEDON, LATE EMBRYOGENESIS ABUNDANT), antioxidative system (CATALASE), mechanical stimuli (TOUCH) and gravitropism (SCARECROW, SHOOT GRAVITROPISM2). Changes in gene expression were detected using quantitative real-time PCR (qRT-PCR). Several of tested genes had increased transcript levels after the influence of simulated microgravity. Specifically, catalase (CAT3), LECs (LEC1), touch (TCH2/CML24), and gravitropism (SGR2) genes achieved significantly increased relative expression (level [≥] 2). The changes in the levels of expression on embryos of Arabidopsis depend on the type of genes and principally on the timing of the influence of the simulated microgravity.

plant biology↗

bioRxiv2018

In vivo phosphatidylserine variations steer Rho GTPase signaling in a cell-context dependent manner

AbstractRho GTPases are master regulators of cell signaling, but how they are regulated depending on the cellular context is unclear. Here, we show that the phospholipid phosphatidylserine acts as a developmentally-controlled lipid rheostat that tunes Rho GTPase signaling in Arabidopsis. Live super-resolution single molecule imaging revealed that RHO-OF-PLANT6 (ROP6) is stabilized by phosphatidylserine into plasma membrane (PM) nanodomains, which is required for auxin signaling. Furthermore, we uncovered that the PM phosphatidylserine content varies during plant root development and that the level of phosphatidylserine modulates the quantity of ROP6 nanoclusters induced by auxin and hence downstream signaling, including regulation of endocytosis and gravitropism. Our work reveals that variations in phosphatidylserine levels are a physiological process that may be leveraged to regulate small GTPase signaling during development.\n\nOne Sentence SummaryPhosphatidylserine acts as a developmentally-controlled lipid rheostat that regulates cellular auxin sensitivity and plant development.

plant biology↗

bioRxiv2018

Common garden experiment reveals altered nutritional values and DNA methylation profiles in micropropagated three elite Ghanaian sweet potato genotypes

Micronutrient deficiency is the cause of multiple diseases in developing countries. Staple crop biofortification is an efficient means to combat such deficiencies in the diets of local consumers. Biofortified lines of sweet potato (Ipomoea batata L. Lam) with enhanced beta-carotene content have been developed in Ghana to alleviate Vitamin A Deficiency. These genotypes are propagated using meristem micropropagation to ensure the generation of virus-free propagules. In vitro culture exposes micropropagated plants to conditions that can lead to the accumulation of somaclonal variation with the potential to generate unwanted aberrant phenotypes. However, the effect of micropropagation induced somaclonal variation on the production of key nutrients by field-grown plants has not been previously studied. Here we assessed the extent of in vitro culture induced somaclonal variation, at a phenotypic, compositional and genetic/epigenetic level, by comparing field-maintained and micropropagated lines of three elite Ghanaian sweet potato genotypes grown in a common garden. Although micropropagated plants presented no observable morphological abnormalities compared to field maintained lines, they presented significantly lower levels of iron, total protein, zinc, and glucose. Methylation Sensitive Amplification Polymorphism analysis showed a high level of in vitro culture induced molecular variation in micropropagated plants. Epigenetic, rather than genetic variation, accounts for most of the observed molecular variability. Taken collectively, our results highlight the importance of ensuring the clonal fidelity of the micropropagated biofortified lines in order to reduce potential losses in the nutritional value prior to their commercial release.

plant biology↗

bioRxiv2018

Ecological occurrence and plant regeneration of embryoid of the endangered and endemic plant Dysosma versipellis in China

