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Results for “Plant Biology”

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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 379 records · Page 21Linked to original sources
bioRxiv2017

Vegetative compatibility groups explain variation in the virulence of Verticillium dahliae on strawberry

Verticillium dahliae infection of strawberry (Fragaria x ananassa) is a major cause of disease-induced wilting in soil-grown strawberries across the world. To understand what components of the pathogen are affecting disease expression, the presence of the known effector VdAve1 was screened in a sample of Verticillium dahliae isolates. Isolates from strawberry were found to contain VdAve1 and were divided into two major clades, based upon their vegetative compatibility groups (VCG); no UK strawberry isolates contained VdAve1. VC clade was strongly related to their virulence levels. VdAve1-containing isolates pathogenic on strawberry were found in both clades, in contrast to some recently published findings.\n\nOn strawberry, VdAve1-containing isolates had significantly higher virulence during early infection, which diminished in significance as the infection progressed. Transformation of a virulent non-VdAve1 containing isolate, with VdAve1 was found neither to increase nor decrease virulence when inoculated on a susceptible strawberry cultivar. There are therefore virulence factors that are epistatic to VdAve1 and potentially multiple independent routes to high virulence on strawberry in V. dahliae lineages.\n\nGenome sequencing a subset of isolates across the two VCGs revealed that isolates were differentiated at the whole genome level and contained multiple changes in putative effector content, indicating that different clonal VCGs may have evolved different strategies for infecting strawberry, leading to different virulence levels in pathogenicity tests. It is therefore important to consider both clonal lineage and effector complement as the adaptive potential of each lineage will differ, even if they contain the same race determining effector.

plant biology↗
bioRxiv2017

Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

Plants respond to seasonal cues, such as the photoperiod, to adapt to current conditions and to prepare for environmental changes in the season to come. To assess photoperiodic responses at the protein level, we quantified the proteome of the model plant Arabidopsis thaliana by mass spectrometry across four photoperiods. This revealed coordinated changes of abundance in proteins of photosynthesis, primary and secondary metabolism, including pigment biosynthesis, consistent with higher metabolic activity in long photoperiods. Higher translation rates in the daytime than the night likely contribute to these changes via rhythmic changes in RNA abundance. Photoperiodic control of protein levels might be greatest only if high translation rates coincide with high transcript levels in some photoperiods. We term this proposed mechanism {acute}translational coincidence{acute}, mathematically model its components, and demonstrate its effect on the Arabidopsis proteome. Datasets from a green alga and a cyanobacterium suggest that translational coincidence contributes to seasonal control of the proteome in many phototrophic organisms. This may explain why many transcripts but not their cognate proteins exhibit diurnal rhythms.

plant biology↗
bioRxiv2017

Novel Computed Tomography-based tools reliably quantify plant reproductive investment

The flower is a bisexual reproductive unit where both genders compete for resources. Counting pollen and ovules in flowers is essential to understand how much is invested in each gender. Classical methods to count very numerous pollen grains and ovules are inefficient when pollen grains are tightly aggregated, and when fertilization rates of ovules are unknown. We thus established novel, Computed-Tomography-based counting techniques. In order to display the potential of our methods in very difficult cases, we counted pollen and ovules across inflorescences of deceptive and rewarding species of European orchids, which possess both very large numbers of pollen grains (tightly aggregated) and ovules. Pollen counts did not significantly vary across inflorescences and pollination strategies, whereas deceptive flowers had significantly more ovules than rewarding flowers. The within inflorescence variance of pollen to ovule ratios in rewarding flowers was four times higher than in deceptive flowers, possibly demonstrating differences in the constraints acting on both pollination strategies. We demonstrate the inaccuracies and limitations of previously established methods, and the broad applicability of our new techniques: they allow measurement of reproductive investment without restriction on object number or aggregation, and without specimen destruction.

plant biology↗
bioRxiv2017

Functional characterization and discovery of modulators of SbMATE, the agronomically important aluminium tolerance transporter from Sorghum bicolor

