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bioRxiv2018

GIGANTEA promotes sorghum flowering by stimulating floral activator gene expression

iv. FundingThis work was supported by USDA-ARS CRIS projects 2030-21000-039-00D and 2030-21000-049-00D to F.G.H.\n\nv. AbstractThe C4 grass Sorghum bicolor is an important grain and subsistence crop, animal forage, and cellulosic biofuel feedstock that is tolerant of abiotic stresses and marginal soils. Sorghum is short-day flowering, an obstacle for adaptation as a grain crop but a benefit as a biofuel feedstock. To identify genes underlying sorghum photoperiodic flowering behavior this study characterized the Sbgi-ems1 nonsense mutation in the sorghum GIGANTEA (SbGI) gene from a sequenced M4 EMS-mutagenized BTx623 population. Sbgi-ems1 plants had reduced stature and leaf blades exhibiting increased lateral growth combined with reduced proximal-distal growth. Mutant plants flowered later than normal siblings under long-day conditions provided by greenhouse or field. Delayed flowering in Sbgi-ems1 plants accompanied by an increase in internode number, indicating an extended vegetative growth phase prior to flowering. Sbgi-ems1 plants had reduced expression of floral activator genes SbCO and SbEhd1 and downstream FT-like florigen genes SbFT, SbCN8, and SbCN12. Therefore, SbGI accelerates flowering by promotion of SbCO and SbEhd1 expression. Circadian clock-associated genes SbTOC1 and SbLHY had disrupted expression in Sbgi-ems1 plants. This work demonstrates SbGI is a key upstream activator in the regulatory networks dictating sorghum flowering time and growth, as well as gene expression regulation within the circadian clock.\n\nSummary StatementSorghum GIGANTEA contributes to flowering time, growth, and the circadian clock with activities opposite to its maize homolog. GI occupies a conserved position within regulatory networks but has plastic activity.

plant biology↗

bioRxiv2018

Characterization of the role of several COPI complex isoforms during the early acceptance of compatible pollen grains in Arabidopsis thaliana.

COPI is a seven subunit coatomer complex, consisting of , {beta}, {beta}', {gamma}, {delta}, {varepsilon}, and {xi}; in A. thaliana, COPI is necessary for retrograde transport from the Golgi to the Endoplasmic Reticulum, Golgi maintenance, and cell-plate formation in plant cells. Vesicle recruitment to the pollen contact point is required for pollen hydration and pollen tube penetration. To determine what other aspects of trafficking may be involved in the stigmatic papillae acceptance of compatible pollen, knock-out lines of several isoforms of the COPI complex were characterized in their roles during compatible pollination. Isoforms that were studied included 1-COPI, {beta}-COPI, {beta}'-COPI, {gamma}-COPI and {varepsilon}-COPI. Each mutant line was characterized in regards to pollen grain adherence, pollen tube penetration, and seed set. Of the mutant lines examined, 1-copi had the strongest phenotype with issues with compatible pollen grain adherence, tube germination and reduction in seed set while other lines had milder but visible retardation in compatible pollen acceptance. The data presented here are the first study of the role of the COPI complex in compatible pollinations and that certain subunit isoforms are required for compatible pollen acceptance.

plant biology↗

bioRxiv2018

Study on physicochemical properties and microbial diversity of flammulina velutipes residue during rapid fermentation

In order to investigate the effects of different mass ratios of corn straw, super absorbent resin (SAR) and cellulose decomposing strains on fermentation of flammulina velutipes residue, the cellulose degradation rate, germination index, bacterial diversity, urease activity, cellulase activity and other indicators were evaluated comprehensively so as to determine the optimal fermentation parameters. The research results indicated that the three factors of corn straw, high water-absorbent resin (SAR), and cellulose-decomposing strains have the tendency to enhance fermentation in the process. In the orthogonal test, the treatment with the highest cellulose degradation rate was T6. By 24 days, all the treated seeds germination Indices (GIs) were higher than 80%, which indicated that they were basically harmless to crops. The cellulase activity and urease activity of each treatment showed the characteristics of first rising and then decreasing as the fermentation time prolonged. In general, the T6 (the added amount of corn straw was 10%, the amount of super absorbent resin was 0.15%, and the amount of cellulose-decomposing strains was 2%) was the suitable mass ratio of additives in the fermentation which provided a certain theoretical support for resource utilization of flammulina velutipes residue.

