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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 343 records · Page 19Linked to original sources

bioRxiv2017

Rice TSV3 Encoding Obg-like GTPase Protein is Essential for Chloroplast Development during the Early Leaf Stage under Cold Stress

The Spo0B-associated GTP-binding (Obg) proteins occupy a wide variety of roles in the viability of nearly all bacteria. Its detailed roles in higher plants have not yet been elucidated. A novel rice thermo-sensitive virescent mutant tsv3 was identified in this study that displayed albino phenotype at 20{degrees}C before the 3-leaf stage while being normal green at 32{degrees}C or even at 20{degrees}C after the 4-leaf stage. The mutant phenotype was aligned with altered chlorophyll (Chl) content and chloroplast development. Map-based cloning and complementation test showed that TSV3 encoded a kind of small GTP binding protein. Subcellular localization revealed that TSV3 was in chloroplast. TSV3 transcripts were highly expressed in leaves and weak or undetectable in other tissues, suggesting the tissue-specific expression. In tsv3 mutant, the transcriptional levels of certain genes associated with biogenesis of chloroplast ribosomes 50S subunit were severely decreased at the 3-leaf-stage under cold stress, but could be recovered to normal levels at a higher temperature (32{degrees}C). The observations from this study indicated that the rice nuclear-encoded TSV3 plays important roles in chloroplast development at early leaf stage under cold stress.

plant biology↗

bioRxiv2017

Temperature and Light Effects on Germination of Peronospora effusa Sporangia

Spinach downy mildew, caused by the biotrophic oomycete Peronospora effusa, is an economically important disease that is found in all spinach growing regions of the US. To effectively predict disease risk we need to understand the response of P. effusa to different environmental conditions. We conducted several germination assays, exposing P. effusa sporangia to different temperature and lighting conditions. Between 5 and 25{degrees}C under constant darkness, germination of P. effusa sporangia on water agar declined. These results were qualitatively different from a previous study of P. effusa germination that found a bimodal response curve, with increased germination at lower and higher temperatures. Time course studies revealed that sporangia consistently germinated within the first twelve hours of plating, regardless of incubation temperature. Sporangia exposed to blue light had significantly reduced germination when compared with those exposed to red, yellow, or no light. Light intensity and color significantly impacted germination, although the effect of color varied by light intensity.

plant biology↗

bioRxiv2017

Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions

Eutrema salsugineum is a model species for the study of plant adaptation to abiotic stresses. Two accessions of E. salsugineum, Shandong (SH) and Yukon (YK), exhibit contrasting morphology, biotic, and abiotic stress tolerance. Transcriptome and metabolic profiling from tissue samples collected during the dark period were used to investigate the molecular and metabolic bases of these contrasting phenotypes. RNA sequencing identified 17,888 expressed genes, of which 157 were not in the published reference genome and 65 were detected for the first time. Differential expression was detected for only 31 genes. The RNA sequencing data contained 14,808 single nucleotide polymorphisms (SNPs) in transcripts, 3,925 of which are newly identified. Among the differentially expressed genes, there were no obvious candidates for the physiological or morphological differences between SH and YK. Metabolic profiling indicated that YK accumulates free fatty acids and long-chain fatty acid derivatives as compared to SH; whereas sugars are more abundant in SH. Metabolite levels suggest that carbohydrate and respiratory metabolism, including starch degradation, is more active during the first half of the dark period in SH. These metabolic differences may explain the greater biomass accumulation in YK over SH. The accumulation of 56% of the identified metabolites was lower in F1 hybrids than the mid-parent averages and the accumulation of 17% of the metabolites in F1 plants transgressed the level in both parents. Concentrations of several metabolites in F1 hybrids agree with previous studies and suggest a role for primary metabolism in heterosis. The improved annotation of the E. salsugineum genome and newly-identified high-quality SNPs will permit accelerated studies using the standing variation in this species to elucidate the mechanisms of its diverse adaptations to the environment.

plant biology↗

bioRxiv2017

An efficient experiment design helps to identify differential expressed genes (DEGs) in RNA-seq data in studies of plant qualitative traits

