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bioRxiv2020

REAP supplemental fertilizer improves greenhouse crop yield

BackgroundMine tailings contain rare earth elements, including lanthanum and cerium, and plant micronutrients including iron. Previous studies have demonstrated that fertilizers containing rare earth elements and/or micronutrients can influence plant physiology, nutrient uptake and crop yield. However, applying the right dose of these fertilizers is critical since the concentration range associated with benefits is often narrow, and overapplication can lead to crop yield reductions. This study aimed to quantify the effects of a water-soluble fertilizer, REAP, on the yield of greenhouse crops. MethodsIn the first experiment, the effects of three concentrations of REAP (100, 250 or 500 ppm) were compared to a control (0 ppm REAP) on growth of lettuce, tomato and pepper growing in soilless media. In the second experiments, the effects of REAP applied at higher rates (500, 1000 and 2000 ppm) were compared to a control (0 ppm REAP) on the growth of lettuce, peppers, tomato and cantaloupe. ResultsIn the first experiment, there were no significant differences in yield between treatments, REAP appeared to promote root development. In the second experiment, there were significant yield increases for all crops treated with REAP. Gas exchange rates and nutrient concentration of tomato plants receiving REAP were not significantly different from the control. These results demonstrated that nutrient elements in REAP, including lanthanum, cerium, and micronutrients, improved the growth and yield of vegetable crops when applied at rates ranging from 500 to 2000 ppm.

plant biology↗

bioRxiv2020

Regulation of Vacuole Morphology by PIEZO Channels in Spreading Earth Moss

The perception of mechanical force is a fundamental property of most, if not all cells. PIEZO channels are plasma membrane-embedded mechanosensitive calcium channels that play diverse and essential roles in mechanobiological processes in animals1,2. PIEZO channel homologs are found in plants3,4, but their role(s) in the green lineage are almost completely unknown. Plants and animals diverged approximately 1.5 billion years ago, independently evolved multicellularity, and have vastly different cellular mechanics5. Here, we investigate PIEZO channel function in the moss Physcomitrium patens, a representative of one of the first land plant lineages. PpPIEZO1 and PpPIEZO2 were redundantly required for normal growth, size, and shape of tip-growing caulonema cells. Both were localized to vacuolar membranes and facilitated the release of calcium into the cytosol in response to hypoosmotic shock. Loss-of-function ({Delta}Pppiezo1/2) and gain-of-function (PpPIEZO2-R2508K and -R2508H) mutants revealed a role for moss PIEZO homologs in regulating vacuole morphology. Our work here shows that plant and animal PIEZO homologs have diverged in both subcellular localization and in function, likely co-opted to serve different needs in each lineage. The plant homologs of PIEZO channels thus provide a compelling lens through which to study plant mechanobiology and the evolution of mechanoperceptive strategies in multicellular eukaryotes.

plant biology↗

bioRxiv2020

Interference of feral radish (Raphanus sativus) resistant to AHAS-inhibiting herbicides in oilseed rape, wheat and sunflower crops

Raphanus sativus (feral radish), a cosmopolitan weed, has developed resistance to acetohydroxyacid synthase (AHAS) inhibitor herbicides in several countries of South America. This study reports the effects of season-long interference of several feral radish densities on grain yield and yield components of oilseed rape, wheat and sunflower, and on feral radish traits under field conditions. Feral radish density treatments consisted of 0, 2, 4, 8 and 16 plants m-2 in oilseed rape, 0, 4 and 12 plants m-2 in wheat, and 0, 1.6, 4, 8 and 16 plants m-2 in sunflower. The number of inflorescences per area, seeds per inflorescence and the seed biomass of crops were reduced with increasing feral radish densities. The rectangular hyperbola model revealed yield losses by up to 100 %, 74.4 % and 12.2 % in oilseed rape, wheat and sunflower, respectively. Feral radish seed production ranged from 4,300 to 31,200, and 1000 to 4,700 seeds m-2 in winter crops and sunflower, respectively. Season-long feral radish interference can result in serious economic losses in oilseed rape, wheat and sunflower. The adverse impact of feral radish on the yield of winter and summer crops and the high feral radish seed and pods production suggests the need for the development and implementation of diverse and effective long-term weed management practices.

plant biology↗

bioRxiv2020

Performance Evaluation and Selection of Improved Tef (Eragrostis tef L) varieties at Main Campus Site Hadiya Zone, Southern Ethiopia