plant biology↗

bioRxiv2018

Studies on effect of gold nanoparticles on Meloidogyne incognita and tomato plants growth and development

The plant parasitic nematodes are one of world major agricultural pest, causing in excess of 157 billion dollars in worldwide damage annually. This study has provided evidence that gold nanoparticles have great utility for management of root-knot nematodes in tomato crop. The effect of gold nanoparticles on Meloidogyne incognita J2 was remarkable under the direct exposure in water, after three hours of incubation of Meloidogyne incognita with GNPs showed the 100% mortality. The lesser survival rate of Meloidogyne incognita in soil treatment showed the strong nematicidal effect of gold nanoparticles. Subsequently, the pot experiment had shown the beneficial effects of gold nanoparticles for intensively managing the root-knot nematode. The Pot experiment not only showed us that GNPs were lethal to root-knot nematodes were also induces growth of tomato plants and didnt have any kind of negative impact on plant growth. In our study, GNPs were found to be safe and lethal to Meloidogyne incognita.

plant biology↗

bioRxiv2018

Real-time whole-plant dynamics of heavy metal transport in Arabidopsis halleri and Arabidopsis thaliana by gamma-ray imaging

Heavy metals such as zinc are essential for plant growth, but toxic at high concentrations. Despite our knowledge of the molecular mechanisms of heavy metal uptake by plants, experimentally addressing the real-time whole-plant dynamics of heavy metal uptake and partitioning has remained a challenge. To overcome this, we applied a high sensitivity gamma-ray imaging system to image uptake and transport of radioactive 65Zn in whole-plant assays of Arabidopsis thaliana and the Zn hyperaccumulator A. halleri. We show that our system can be used to quantitatively image and measure uptake and root-to-shoot translocation dynamics of zinc in real time. In the metal hyperaccumulator Arabidopsis halleri, 65Zn uptake and transport from its growth media to the shoot occurs rapidly and on time scales similar to those reported in rice. In transgenic A. halleri plants in which expression of the zinc transporter gene HMA4 is suppressed by RNAi, 65Zn uptake is completely abolished.\n\nHIGHLIGHTWe have used gamma-ray imaging to visualize the stark differences of real-time whole-plant dynamics of zinc root-to-shoot transport in heavy metal hyperaccumulating and non-accumulating Arabidopsis.

plant biology↗

bioRxiv2018

A florigen paralog is required for short-day vernalization in a pooid grass

Perception of seasonal cues is critical for reproductive success in many plants. Exposure to winter cold is a cue that can confer competence to flower in the spring via a process known as vernalization. In certain grasses, exposure to short days is another winter cue that can lead to a vernalized state. In Brachypodium distachyon, we find that natural variation for the ability of short days to confer competence to flower is due to allelic variation of the florigen paralog FT-like9 (FTL9). An active FTL9 allele is required for the acquisition of floral competence, demonstrating a novel role for a member of the florigen family of genes. Loss of the short-day vernalization response appears to have arisen once in B. distachyon and spread through diverse lineages indicating that this loss has adaptive value, perhaps by delaying spring flowering until the danger of cold damage to flowers has subsided.

plant biology↗

bioRxiv2018

Pathogen Detection and Microbiome Analysis of Infected Wheat Using a Portable DNA Sequencer