In this study, we conducted comparative transcriptome analysis between homozygous dominant parent and heterozygous F1 hybrid with homozygous recessive parent in qualitative trait study of common wheat (Triticum aestivum L.). Two sets of near-isogenic lines (NILs) were used: one set of NILs carrying powdery mildew resistance and susceptible Pm2 alleles, the other set of NILs carrying different awn inhibition gene B1 alleles. The results demonstrated that 2,932 DEGs were identified between L031 (Pm2Pm2) and Chancellor (pm2pm2), while 1,494 DEGs presented between F1 hybrid (Pm2pm2) and Chancellor, the co-regulated DEGs were 1,028. For the wheat awn inhibition gene B1 test, 720 DEGs were identified between SN051-2 (B1B1) and SN051-1 (b1b1), and 231 DEGs were identified between F1 hybrid (B1b1) and SN051-1, the co-regulated DEGs were 180. Hierarchical clustering analysis of co-regulated DEGs showed that dominant parent and F1 hybrid were clustered as the nearest neighbors, while recessive parent showed an apparent departure. The results showed that the overlapping DEGs between dominant parent and F1 hybrid with recessive parent reduced the number of interested DEGs to only one-quarter (or one-third) of that between dominant and recessive parent, these overlapping loci could provide insights into molecular mechanisms that are affected by causal mutations.

plant biology↗

bioRxiv2018

HRS1/HHOs GARP transcription factors and reactive oxygen species are regulators of Arabidopsis nitrogen starvation response.

Plants need to cope with strong variations in the nitrogen content of the soil solution. Although many molecular actors are being discovered concerning how plants perceive NO3- provision, it is less clear how plants recognize a lack of Nitrogen. Indeed, following N removal plants activate their Nitrogen Starvation Response (NSR) being characterized in particular by the activation of very high affinity nitrate transport systems (NRT2.4, NRT2.5) and other sentinel genes such as GDH3. Here we show using a combination of functional genomics (via TF perturbation) and molecular physiology studies, that the GARP Transcription Factors (TFs) belonging the HHO sub-family are important regulators of the NSR through two potential mechanisms. First, HHOs directly repress NRT2.4 and NRT2.5 high-affinity nitrate transporters. Genotypes affected in HHO genes (mutants and overexpressors) display modified high-affinity nitrate transport activities opening interesting perspectives in biotechnology applications. Second, we show that Reactive Oxygen Species (ROS) are important to control NSR in wild type plants and that HRS1 and HHO1 overexpressors are affected in their ROS content, defining a potential feedforward branch of the signaling pathway. Taken together our results define two new classes of molecular actors in the control of NSR including ROS and the first transcription factors to date. This work (i) opens perspectives on a poorly understood nutrient related signaling pathway, and (ii) defines targets for molecular breeding of plants with enhanced NO3- uptake.

plant biology↗

bioRxiv2017

Elemental Accumulation in Kernels of the Maize Nested Association Mapping Panel Reveals Signals of Gene by Environment Interactions

Elemental accumulation in seeds is the product of a combination of environment and a wide variety of genetically controlled physiological processes. We measured the kernel elemental composition of the Nested Association Mapping (NAM) of maize (Zea mays L.) grown in 4 different environments. Analysis of variance revealed strong effects of genotype, environment and genotype by environment interactions. Using Joint-linkage mapping on a set of 7000 markers we identified 354 quantitative trait loci (QTL) across 20 elements, four environments and a combination of the environments. Leveraging 20 M SNPs derived from genome resequencing on the parents of the population, genome-wide association mapping studies (GWAS) detected 8573 loci. While most of the GWAS SNPs were located near genes not previously implicated in elemental regulation, several SNPs were located next to orthologs of well-characterized elemental regulation genes.