Tef [Eragrostis tef (Zucc.) Trotter] is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. It is, a tetraploid with 40 chromosomes (2n = 4x = 40), belongs to the family Poaceae and, together with finger millet (Eleusine coracana Gareth.), to the subfamily Chloridoideae. It was originated and domesticated in Ethiopia. The experiment was conducted to identify, select and recommend adaptable, high yielding, Insect pest and disease resistant twelve released and one local variety at Main Campus Site Hadiya zone of SNNPR. Twelve tef varieties were evaluated in RCBD with three replications on station of Main Campus Site during main cropping season of 2019/2020. Analysis of variance revealed that there were significant differences among tef varieties, Culm length, panicle length, plant height, days to heading, days to maturity, grain filling period, primary panicle brunch, grain yield, biomass yield and harvest index at Main Campus site. Based on the obtained result, the improved tef varieties namely; DZ-Cr-438 DZ-Cr-974 (Dukem), DZ-01-899 (Gimbechu) and DZ-01-196 (Magna) at Main Campus site. Therefore, these varieties showed better performance for most of the studied characters including grain yield. Therefore, these varieties were selected and recommended for the study area and similar ecologies of Hadiya Zone. This finding, being the result of one year with single location, it is recommended that the experiment should be repeated at multi locations for several years to confirm the obtained results.

plant biology↗

bioRxiv2020

A giant cell enhancer achieves cell-type specificity through activation via TCP and repression by Dof transcription factors

Proper pattern formation relies on the tight coordination of cell fate specification and cell cycle regulation in growing tissues. How this can be organized at enhancers that activate gene expression necessary for differentiation is not well understood. One such example is the patterning of the Arabidopsis thaliana sepal epidermis where giant cell fate specification is associated with the endoreduplication cell cycle. Previously, we identified an enhancer region capable of driving giant cell-specific expression. In this study, we use the giant cell enhancer as a model to understand the regulatory logic that promotes cell-type specific expression. Our dissection of the enhancer revealed that giant cell specificity is achieved primarily through the combination of two elements: an activator and a repressor. TCP transcription factors are involved in activation of non-specific expression throughout the epidermis with higher expression in endoreduplicated giant cells than small cells. Dof transcription factors act via the second element to repress activity of the enhancer and limit expression to giant cells. Thus, we find that cell-type specific expression emerges from the combined activities of two broadly acting enhancer elements.

plant biology↗

bioRxiv2020

Racing against stomatal attenuation: rapid CO2 response curves more reliably estimate photosynthetic capacity than steady state curves in a low conductance species

A/Ci curves are an important gas-exchange-based approach to understanding the regulation of photosynthesis, describing the response of net CO2 assimilation (A) to leaf internal concentration of CO2 (Ci). Low stomatal conductance species pose a challenge to the measurement of A/Ci curves by reducing the signal-to-noise ratio of gas exchange measures. Additionally, the stomatal attenuation effect of elevated ambient CO2 leads to further reduction of conductance and may lead to erroneous interpretation of high Ci responses of A. Rapid A/Ci response (RACiR) curves offer a potential practice to develop A/Ci curves faster than the stomatal closure response to elevated CO2. We used the moderately low conductance Citrus to compare traditional steady state (SS) A/Ci curves with RACiR curves. SS curves failed more often than RACiR curves. Overall parameter estimates were the same between SS and RACiR curves. When low stomatal conductance values were removed, triose-phosphate utilization (TPU) limitation estimates increased. Overall RACiR stomatal conductance values began and remained higher than SS values. Based on the comparable resulting parameter estimates, higher likelihood of success and reduced measurement time, we propose RACiR as a valuable tool to measure A/Ci responses in low conductance species.

plant biology↗

bioRxiv2020

Nutri rich cattle feed (NuCa feed) supplement with improved fiber content free of anti-nutritional factor Phytic acid

Most of the commercial ruminant feeds comprise Corn meal, Groundnut cake, Maize etc., which contain anti-nutritional factors called Phytates. They have high binding affinity to cationic minerals. This results in decrease in activity of the cattle by making minerals unavailable for absorption in the intestine. Many of the feed industries add Phytase enzyme that degrades the Phytic acid. Addition of Phytase enzyme is very complex method and increases the cost of the feed. If Phytase is not added, Phytic acid enters the ecosystem through the dung and due to microbial degradation, the Phytic acid gets converted into Phosphates. Phosphate abundance in water bodies leads to Eutrophication, which is a serious ecological issue. And also, in many parts of the country, post-harvest Paddy straw is burnt unused. This intentional stubble burning causes air pollution. We combined paddy straw and Azolla along with jaggery to prepare animal feed supplement. The feed pellets were evaluated for their nutritional composition and efficacy. The efficacy of the developed feed was evaluated by feeding it to milch cows and compared with regular feed for a period of 15 days. The Azolla-Hay feed improved the milk yield and also quality of the milk in comparison to the control group. This study revealed that Azolla in combination with paddy straw powder can be low-cost feed alternative especially during the lean period where the availability of feed is scarce.