In this study, the effective callus culture, somatic embryogenesis, and plant regeneration system of Dysosma versipellis, which is an endangered and endemic plant in China, were established under specific culture conditions. Using the D. versipellis leaves, petioles, and roots as explants, DPS software orthogonal design method and SPSS Duncans multiple range test were used to investigate their effects of D. versipellis on callus formation, embryoid induction, and plant regeneration by adding different phytohormones. Results showed that leaves and petioles were the most suitable materials in inducing callus. The effect of phytohormone on callus formation followed the order of 2,4-dichlorophenoxyacetic acid (2,4-D)>thidiazuron (TDZ)> kinetin>naphthylacetic acid (NAA)>2-ip. The best medium for callus formation was MS+2,4-D 1 mg/L+NAA 0.05 mg/L+TDZ 0.5 mg/L+2-ip 1 mg/L. The optimal medium to induce the formation of granular callus embryoid was MS+0.5 mg/L 6-BA+0.1 mg/L NAA, and the induction rate was 71.33%. The embryoid rooting and plant regeneration medium was MS+0.5 mg/L IBA+0.5 mg/L GA3. The optimal medium formula obtained in this study was suitable for the rapid induction of callus, embryoid, and plant regeneration of D. versipellis under in vitro culture conditions. Further study on the action mechanism, signal regulation mechanism, and artificial seed production of fungal elicitors affecting the accumulation of podophyllotoxin is important.

plant biology↗

bioRxiv2018

Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia

Grain yield is a trait of paramount importance in the breeding of all cereals. In wheat (Triticum aestivum L.), yield has steadily increased since the Green Revolution, though the current rate of increase is not forecasted to keep pace with demand due to growing world population and affluence. While several genome-wide association studies (GWAS) on yield and related component traits have been performed in wheat, the previous lack of a reference genome has made comparisons between studies difficult. In this study, a GWAS for yield and yield-related traits was carried out on a population of 324 soft red winter wheat lines across a total of four rain-fed environments in the state of Virginia using single-nucleotide polymorphism (SNP) marker data generated by a genotyping-by-sequencing (GBS) protocol. Two separate mixed linear models were used to identify significant marker-trait associations (MTAs). The first was a single-locus model utilizing a leave-one-chromosome-out approach to estimating kinship. The second was a sub-setting kinship multi-locus method (FarmCPU). The single-locus model identified nine significant MTAs for various yield-related traits, while the FarmCPU model identified 74 significant MTAs. The availability of the wheat reference genome allowed for the description of MTAs in terms of both genetic and physical positions, and enabled more extensive post-GWAS characterization of significant MTAs. The results indicate promising avenues for increasing grain yield by exploiting variation in traits relating to the number of grains per unit area, as well as phenological traits influencing grain-filling duration of genotypes.

plant biology↗

bioRxiv2018

Effects of Biogas Slurry on Fruit Economic Traits and Soil Nutrient of Camellia oleifera Abel

Soil nutrients play a principal role in Camellia oleifera Abel (oil-seed camellia) production. Camellia oleifera absorbs nutrients from surrounding soils and its production is highly influenced by nutrients or fertilization. In this study, we investigated the effects of biogas slurry applications on soil nutrients and economic traits of C. oleifera fruits. Five different amounts of fertilizing biogas slurry (0, 10, 20, 30, or 40 kg/plant/year from three applications per year) were applied to C. oleifera plants in 2015 and 2016. Rhizosphere soil nutrients and C. oleifera fruit economic traits (yield, seed rate, and oil yield)were measured. Fertilization with biogas slurryincreasedsoil organic matter, available nitrogen (N), phosphorus (P), and potassium (K) in both 2015 and 2016. Increases in soil available N, P, and Kwere largest at the highest slurry application rate and second largest at the second highest application rate. Fruit economic traits were maximized at the two highest application rates. Oil yield was correlated withsoil available P in 2015 and 2016, and soil organic matter in 2015. Fertilization with biogas slurry decreased saturated fatty acid content in fruit but had no effect on unsaturated fatty acid content. In conclusion, fertilization with biogas slurry increases rhizosphere soil nutrients and fruit economic traits of C. oleifera with the rates of at least 30 kg/plant/year having the most positive effects.

plant biology↗

bioRxiv2018

Transcriptome dynamics in developing leaves from C3 and C4 Flaveria species reveal determinants of Kranz anatomy