plant biology↗

bioRxiv2017

Widespread sampling biases in herbaria revealed from large-scale digitization

O_LINon-random collecting practices may bias conclusions drawn from analyses of herbarium records. Recent efforts to fully digitize and mobilize regional floras offer a timely opportunity to assess commonalities and differences in herbarium sampling biases.\nC_LIO_LIWe determined spatial, temporal, trait, phylogenetic, and collector biases in [~]5 million herbarium records, representing three of the most complete digitized floras of the world: Australia (AU), South Africa (SA), and New England (NE).\nC_LIO_LIWe identified numerous shared and unique biases among these regions. Shared biases included specimens i) collected close to roads and herbaria; ii) collected more frequently during spring; iii) of threatened species collected less frequently; and iv) of close relatives collected in similar numbers. Regional differences included i) over-representation of graminoids in SA and AU and of annuals in AU; and ii) peak collection during the 1910s in NE, 1980s in SA, and 1990s in AU. Finally, in all regions, a disproportionately large percentage of specimens were collected by a few individuals. These mega-collectors, and their associated preferences and idiosyncrasies, may have shaped patterns of collection bias via founder effects.\nC_LIO_LIStudies using herbarium collections should account for sampling biases and future collecting efforts should avoid compounding these biases.\nC_LI

plant biology↗

bioRxiv2017

A transcription factor binding atlas for photosynthesis in cereals identifies a key role for coding sequence in the regulation of gene expression

The majority of plants use C3 photosynthesis, but over sixty independent lineages of angiosperms have evolved the C4 pathway. In most C4 species, photosynthesis gene expression is compartmented between mesophyll and bundle sheath cells. We performed DNaseI-SEQ to identify genome-wide profiles of transcription factor binding in leaves of the C4 grasses Zea mays, Sorghum bicolor and Setaria italica as well as C3 Brachypodium distachyon. In C4 species, while bundle sheath strands and whole leaves shared similarity in the broad regions of DNA accessible to transcription factors, the short sequences bound varied. Transcription factor binding was prevalent in gene bodies as well as promoters, and many of these sites could represent duons that impact gene regulation in addition to amino acid sequence. Although globally there was little correlation between any individual DNaseI footprint and cell-specific gene expression, within individual species transcription factor binding to the same motifs in multiple genes provided evidence for shared mechanisms governing C4 photosynthesis gene expression. Furthermore, interspecific comparisons identified a small number of highly conserved transcription factor binding sites associated with leaves from species that diverged around 60 million years ago. These data therefore provide insight into the architecture associated with C4 photosynthesis gene expression in particular and characteristics of transcription factor binding in cereal crops in general.\n\nOne sentence summaryGenome-wide patterns of transcription factor binding in vivo defined by DNaseI for leaves of C3 and C4 grasses

plant biology↗

bioRxiv2017

Compositional shifts in the root microbiota track the life-cycle of field-grown rice plants

Bacterial communities associated with roots impact the health and nutrition of the host plant. While a multitude of static factors are known to influence the composition of the root-associated microbiota, the dynamics of these microbial assemblies over the plant life cycle are poorly understood. Here, we use dense temporal sampling of spatial compartments to characterize the root-associated microbiota of field grown rice (Oryza sativa) over the course of three consecutive growing seasons and two sites in diverse geographic regions. The root microbiota was found to be highly dynamic during the vegetative phase of plant growth, then stabilizes compositionally for the remainder of the life cycle. Bacterial taxa conserved between field sites can be used as predictive features of rice plant age by modeling using a random forests approach. The age-prediction models were used to reveal that drought stressed plants have developmentally delayed microbiota compared to unstressed plants. Further, by using genotypes with varying developmental rates, we show that shifts in the microbiome are correlated with rates of developmental transitions rather than age alone, such that different microbiota compositions reflect juvenile and adult life stages. These results suggest a model for successional dynamics of the root-associated microbiota over the plant life cycle.

plant biology↗

bioRxiv2017

Zinc availability modulates plant growth and immune responses via AZI1

Zinc is an essential micronutrient for all living organisms and is involved in a plethora of processes including growth and development, and immunity. However, it is unknown if there is a common genetic and molecular basis underlying multiple facets of zinc function. Here we used natural variation in Arabidopsis thaliana to study the role of zinc in regulating growth. We identify allelic variation of the systemic immunity gene AZI1 as a key for determining root growth responses to low zinc conditions. We further demonstrate that this gene is important for modulating root growth depending on the zinc and defence status. Finally, we show that the interaction of the immunity signal azelaic acid and zinc level to regulate root growth is conserved in rice. This work demonstrates that there is a common genetic and molecular basis for multiple zinc dependent processes and that nutrient cues can determine the balance of plant growth and immune responses in plants.