plant biology↗

bioRxiv2020

Dissection of PRC1 and PRC2 recruitment in Arabidopsis connects EAR repressome to PRC2 anchoring

PcG complexes ensure that every cell in an organism expresses the genes needed at a particular stage, time or condition. However, it is still not fully understood how PRC1 and PRC2 are recruited to target genes in plants. Recent results in Arabidopsis support that PRC2 recruitment is mediated by different TFs. However, it is unclear how all these TFs interact with PRC2 and whether they can also recruit PRC1 activity. Here, by using a system to in vivo bind selected factors to a synthetic promoter lacking the complexity of PcG target promoters, we show that while VAL1 binding recapitulates PRC1 and PRC2 marking, the binding of other TFs only render PRC2 marking. Interestingly, all these TFs contain an EAR domain that acts as docking point for PRC2 and HDACs, connecting two different repressive mechanisms. Furthermore, we show that different TFs act synergistically in PRC2 anchoring to maintain a long-term repression.

plant biology↗

bioRxiv2020

RNA-Seq analysis of genes affected by Cyclophilin A/DIAGEOTROPICA (DGT) in tomato root development

Cyclophilin A/DIAGEOTROPICA (DGT) has been linked to auxin-regulated development in tomato and appears to affect multiple developmental pathways. Loss of DGT function results in a pleiotropic phenotype that is strongest in the roots, including shortened roots with no lateral branching. Here, we present an RNA-Seq dataset comparing the gene expression profiles of wildtype ( Ailsa Craig) and dgt tissues from three spatially separated developmental stages of the tomato root tip, with three replicates for each tissue and genotype. We also identify differentially expressed genes, provide an initial comparison of genes affected in each genotype and tissue, and provide the pipeline used to analyze the data. Further analysis of this dataset can be used to gain insight into the effects of DGT on various root developmental pathways in tomato.

plant biology↗

bioRxiv2020

Two distinct phases of chloroplast biogenesis during de-etiolation in Arabidopsis thaliana

Light triggers chloroplast differentiation whereby the etioplast transforms into a photosynthesizing chloroplast and the thylakoid rapidly emerges. However, the sequence of events during chloroplast differentiation remains poorly understood. Using Serial Block Face Scanning Electron Microscopy (SBF-SEM), we generated a series of chloroplast 3D reconstructions during differentiation, revealing chloroplast number and volume and the extent of envelope and thylakoid membrane surfaces. Furthermore, we used quantitative lipid and whole proteome data to complement the (ultra)structural data, providing a time-resolved, multi-dimensional description of chloroplast differentiation. This showed two distinct phases of chloroplast biogenesis: an initial photosynthesis-enabling Structure Establishment Phase followed by a Chloroplast Proliferation Phase during cell expansion. Moreover, these data detail thylakoid membrane expansion during de-etiolation at the seedling level and the relative contribution and differential regulation of proteins and lipids at each developmental stage. Altogether, we establish a roadmap for chloroplast differentiation, a critical process for plant photoautotrophic growth and survival.

plant biology↗

bioRxiv2020

Atomic structures of respiratory complex III2 , complex IV and supercomplex III2+IV from vascular plants

Mitochondrial complex III (CIII2) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III2+IV), play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII2, CIV and SC III2+IV from Vigna radiata determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII2 and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII2 revealed long-range, coordinated movements across the complex, as well as the motion of CIII2s iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H-channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits, angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes, generate new mechanistic hypotheses and allow for the generation of more selective agricultural inhibitors.

plant biology↗

bioRxiv2020

Identifying seaweeds species of Chlorophyta, Ochrophyta and Rhodophyta using DNA barcodes

Strengthening the DNA barcode database is important for a species level identification, which was lacking for seaweeds. We made an effort to collect and barcode seaweeds occurring along Southeast coast of India. We barcoded 31 seaweeds species belonging to 21 genera, 14 family, 12 order of 3 phyla (viz., Chlorophyta, Phaeophyta and Rhodophyta). We found 10 species in 3 phyla and 2 genera (Anthophycus and Chnoospora) of Phaeophyta were barcoded for the first time. Uncorrected p-distance calculated using K2P, nucleotide diversity and Tajimas test statistics reveals highest values among the species of Chlorophyta. Over all K2P distance was 0.36. The present study revealed the potentiality of rbcL gene sequences in identification of all 3 phyla of seaweeds. We also found that the present barcode reference libraries (GenBank and BOLD) were insufficient in seaweeds identification and more efforts were needed for strengthening local seaweed barcode library to benefit rapids developing field such as environmental DNA barcoding. We also show that the constructed barcode library could aid various industrial experts involved in seaweed bio-resource exploration and taxonomy/non-taxonomic researches involved in climate, agriculture and epigenetics research in precise seaweed identification. Since the rise of modern high-throughput sequencing technologies is significantly altering bio-monitoring applications and surveys, reference datasets such as ours will become essential in ecosystems health assessment and monitoring.