C4 species have evolved more than 60 times independently from C3 ancestors. This multiple and parallel evolution of the complex C4 trait indicates common underlying evolutionary mechanisms that might be identified by comparative analysis of closely related C3 and C4 species. Efficient C4 function depends on a distinctive leaf anatomy that is characterized by enlarged, chloroplast rich bundle sheath cells and a narrow vein spacing. To elucidate molecular mechanisms generating this so called Kranz anatomy, we analyzed a developmental series of leaves from the C4 plant Flaveria bidentis and the closely related C3 species Flaveria robusta using leaf clearing and whole transcriptome sequencing. Applying non-negative matrix factorization on the data identified four different zones with distinct transcriptome patterns in growing leaves of both species. Comparing these transcriptome patterns revealed an important role of auxin metabolism and especially auxin homeostasis for establishing the high vein density typical for C4 leaves.

plant biology↗

bioRxiv2018

Sustaining yam yields amidst climate threat in the forest - savannah transition zone of Ghana

With about 70% of yam tuber been water, yield is critically affected during bulking as a result of onset of temporal drought. As a consequence of climate change, farmers who are into Dioscorea rotundata (white yam) production for local and international market lose their investments mainly due to erratic precipitation, drought spells culminating into low yields of just 12t/ha compared to the potential of about 22-49t/ha depending on the variety. Innovative land uses technologies with higher and sustained productivity for yam production are imperative. This study verifies improved agronomic package for sustainable yam production in yam growing areas in the forest - savannah transition zone of Ghana during the 2015 and 2016 cropping seasons. The improved agronomic package included use of ridging as seedbed, seed treatment before planting, fertilizer application at a rate of 30:30:36 N:P205:K20 kg/ha plus 15 kg/ha Mg and 20 kg/ha S as MgSO4 and the use of minimum stakes (trellis; 30-50% less number of stakes used by farmers staking). This was compared with farmers practice which consisted of mounding, no fertilizer application and no seed treatment. The results revealed significant (P [≤] 0.01) yam yields of more than 60% difference between the improved agronomic practice and farmers practice from Ejura, Atebubu and Kintampo yam growing communities. Adoption of improved agronomic practices does not only sustain yam production and address deforestation but also provide higher returns on investments promoting climate resilience by small holders.

plant biology↗

bioRxiv2018

CRISPR-TSKO facilitates efficient cell type-, tissue-, or organ-specific mutagenesis in Arabidopsis

Detailed functional analyses of many fundamentally-important plant genes via conventional loss-of-function approaches are impeded by severe pleiotropic phenotypes. In particular, mutations in genes that are required for basic cellular functions and/or reproduction often interfere with the generation of homozygous mutant plants, precluding further functional studies. To overcome this limitation, we devised a CRISPR-based tissue-specific knockout system, CRISPR-TSKO, enabling the generation of somatic mutations in particular plant cell types, tissues, and organs. In Arabidopsis, CRISPR-TSKO mutations in essential genes caused well-defined, localized phenotypes in the root cap, stomatal lineage, or entire lateral roots. The underlying modular cloning system allows for efficient selection, identification, and functional analysis of mutant lines directly in the first transgenic generation. The efficacy of CRISPR-TSKO opens new avenues to discover and analyze gene functions in spatial and temporal contexts of plant life while avoiding pleiotropic effects of system-wide loss of gene function.

plant biology↗

bioRxiv2018

The study of hormonal metabolism of Trincadeira and Syrah cultivars indicates new roles of salicylic acid, jasmonates, ABA and IAA during grape ripening and upon infection with Botrytis cinerea