plant biology↗

bioRxiv2017

Biomass increase under zinc deficiency caused by delay of early flowering in Arabidopsis

Plants generally produce more biomass when all nutrients are available in sufficient amounts. In addition to environmental constraints, genetic and developmental factors, such as the transition from vegetative to reproductive growth, restrict maximal yield. Here we report the peculiar observation that a subset of early flowering Arabidopsis thaliana accessions produced larger shoot rosette diameters when grown in zinc (Zn)-deficient conditions, compared with Zn-sufficient conditions. This was associated with early flowering that restricted the leaf length under Zn sufficiency. Zinc deficiency repressed FLOWERING LOCUS T (FT) expression, a major regulator of flowering. Repression or loss of FT increased the rosette diameter by a delay of the transition to flowering, a longer phase of leaf proliferation and increased leaf number. The transition to flowering reduced, but not terminated, the proliferation of established leaves. The size of individual leaf mesophyll cells was not affected by Zn deficiency or loss of FT, indicating that the larger rosette diameter was caused by maintained proliferation of vegetative tissue. As a consequence, early flowering accessions under Zn deficiency grew larger rosette diameters due to a delay of flowering, which explains the unusual increase of vegetative biomass under nutrient deficiency.\n\nHighlightAn increase in biomass of some Arabidopsis accessions under Zn-deficiency is caused by retardation of flowering, prolonging vegetative growth.\n\nAbbreviations

plant biology↗

bioRxiv2017

Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules

The transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how many cis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the Assay for Transposase-Accessible Chromatin (ATAC-seq) in four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite 10-fold variation in intergenic space among species, the majority of open chromatin regions lie within 3 kb upstream of a transcription start site in all species. We find a common set of four TFs that appear to regulate conserved gene sets in the root tips of all four species, suggesting that TF-gene networks are generally conserved. Comparative ATAC-seq profiling of Arabidopsis root hair and non-hair cell types revealed extensive similarity as well as many cell type-specific differences. Analyzing TF binding sites in differentially accessible regions identified a MYB-driven regulatory module unique to the hair cell, which appears to control both cell fate regulators and abiotic stress responses. Our analyses revealed common regulatory principles among species and shed light on the mechanisms producing cell type-specific transcriptomes during development.

plant biology↗

bioRxiv2017

An updated infrageneric classification of the oaks: review of previous taxonomic schemes and synthesis of evolutionary patterns