Fungal diseases of plants are responsible for major losses in agriculture, highlighting the need for rapid and accurate identification of plant pathogens. Disease outcomes are often defined not only by the main pathogen but are influenced by diverse microbial communities known as the microbiome at sites of infection. Here we present the first use of whole genome sequencing from a portable DNA sequencing device as a method for detection of fungal pathogens from wheat (Triticum aestivum). The data revealed that our method is robust and applicable to the diagnosis of fungal diseases including wheat stripe rust (caused by Puccinia striiformis f. sp. tritici), septoria tritici blotch (caused by Zymoseptoria tritici) and yellow leaf spot (caused by Pyrenophora tritici repentis). We also identified a bacterial genus Pseudomonas co-present with Puccinia and Zymoseptoria infections but not Pyrenophora infections. One limitation of the method is the over-representation of redundant wheat genome sequences in the sample. This could be addressed by amplicon-based sequencing approaches in future studies. Our work outlines a new approach for the detection of a broad range of plant pathogens and associated microbes using a portable sequencer, providing the basis for future development of a system for on-site disease monitoring.

plant biology↗

bioRxiv2018

AhRLK1, a CLAVATA1-like leucine-rich repeat receptor-like kinase of peanut, confers increased resistance to bacterial wilt in tobacco

Bacterial wilt caused by Ralstonia solanacearum is a devastating disease that infects hundreds of plant species. Host factors involved in disease resistance and pathogenesis remain poorly characterized. An up regulated and leucine-rich repeat receptor-like kinase characterized as CLAVATA1 and named AhRLK1 was obtained by microarray analysis in response to R. solanacearum in peanut. AhRLK1 contained presumably, a signal peptide, ten leucine-rich repeat (LRR) domains and conserved motifs of intracellular kinases. For subcellular localization, the AhRLK1 protein was visualized only in the plasma membrane. After inoculation with R. solanacearum, AhRLK1 was constantly up regulated in the susceptible variety Xinhuixiaoli but showed little changed in the resistant cultivar Yueyou92. Different hormones, including salicylic acid, abscisic acid, methyl jasmonate, and ethephon, induced expression, but expression was completely down regulated under cold and drought treatments. Transient overexpression provoked a hypersensitive response (HR) in Nicotiana benthamiana following agro-infiltration. Furthermore, in transgenic tobacco with overexpression of the gene, the resistance to R. solanacearum increased significantly. By contrast, most representative defense-responsive genes in HR, SA, JA and ET signal pathways such as NtHIN1, NtPR2, NtLOX1, and NtACS6, among others, were considerably up regulated in the AhRLK1 transgenic lines. Additionally, the EDS1 and PAD4 in the R gene signal were also up regulated in transgenic plants, but the NDR1 and NPR1 genes were down regulated. Accordingly, we suggest that AhRLK1 increases the defense response to R. solanacearum via HR and hormone defense signalling, associated with the EDS1 pathway of R gene signalling. The results provide new understanding of CLV1 function and will contribute to genetic enhancement of peanut.

plant biology↗

bioRxiv2018

Effect of Thiobacillus and superabsorbent on essential oil components in Thyme species

Optimal nutrition along with non-stress conditions has a significant impact on the quantity and quality of essential oil in medicinal plants. The objective of this research was to examine the possibility of improving the quantity and quality of essential oil in thyme through nutrition of the seedlings using Thiobacillus bio-fertilizer and treatment by Superabsorbent. For this purpose, seedlings of two thyme species (Thymus vulgaris and Thymus daenensis) were sown in pots and exposed to different levels of Thiobacillus and superabsorbent. Results of Gas Chromatography Mass Spectrometry (GC/MS) revealed that the main compounds detected for T. vulgaris were thymol (31.5%), p-cymene (23.4%),{gamma} -terpinene (13.9%), linalool (38.3%) and carvacrol (2.7%) while the main compounds of T. daenensis were thymol (51.2%), o-cymene (12.9%),{gamma} -terpinene (4.5%), linalool (1.7%) and borneol (3.1%). Furthermore, the application of Thiobacillus had a significant effect on -pinene content (p = 0.05). Moreover, the interaction between superabsorbent and Thiobacillus significantly changed the percentage of thymol, borneol, and caryophyllene. In conclusion, the mean of essence components in T. vulgaris was more than T. daenensis with the exception of thymol and caryophyllene.

plant biology↗

bioRxiv2018

Altered Gene Regulatory Networks are Associated with the Transition from C3 to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae)