Hormones play an important role in fruit ripening and in response to biotic stress. Nevertheless, analyses of hormonal profiling during plant development and defense are scarce. In this work, changes in hormonal metabolism in grapevine (Vitis vinifera) were compared between a susceptible (Trincadeira) and a tolerant (Syrah) variety during grape ripening and upon infection with Botrytis cinerea. Infection of grapes with the necrotrophic pathogen Botrytis cinerea leads to significant economic losses worldwide.\n\nPeppercorn-sized fruits were infected in the field and mock-treated and infected berries were collected at green, veraison and harvest stages for hormone analysis and targeted qPCR analysis of genes involved in hormonal metabolism and signaling. Results indicate a substantial reprogramming of hormonal metabolism during grape ripening and in response to fungal attack. Syrah and Trincadeira presented differences in the metabolism of abscisic acid (ABA), indole-3-acetic acid (IAA) and jasmonates during grape ripening that may be connected to fruit quality. On the other hand, high basal levels of salicylic acid (SA), jasmonates and IAA at an early stage of ripening, together with activated SA, jasmonates and IAA signaling, likely enable a fast defense response leading to grape resistance/ tolerance towards B. cinerea.\n\nThe balance among the different phytohormones seems to depend on the ripening stage and on the intra-specific genetic background and may be fundamental in providing resistance or susceptibility. In addition, this study indicated the involvement of SA and IAA in defense against necrotrophic pathogens and gains insights into possible strategies for conventional breeding and/or gene editing aiming at improving grape quality and grape resistance against Botrytis cinerea.

plant biology↗

bioRxiv2018

Excess light priming in Arabidopsis thaliana with altered DNA methylomes

Plants must continuously react to the ever-fluctuating nature of their environment. Repeated exposure to stressful conditions can lead to priming, whereby prior encounters heighten a plants ability to respond to future events. A clear example of priming is provided by the model plant Arabidopsis thaliana (Arabidopsis), in which photosynthetic and photoprotective responses are enhanced following recurring light stress. While there are various post-translational mechanisms underpinning photoprotection, an unresolved question is the relative importance of transcriptional changes towards stress priming and, consequently, the potential contribution from DNA methylation - a heritable chemical modification of DNA capable of influencing gene expression. Here, we systematically investigate the potential molecular underpinnings of physiological priming against recurring excess-light (EL), specifically DNA methylation and transcriptional regulation: the latter having not been examined with respect to EL priming. The capacity for physiological priming of photosynthetic and photoprotective parameters following a recurring EL treatment was not impaired in Arabidopsis mutants with perturbed establishment, maintenance, or removal of DNA methylation. Importantly, no differences in development or basal photoprotective capacity were identified in the mutants that may confound the above result. Little evidence for a causal transcriptional component of physiological priming was identified; in fact, most alterations in primed plants presented as a transcriptional dampening in response to an additional EL exposure, likely a consequence of physiological priming. However, a set of transcripts uniquely regulated in primed plants provide preliminary evidence for a novel transcriptional component of recurring EL priming, independent of physiological changes. Thus, we propose that physiological priming of recurring EL in Arabidopsis occurs independently of DNA methylation; and that the majority of the associated transcriptional alterations are a consequence, not cause, of this physiological priming.\n\nOne sentence summaryPhotoprotection and priming against recurring excess light is functional despite impaired maintenance of the DNA methylome.

plant biology↗

bioRxiv2018

The Flowering Hormone Florigen Accelerates Secondary Cell Wall Biogenesis to Harmonize Vascular Maturation with Reproductive Development

The protein hormone florigen is a universal systemic inducer of flowering and a generic growth terminator across meristems. To understand the developmental rational for its pleiotropic functions and to uncover the deep cellular systems mobilized by florigen beyond flowering we explored termination of radial expansion of stems. Employing the power of tomato genetics along with RNAseq and histological validations we show that endogenous, mobile, or induced florigen accelerates secondary cell wall biogenesis (SCWB), and hence vascular maturation, independently of flowering. This finding is supported by a systemic florigen antagonist from the non-flowering Ginkgo biloba, which arrests SCWB and by MADS and MIF genes downstream of florigen that similarly suppress or enhance, respectively, vascular maturation independent of flowering. We also show that florigen is remarkably stable and distributed to all organs regardless of existing endogenous levels. By accelerating SCWB, florigen reprograms the distribution of resources, signals and mechanical loads required for the ensuing reproductive phase it had originally set into motion.\n\nDevelopmental HighlightsO_LIFlorigen accelerates SCWB: A prime case for a long-range regulation of a complete metabolic network by a plant hormone.\nC_LIO_LIThe dual acceleration of flowering and vascular maturation by Florigen provides a paradigm for a dynamic regulation of global, independent, developmental programs.\nC_LIO_LIThe growth termination functions of florigen and the auto-regulatory mechanism for its production and distribution provide a communication network enveloping the shoot system.\nC_LIO_LIA stable florigen provides a possible mechanism for the quantitative regulation of flowering\nC_LIO_LILateral stimulation of xylem differentiation links the phloem-travelling florigen with the annual rings in trunks.\nC_LIO_LIMADS genes are common relay partners in Florigen circuits; vascular maturation in stems and reproductive transition in apical meristems.\nC_LI