In this paper, we review major classification schemes proposed for oaks by John Claudius Loudon, Anders Sandoe Orsted, William Trelease, Otto Karl Anton Schwarz, Aimee Antoinette Camus, Yuri Leonardovich Menitsky, and Kevin C. Nixon. Classifications of oaks (Fig. 1) have thus far been based entirely on morphological characters. They differed profoundly from each other because each taxonomist gave a different weight to distinguishing characters; often characters that are homoplastic in oaks. With the advent of molecular phylogenetics our view has considerably changed. One of the most profound changes has been the realisation that the traditional split between the East Asian subtropical to tropical subgenus Cyclobalanopsis and the subgenus Quercus that includes all other oaks is artificial. The traditional concept has been replaced by that of two major clades, each comprising three infrageneric groups: a Palearctic-Indomalayan clade including Group Ilex (Ilex oaks), Group Cerris (Cerris oaks) and Group Cyclobalanopsis (cycle-cup oaks), and a predominantly Nearctic clade including Group Protobalanus (intermediate or golden cup oaks), Group Lobatae (red oaks) and Group Quercus (white oaks, with most species in America and some 30 species in Eurasia). The main morphological feature characterising these phylogenetic lineages is pollen morphology, a character overlooked in traditional classifications. This realisation, along with the now available (molecular-)phylogenetic framework, opens new avenues for biogeographic, ecological and evolutionary studies and a re-appraisal of the fossil record. We provide an overview about recent advances in these fields and outline how the results of these studies contribute to the establishment of a unifying systematic scheme of oaks. Ultimately, we propose an updated classification of Quercus recognising two subgenera with eight sections. This classification considers morphological traits, molecular-phylogenetic relationships, and the evolutionary history of one of the most important temperate woody plant genera.\n\nO_FIG O_LINKSMALLFIG WIDTH=156 HEIGHT=200 SRC=\"FIGDIR/small/168146_fig1.gif\" ALT=\"Figure 1\">\nView larger version (49K):\norg.highwire.dtl.DTLVardef@d5a05org.highwire.dtl.DTLVardef@91295forg.highwire.dtl.DTLVardef@3338fcorg.highwire.dtl.DTLVardef@e24a58_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Classification schemes for Quercus from Loudon to Nixon (see Appendix). Colour coding denotes the actual systematic affiliation of species included in each taxon: of the Old World or mid-latitude clade section Cyclobalanopsis (cycle-cup oaks, yellow), section Cerris (Cerris oaks; orange), and section Ilex (Ilex oaks; green); and of the New World or high-latitude clade section Quercus (white oaks s.str.; blue), sections Virentes (cyan) and Ponticae (dark blue), section Protobalanus (intermediate oaks; purple), and section Lobatae (red oaks; red). Colour gradients are proportional, i.e. reflect the proportion of species with different systematic affiliation included in each taxon. Note: Menitsky (1984) and Trelease (1924) only treated the Eurasian and American oaks, respectively, and provided classifications in (nearly) full agreement with current phylogenies.\n\nC_FIG

plant biology↗

bioRxiv2017

Vacuolar invertase activity shapes photosynthetic stress response of Arabidopsis thaliana and stabilizes central energy supply

Stabilization of the central carbohydrate and energy metabolism plays a key role in plant stress response. As the primary photosynthetic products, carbohydrates are substrate for numerous metabolic and stress-protective reactions. Further, they have been shown to be involved in diverse signalling processes finally affecting and regulating plant stress response on a whole plant level. Sucrose metabolism is known to be central to many stress-related processes and enzymes catalysing its biosynthesis, transport and degradation have been shown to significantly impact stress resistance and acclimation output. However, due to the cyclic structure of sucrose metabolism involving sucrose cleavage in multiple compartments as well as energy-demanding re-synthesis via hexose phosphorylation, it is challenging to derive an unambiguous picture of its contribution to stress reactions. In the present study, a combined stress experiment comprising cold and high-light identified metabolism of sucrose and fumaric acid to significantly separate the stress response of a cold susceptible and a tolerant natural accession of Arabidopsis thaliana. Kinetic modelling and simulation of subcellular rates of invertase-driven sucrose cleavage revealed a contrasting picture between the susceptible and the tolerant accession pointing to an important role of vacuolar invertase during initial stress response. Using a T-DNA insertion mutant with a dramatically reduced invertase activity provided evidence for a central role of the enzyme in stabilizing photosynthesis and the central energy metabolism during freezing and high-light stress. Reducing vacuolar invertase activity to about 3% of the wild type resulted in a strong increase of ADP and ATP levels indicating a severe effect on cytosolic and plastidial energy balance. Together with a significant decrease of maximum quantum yield of photosystem II (Fv/Fm) these results suggest that vacuolar invertase activity stabilizes cytosolic energy metabolism by supplying hexose equivalents being phosphorylated in the cytosol. Finally, the accompanying ATP consumption is essential for cytosolic phosphate balance which directly affects photosynthetic performance by the supply of ADP being crucial for photosynthetic ATP production.

plant biology↗

bioRxiv2017

Conventional and hyperspectral time-series imagingof maize lines widely used in field trials