plant biology↗

bioRxiv2020

Quantitative imaging of RNA polymerase II activity in plants reveals the single-cell basis of tissue-wide transcriptional dynamics

The responses of plants to their environment often hinge on the spatiotemporal dynamics of transcriptional regulation. While live-imaging tools have been used extensively to quantitatively capture rapid transcriptional dynamics in living animal cells, lack of implementation of these technologies in plants has limited concomitant quantitative studies. Here, we applied the PP7 and MS2 RNA-labeling technologies for the quantitative imaging of RNA polymerase II activity dynamics in single cells of living plants as they respond to experimental treatments. Using this technology, we count nascent RNA transcripts in real-time in Nicotiana benthamiana (tobacco) and Arabidopsis thaliana (Arabidopsis). Examination of heat shock reporters revealed that plant tissues respond to external signals by modulating the number of cells engaged in transcription rather than the transcription rate of active cells. This switch-like behavior, combined with cell-to-cell variability in transcription rate, results in mRNA production variability spanning three orders of magnitude. We determined that cellular heterogeneity stems mainly from the stochasticity intrinsic to individual alleles. Taken together, our results demonstrate that it is now possible to quantitatively study the dynamics of transcriptional programs in single cells of living plants.

plant biology↗

bioRxiv2020

Plant NLR targets P-type ATPase for executing plasma membrane depolarization leading to calcium influx and cell death

Hypersensitive response (HR) is a robust immune response mediated by plant nucleotide-binding and leucine-rich repeat receptor (NLR). However, the early molecular event linking NLR to cell death is obscure. Here we demonstrate that NLR targets plasma membrane H+-ATPases (PMA) generating electrochemical potential across the membrane. CCA309, an autoactive N-terminal domain of pepper coiled-coil NLR (CNL), associates with PMAs and its autoactivity is affected by silencing or overexpression of PMA. CCA309-induced extracellular alkalization accompanied with membrane depolarization is followed by calcium influx and cell death. CCA309 interacts with C-terminal regulatory domain of PMA and 14-3-3 negatively affects CCA309-induced cell death. Moreover, pharmacological experiments with fusicoccin, an irreversible PMA activator, confirmed that CC- and CNL-mediated cell death occurred through inhibiting PMA. We propose PMAs as the primary target of plasma membrane-associated CNL to disrupt electrochemical homeostasis leading to HR cell death.

plant biology↗

bioRxiv2020

Neither the availability of D2 nor CP43 limits the biogenesis of PSII in tobacco

The pathway of photosystem II assembly is well understood and multiple auxiliary proteins supporting it have been identified. By contrast, little is known about rate-limiting steps controlling PSII biogenesis. In the green alga Chlamydomonas reinhardtii, biosynthesis of the chloroplast-encoded D2 reaction center subunit (PsbD) limits PSII accumulation. To determine the importance of D2 synthesis for PSII accumulation in vascular plants and elucidate the contributions of transcriptional and translational regulation, the 5-untranslated region of psbD was modified via chloroplast transformation in tobacco. A drastic reduction in psbD mRNA abundance resulted in a strong decrease of PSII content, impaired photosynthetic electron transport, and retarded growth under autotrophic conditions. Overexpression of the psbD mRNA also increased transcript abundance of psbC (the CP43 inner antenna protein), which is co-transcribed with psbD. Because translation efficiency remained unaltered, translation output of pbsD and psbC increased with mRNA abundance. However, this did not result in increased PSII accumulation. The introduction of point mutations into the Shine-Dalgarno-like sequence or start codon of psbD decreased translation efficiency without causing pronounced effects on PSII accumulation and function. These data show that neither transcription nor translation of psbD and psbC are rate-limiting for PSII biogenesis in vascular plants, and that PSII assembly and accumulation in tobacco are controlled by different mechanisms than in Chlamydomonas. One sentence summaryPSII biogenesis in tobacco is neither limited by transcript accumulation nor translation of psbD and psbC.