plant biology↗

bioRxiv2018

Physiological regulation of bud burst in grapevine

The physiological constraints on bud burst in woody perennials, including the prerequisite for vascular development remain unresolved. Both light and tissue oxygen status have emerged as important cues for vascular development in other systems, however, light requirement appears to be facultative in grapevine, and the information related to the spatial variability of oxygen in buds is unclear. Here, we analysed apoplastic development at early stages of grapevine bud burst and combined molecular modelling with histochemical techniques to determine the pore size of cell walls in grapevine buds. The data demonstrate that quiescent grapevine buds were impermeable to apoplastic dyes (acid fuchsin and eosin Y) until after bud burst was established. The molecular exclusion size was calculated to be 2.1 nm, which would exclude most macromolecules except simple sugars and phytohormones. In vivo experiments show that grapevine buds were able to resume growth even following excision from the cane, and that the outer scales of grapevine buds may participate in the biochemical repression of bud burst. Furthermore, we demonstrate that the tissue oxygen partial pressure data correlated well with structural heterogeneity within the bud and differences in tissue density. These data consolidate evidence that the meristematic core becomes rapidly oxygenated during bud burst. Taken together, and when put in the context of earlier studies, these data provide solid evidence that the physiological and biochemical events that initiate bud burst reside within the bud, and question the role of long distance signalling in this developmental transition.\n\nHighlightsO_LIThe apoplastic pore size between the grapevine bud and the mother vine is dynamically regulated in the transition to bud burst.\nC_LIO_LIThe molecular exclusion size of the apoplastic connection between the bud and cane is calculated 2.1 nm prior to the initiation of bud burst.\nC_LIO_LIThe structural heterogeneity of the bud explains the spatial variance in tissue oxygen status, and the meristematic core is oxygenated during the initiation of bud burst.\nC_LIO_LILong distance maternal signals are not a requirement for bud burst.\nC_LI

plant biology↗

bioRxiv2018

A stress-response-related inter-compartmental signalling pathway regulates embryonic cuticle integrity in Arabidopsis

The embryonic cuticle is necessary for normal seed development and seedling establishment in Arabidopsis. Although mutants with defective embryonic cuticles have been identified, neither the deposition of cuticle material, nor its regulation, has been described during embryogenesis. Here we use electron microscopy, lipid staining and permeability assays to show that cuticle deposition initiates de novo in patches on globular embryos. By combining these techniques with genetics and gene expression analysis, we show that successful patch coalescence to form a continuous cuticle requires a signalling involving the endosperm-specific subtilisin protease ALE1 and the receptor kinases GSO1 and GSO2, which are expressed in the developing embryonic epidermis. Transcriptome analysis shows that this pathway regulates stress-related gene expression in seeds. Consistent with these findings we show genetically, and through activity analysis, that the stress-associated MPK6 protein acts downstream of GSO1 and GSO2 in the developing embryo. We propose that a stress-related signalling pathway has been hijacked in some angiosperm seeds through the recruitment of endosperm-specific components. Our work reveals the presence of an inter-compartmental dialogue between the endosperm and embryo that ensures the formation of an intact and functional cuticle around the developing embryo through an \"auto-immune\" type interaction.

plant biology↗