Crassulacean acid metabolism (CAM) photosynthesis is a modification of the core C3 photosynthetic pathway that improves the ability of plants to assimilate carbon in water-limited environments. CAM plants fix CO2 mostly at night, when transpiration rates are low. All of the CAM pathway genes exist in ancestral C3 species, but the timing and magnitude of expression are greatly altered between C3 and CAM species. Understanding these regulatory changes is key to elucidating the mechanism by which CAM evolved from C3. Here we use two closely related species in the Orchidaceae, Erycina pusilla (CAM) and Erycina crista-galli (C3), to conduct comparative transcriptomic analyses across multiple time points. Clustering of genes with expression variation across the diel cycle revealed some canonical CAM pathway genes similarly expressed in both species, regardless of photosynthetic pathway. However, gene network construction indicated that 149 gene families had significant differences in network connectivity and were further explored for these functional enrichments. Genes involved in light sensing and ABA signaling were some of the most differently connected genes between the C3 and CAM Erycina species, in agreement with the contrasting diel patterns of stomatal conductance in C3 and CAM plants. Our results suggest changes to transcriptional cascades are important for the transition from C3 to CAM photosynthesis in Erycina.

plant biology↗

bioRxiv2018

pH gradient mitigation in the leaf cell secretory pathway alters the defense response of Nicotiana benthamiana to agroinfiltration

Partial neutralization of the Golgi lumen pH by ectopic expression of influenza virus M2 proton channel stabilizes acid-labile and protease-susceptible recombinant proteins in the plant cell secretory pathway. Here, we assessed the impact of M2 channel expression on the proteome of Nicotiana benthamiana leaf tissue infiltrated with the bacterial gene vector Agrobacterium tumefaciens, keeping in mind the key role of pH homeostasis on secreted protein processing and the involvement of protein secretion processes in plant cells upon microbial challenge. The proteomes of leaves agroinfiltrated with an empty vector or with an M2 channel-encoding vector were compared with the proteome of non-infiltrated leaves using a iTRAQ quantitative proteomics procedure. Leaves infiltrated with the empty vector had a low soluble protein content compared to non-infiltrated leaves, associated with a strong decrease of photosynthesis-associated proteins (including Rubisco) and a parallel increase of stress-related secreted proteins (including pathogenesis-related proteins, protease inhibitors and molecular chaperones). M2 expression partly compromised these alterations of the proteome to restore original soluble protein and Rubisco contents, associated with higher levels of translation-associated (ribosomal) proteins and reduced levels of stress-related proteins in the apoplast. Proteome changes in M2-expressing leaves were determined both transcriptionally and post-transcriptionally, to alter the steady-state levels of proteins not only along the secretory pathway but also in other cellular compartments including the chloroplast, the cytoplasm, the nucleus and the mitochondrion. These data illustrate the cell-wide influence of Golgi lumen pH homeostasis on the leaf proteome of N. benthamiana plants responding to microbial challenge. They underline in practice the relevance of carefully considering the eventual off-target effects of accessory proteins used to modulate specific cellular or metabolic functions in plant protein biofactories.

plant biology↗

bioRxiv2018

Classifying cold stress responses of inbred maize seedlings using RGB imaging

Increasing the tolerance of maize seedlings to low temperature episodes could mitigate the effects of increasing climate variability on yield. To aid progress toward this goal, we established a growth chamber-based system for subjecting seedlings of 40 maize inbred genotypes to a defined, temporary cold stress while collecting digital profile images over a 9-day time course. Image analysis performed with PlantCV software quantified shoot height, shoot area, 14 other morphological traits, and necrosis identified by color analysis. Hierarchical clustering of changes in growth rates of morphological traits and quantification of leaf necrosis over two time intervals resulted in three clusters of genotypes, which are characterized by unique responses to cold stress. For any given genotype, the set of traits with similar growth rates is unique. However, the patterns among traits are different between genotypes. Cold sensitivity was not correlated with the latitude where the inbred varieties were released suggesting potential further improvement for this trait. This work will serve as the basis for future experiments investigating the genetic basis of recovery to cold stress in maize seedlings.