plant biology↗

bioRxiv2020

Climate change alters plant-herbivore interactions

Plant-herbivore interactions have evolved in response to co-evolutionary dynamics, along with selection driven by abiotic conditions. We examine how abiotic factors influence trait expression in both plants and herbivores to evaluate how climate change will alter this long-standing interaction. The paleontological record documents increased herbivory during periods of global warming in the deep past. In phylogenetically-corrected meta-analyses, we find that elevated temperatures, CO2 concentration, drought stress and nutrient conditions directly and indirectly induce greater herbivore consumption, primarily in agricultural systems. Additionally, elevated CO2 delays herbivore development, but increased temperatures accelerate development. For annual plants, higher temperatures, CO2, and drought stress increase foliar herbivory, and our meta-analysis suggests that greater temperatures and drought may heighten florivory in perennials. Human actions are causing concurrent shifts in CO2, temperature, precipitation regimes and nitrogen deposition, yet few studies evaluate interactions among these changing conditions. We call for additional multifactorial studies that simultaneously manipulate multiple climatic factors, which will enable us to generate more robust predictions of how climate change could disrupt plant-herbivore interactions. Finally, we consider how shifts in insect and plant phenology and distribution patterns could lead to ecological mismatches, and how these changes may drive future adaptation and coevolution between interacting species.

plant biology↗

bioRxiv2020

Perturbations of the AMI1 IAM-amidohydrolase expression trigger plant stress responses in Arabidopsis thaliana

The evolutionary success of plants relies to a large extent on their extraordinary ability to adapt to changes in their environment. These adaptations require that plants balance their growth with their stress responses. Plant hormones are crucial mediators orchestrating the underlying adaptive processes. However, whether and how the growth-related hormone auxin and the stress-related hormones jasmonic acid (JA), salicylic acid, and abscisic acid (ABA) are coordinated remains largely elusive. Here, we analyze the physiological role of AMIDASE 1 (AMI1) in plant growth and its possible connection to plant adaptations to abiotic stresses. AMI1 contributes to cellular auxin homeostasis by catalyzing the conversion of indole-acetamide into the major plant auxin indole-3-acetic acid. Functional impairment of AMI1 increases the plants stress status rendering mutant plants more susceptible to abiotic stresses. Transcriptomic analysis of ami1 mutants disclosed the reprogramming of a considerable number of stress-related genes, including JA and ABA biosynthesis genes. The ami1 mutants exhibit only moderately repressed growth, but an enhanced ABA accumulation, which suggests a role for AMI1 in the crosstalk between auxin and ABA. Altogether, our results suggest that AMI1 is involved in coordinating the trade-off between plant growth and stress responses, balancing auxin with ABA homeostasis. HIGHLIGHTThe IAM amidohydrolase AMI1 catalyzes the conversion of IAM into IAA in vivo. Expression of AMI1 is specifically repressed by osmotic stress conditions, which triggers ABA biosynthesis through the induction of NCED3, thereby linking auxin homeostasis with plant stress responses.

plant biology↗

bioRxiv2020

F-box protein At1g08710 negatively regulates root length and imparts drought stress tolerance in Arabidopsis thaliana.

Plants experience abiotic stresses throughout their life cycle and accordingly respond to tide over the unfavorable conditions. Drought or water deficit is one such condition to which plants respond in various ways including the ubiquitin proteasome system (UPS). Ubiquitin E3 ligases are a diverse family of protein complexes of which Skp1{square}Cullin{square}F{square}box (SCF) class mediate the ubiquitination and subsequent proteolytic turnover of proteins. F{square}box protein subunit plays crucial role in imparting specificity for selective degradation of target proteins. Here we report the function of Arabidopsis F-box protein At1g08710 in drought stress adaptation. As F-box protein is a constituent of SCF complex, here it is shown interacting with ASK1 and Cullin1. F-box protein localizes to both nucleus and membrane. F-box gene transcript accumulates highly in root and is altered in response to drought stress conditions. F-box protein interacts with a transcriptional co-activator protein ADA2b. F-box mutant plants displayed better growth under drought stress conditions compared to the wild type with a reduced accumulation of H2O2 and malondialdehyde (MDA). Drought responsive genes RD29A, RD22, ABI3 expression is also induced in F-box mutant plants. These results indicate F-box protein At1g08710 plays a role in drought stress adaptation in Arabidopsis thaliana. HighlightsO_LIF-box gene At1g08710 encodes a nuclear, membrane localized protein. C_LIO_LIF-box protein At1g08710 interacts with transcriptional co-activator protein ADA2b. C_LIO_LIF-box protein imparts drought stress tolerance by modulating H2O2 and MDA content. C_LIO_LIDrought response genes RD29A, RD22, ABI3 expression is induced in F-box mutant plants. C_LI

plant biology↗