Maize (Zea mays ssp. mays) is one of three crops, along with rice and wheat, responsible for more than 1/2 of all calories consumed around the world. Increasing the yield and stress tolerance of these crops is essential to meet the growing need for food. The cost and speed of plant phenotyping is currently the largest constraint on plant breeding efforts. Datasets linking new types of high throughput phenotyping data collected from plants to the performance of the same genotypes under agronomic conditions across a wide range of environments are essential for developing new statistical approaches and computer vision based tools. A set of maize inbreds - primarily recently off patent lines - were phenotyped using a high throughput platform at University of Nebraska-Lincoln. These lines have been previously subjected to high density genotyping, and scored for a core set of 13 phenotypes in field trials across 13 North American states in two years by the Genomes to Fields consortium. A total of 485 GB of image data including RGB, hyperspectral, fluorescence and thermal infrared photos has been released. Correlations between image-based measurements and manual measurements demonstrated the feasibility of quantifying variation in plant architecture using image data. However, naive approaches to measuring traits such as biomass can introduce nonrandom measurement errors confounded with genotype variation. Analysis of hyperspectral image data demonstrated unique signatures from stem tissue. Integrating heritable phenotypes from high-throughput phenotyping data with field data from different environments can reveal previously unknown factors influencing yield plasticity.

plant biology↗

bioRxiv2017

Endogenous synthesis of pyrethrins by cannabis

Pyrethrins are a class of natural terpenoid pesticides produced by Tanacetum cinerariifolium, commonly known as chrysanthemum. Here we present evidence that cannabis may be able to produce pyrethrins endogenously. Flower from a cannabis plant grown in a closed hydroponic environment contained 2.48 parts per million pyrethrin I by weight. A comparison of the genetics of T. cinerariifolium and Cannabis demonstrates Cannabis homologues of the genes that contribute to pyrethrins production in T. cinerariifolium. This provides a plausible pathway for the biosynthesis of pyrethrins in cannabis. Although preliminary, these data indicate a potentially significant confounding variable in both cannabis research and regulations on allowable pyrethrins residues in cannabis products.

plant biology↗

bioRxiv2017

Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legume Parasponia

Rhizobium nitrogen-fixing nodules are a well-known trait of legumes, but nodules also occur in other plant lineages either with rhizobium or the actinomycete Frankia as microsymbiont. The widely accepted hypothesis is that nodulation evolved independently multiple times, with only a few losses. However, insight in the evolutionary trajectory of nodulation is lacking. We conducted comparative studies using Parasponia (Cannabaceae), the only non-legume able to establish nitrogen fixing nodules with rhizobium. This revealed that Parasponia and legumes utilize a large set of orthologous symbiosis genes. Comparing genomes of Parasponia and its non-nodulating relative Trema did not reveal specific gene duplications that could explain a recent gain of nodulation in Parasponia. Rather, Trema and other non-nodulating species in the Order Rosales show evidence of pseudogenization or loss of key symbiosis genes. This demonstrates that these species have lost the potential to nodulate. This finding challenges a long-standing hypothesis on evolution of nitrogen-fixing symbioses, and has profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.

plant biology↗

bioRxiv2017

Maize leaf functional responses to drought episode and rewatering

Effects of crop growth and physiological activity to drought and irrigation regimes have been extensively studied; however, the responses of plant growth, morphological and photosynthetic behaviors to drought episodes and thereafter rewatering receive a less attention. This field experiment was carried out directly in situ at an agricultural ecosystem research station during 2015-2016, in a northeastern China, on the renowned northeastern maize production belt, where is being threatened by severe drought. A field automatic rain-shelter was used, and five irrigation regimes including control, four drought episodes, and rewatering treatments were established. The chlorophyll contents (SPAD values), light-saturated photosynthetic rate (Asat), and photosystem II actual quantum yield ({Phi}PSII), maximum quantum yield (Fv'/Fm') decreased at lower leaf positions and with plant development. Episodic drought effects on plant growth, leaf morphological traits and photosynthetic processes at both vegetative and reproductive stages were severely remarked, particularly at late development stage and with longer drought duration. The recovery of leaf functional traits of the plants experienced historical-drought following re-irrigating was not fully restored to the level of the plants subjected to ample and normal water status; and the strength of recovery was proportional to the persistence of pre-drought episodes. The relationship of Asat with SPAD depends on water status and plant development. A principal component analysis can well denote the change patterns in responses to water status treatments with plant development. The results may give an insight into how to understand the maize traits responses to drought episode and rewatering, and this also might assist the drought-stricken crops to cope with future climatic change.

plant biology↗