plant biology↗

bioRxiv2018

Nitrate inhibition of nodule formation in Medicago truncatula is mediated by ACC SYNTHASE 10

Legumes form a mutualistic endosymbiosis with nitrogen-fixing rhizobia. These rhizobia are housed intracellularly in specialised lateral root organs, called nodules. Initiation of these nodules is triggered by bacterial derived signalling molecules, lipochitooligosaccharides (LCO). The process of nitrogen fixation is highly energy-demanding and therefore nodule initiation is tightly regulated. Nitrate is a potent inhibitor of nodulation. However, the precise mechanisms by which nitrate inhibits nodulation is poorly understood. Here, we demonstrate that in Medicago truncatula nitrate interferes with the transcriptional regulation of the ethylene biosynthesis gene ACC SYNTHASE 10. ACSs commit the rate limiting step in ethylene biosynthesis and in M. truncatula ACS10 is highly expressed in the zone of the root where nodulation occurs. Our results show that a reduction in ACS10 expression in response to LCO exposure correlates with the ability to form nodules. In addition, RNAi-mediated knockdown of ACS10 confers nodulation ability under otherwise inhibitory nitrate conditions. This discovery sheds new light on how ethylene is involved in the inhibition of nodulation by nitrate, bringing us one step closer to understanding how plants regulate their susceptibility towards rhizobia.

plant biology↗

bioRxiv2018

Triose phosphate utilization and beyond: from photosynthesis to end-product synthesis

During photosynthesis plants fix CO2 from the atmosphere onto ribulose-bisphosphate producing 3-phosphoglycerate, which is reduced to triose phosphates (TPs). The TPs are then converted into the end products of photosynthesis. When a plant is photosynthesizing very quickly it may not be possible to commit photosynthate to end product as fast as it is produced, causing a decrease in available phosphate and limiting the rate of photosynthesis to the rate of triose phosphate utilization (TPU). The occurrence of an observable TPU limitation is highly variable based on species and especially growth conditions, with TPU capacity seemingly regulated to be in just slight excess of the likely photosynthetic rate. The physiological effects of TPU limitation are discussed with an emphasis on interactions between the Calvin-Benson cycle and the light reactions. Methods for detecting TPU-limited data from gas exchange data are detailed, and the impact on modeling of some physiological effects are shown. Special consideration is given to common misconceptions about TPU.\n\nHighlightPhotosynthetic triose phosphate utilization limitation is discussed, highlighting misleading points in physiology and focusing on regulation.

plant biology↗

bioRxiv2018

Unleashing floret fertility by a mutated homeobox gene improved grain yield during wheat evolution under domestication

Floret fertility is a key trait to determine the number of grains per inflorescence in cereals. During wheat (Triticum sp.) evolution, floret fertility has been increased and current bread wheat (T. aestivum L.) produces three to five grains per spikelet; however, little is known about the genetic basis controlling floret fertility. Here we identify the quantitative trait locus Grain Number Increase 1 (GNI1), encoding a homeodomain leucine zipper class I (HD-Zip I) transcription factor. GNI1 evolved in the Triticeae through gene duplication and functionalization. GNI1 was predominantly expressed in the most apical floret primordia and parts of the rachilla, suggesting that GNI1 inhibits rachilla growth and development. GNI1 expression decreased during wheat evolution, and as a consequence, more fertile florets and grains per spikelet are being produced. Genetic analysis revealed that the reduced-function allele of GNI1-A contributes to increase the number of fertile florets per spikelet. The knockdown of GNI1 in transgenic hexaploid wheat improved fertile floret and grain number. Furthermore, wheat plants carrying the impaired allele increased grain yield under field conditions. Our findings illuminate that gene duplication and functionalization generated evolutionary novelty for floret fertility (i.e. reducing floral numbers) while the mutations towards increased grain production were under selection during wheat evolution under domestication.\n\nSignificance StatementGrain number is a fundamental trait for cereal grain yield; but its underlying genetic basis is mainly unknown in wheat. Here we show for the first time a direct link between increased floret fertility, higher grain number per spike and higher plot-yields of wheat in the field. We have identified GNI1 gene encoding an HD-Zip I transcription factor responsible for increased floret fertility. The wild type allele imposes an inhibitory role specifically during rachilla development, indicating that expression of this protein actively shuts-down grain yield potential; whereas, the reduced-function allele enables more florets and grains to be produced. GNI1 evolved through gene duplication in Triticeae and its mutations were under parallel human selection during wheat and barley evolution under domestication.

plant biology↗

bioRxiv2018

Defining the developmental program leading to meiosis in maize

In multicellular organisms, the entry into meiosis is a complex process characterized by increasing levels of meiotic specialization. We used single-cell RNA-sequencing to reconstruct the developmental program into meiosis in maize. We observed a smooth continuum of expression stages leading up to meiosis, followed by a sharp reorganization of the transcriptome in early meiotic prophase. This latter transcriptional shift was dramatic, with 26.7% of expressed genes changing by 2 fold or more, and occurred just prior to a proposed cell cycle checkpoint. Changes in cell physiology accompanied the nuclear events of meiosis, including a decrease in protein translation capacity and increase in membrane-bound organelles. We further identified differences in gene expression between the mitotic and meiotic cell cycles. Our results uncover a multi-step pathway into meiosis and highlight the power of single cell RNA-seq to define developmental transitions.

plant biology↗

bioRxiv2018

Root endophytes improve physiological performance and yield in crops under salt stress by up-regulating the foliar sodium concentration

Increase in the soil salinity will be a conspicuous constraint for both native plant communities as well as several crops worldwide. In this context plant root-associated fungi appear as a new strategy to improve ecophysiological performance and yield of crops under abiotic stress. Here, we evaluated how the inoculation of fungal endophytes isolated from Antarctic plants can improve the ecophysiological performance in cultivars of tomato and lettuce, grown under different salt conditions. In addition, we assessed if the expression of the NHX1 gene that is related with salt tolerance is enhanced in presence of fungal endophytes. Finally, we evaluated the regulation the nutritional status and specifically the Na+ content in leaves. Overall, those individuals with presence of endophytes showed higher ecophysiological performance. In addition, the presence of fungal endophytes was correlated with a higher regulation of ion homeostasis by enhanced expression of NHX1 gene. Our results suggest that presence of fungal endophytes could minimize the negative effect of salt by improving osmotic tolerance through ecophysiological and molecular mechanisms. Thus, root-endophytes might be a successful biotechnological tool to maintain high levels of ecophysiological performance and productivity in zones under osmotic stress, acting as potential solution to maintain the global food security.\n\nHighlightWe showed that functional symbiosis improve the physiological performance and yield in crops subjected to salinity, by biochemical and molecular mechanisms. Thus, here we pointed a successful strategy to meet the future challenges for help to maintain the food security.

plant biology↗

bioRxiv2018

Multi-lab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

O_LIThere is a dynamic reciprocity between plants and their environment: On one hand, the physiochemical properties of soil influence plant morphology and metabolism, while on the other, root morphology and exudates shape the environment surrounding roots. Here, we investigate both of these aspects as well as the reproducibility of these responses across laboratories.\nC_LIO_LIThe model grass Brachypodium distachyon was grown in phosphate-sufficient and phosphate-deficient mineral media, as well as in sterile soil extract, within fabricated ecosystem (EcoFAB) devices across four laboratories.\nC_LIO_LITissue weight and phosphate content, total root length, root tissue and exudate metabolic profiles were found to be consistent across laboratories and distinct between experimental treatments. Plants grown in soil extract were morphologically and metabolically distinct in all laboratories, with root hairs four times longer compared to other growth conditions. Further, plants depleted half of the investigated metabolites from the soil extract.\nC_LIO_LITo interact with their environment, plants not only adapt morphology and release complex metabolite mixtures; they also selectively deplete a range of soil-derived metabolites. The EcoFABs utilized here generated high inter-laboratory reproducibility, demonstrating that their value in standardized investigations of plant traits.\nC_LI

plant biology↗