About 50% of the worlds arable land is strongly acidic (soil pH < 5). The low pH of these soils solubilizes root-toxic ionic aluminium (Al3+) species from clay minerals, driving the evolution of various counteractive adaptations in cultivated crops. The food crop Sorghum bicolor, for example, upregulates the membrane-embedded transporter protein SbMATE in its roots. SbMATE mediates efflux of the anionic form of the organic acid, citrate, into the soil rhizosphere, chelating Al3+ ions and thereby imparting Al-resistance based on excluding Al+3 from the growing root tip. Here, we use electrophysiological, radiolabeled, and fluorescence-based transport assays in two heterologous expression systems to establish a broad substrate recognition profile of SbMATE, showing the transport of 14C- citrate anion, as well as the organic monovalent cation, ethidium, but not the divalent ethidium-derivative, propidium. The transport cycle is proton and/or sodium-driven, and shares certain molecular mechanisms with bacterial MATE-family transporters. We further complement our transport assays by directly measuring substrate binding to detergent-purified SbMATE protein. Finally, we use the functionally-folded, purified membrane protein as an antigen to discover high-affinity, native conformation-binding and transport function-altering nanobodies using an animal-free, mRNA/cDNA display technology. Our results demonstrate the utility of using Pichia pastoris as an efficient eukaryotic host to express large quantities of functional plant transporter proteins for in vitro characterization. The nanobody discovery approach is applicable to other low immunogenic plant proteins.

plant biology↗
bioRxiv2017

Raspberry Pi Powered Imaging for Plant Phenotyping

O_LIPremise of the study: Image-based phenomics is a powerful approach to capture and quantify plant diversity. However, commercial platforms that make consistent image acquisition easy are often cost-prohibitive. To make high-throughput phenotyping methods more accessible, low-cost microcomputers and cameras can be used to acquire plant image data.\nC_LIO_LIMethods and Results: We used low-cost Raspberry Pi computers and cameras to manage and capture plant image data. Detailed here are three different applications of Raspberry Pi controlled imaging platforms for seed and shoot imaging. Images obtained from each platform were suitable for extracting quantifiable plant traits (shape, area, height, color) en masse using open-source image processing software such as PlantCV.\nC_LIO_LIConclusion: This protocol describes three low-cost platforms for image acquisition that are useful for quantifying plant diversity. When coupled with open-source image processing tools, these imaging platforms provide viable low-cost solutions for incorporating high-throughput phenomics into a wide range of research programs.\nC_LI

plant biology↗
bioRxiv2017

ARIGAN: Synthetic Arabidopsis Plants using Generative Adversarial Network

In recent years, there has been an increasing interest in image-based plant phenotyping, applying state-of-the-art machine learning approaches to tackle challenging problems, such as leaf segmentation (a multi-instance problem) and counting. Most of these algorithms need labelled data to learn a model for the task at hand. Despite the recent release of a few plant phenotyping datasets, large annotated plant image datasets for the purpose of training deep learning algorithms are lacking. One common approach to alleviate the lack of training data is dataset augmentation. Herein, we propose an alternative solution to dataset augmentation for plant phenotyping, creating artificial images of plants using generative neural networks. We propose the Arabidopsis Rosette Image Generator (through) Adversarial Network: a deep convolutional network that is able to generate synthetic rosette-shaped plants, inspired by DC-GAN (a recent adversarial network model using convolutional layers). Specifically, we trained the network using A1, A2, and A4 of the CVPPP 2017 LCC dataset, containing Arabidopsis Thaliana plants. We show that our model is able to generate realistic 128 x 128 colour images of plants. We train our network conditioning on leaf count, such that it is possible to generate plants with a given number of leaves suitable, among others, for training regression based models. We propose a new Ax dataset of artificial plants images, obtained by our ARIGAN. We evaluate this new dataset using a state-of-the-art leaf counting algorithm, showing that the testing error is reduced when Ax is used as part of the training data.

plant biology↗
bioRxiv2017

Tissue specific auxin biosynthesis regulates leaf vein patterning

The plant hormone auxin (indole-3-acetic acid, IAA) has a profound influence over plant cell growth and differentiation. Current understanding of vein development in leaves is based on the canalization of auxin into self-reinforcing streams which determine the sites of vascular cell differentiation. However, the role of auxin biosynthesis during leaf development in the context of leaf vein patterning has not been much studied so far. Here we characterize the context specific importance of auxin biosynthesis, auxin transport and mechanical regulations in a growing leaf. We show that domains of auxin biosynthesis predict the positioning of vascular cells. In mutants that have reduced capacity in auxin biosynthesis, leaf vein formation is decreased. While exogenous application of auxin does not compensate the loss of vein formation in auxin biosynthesis mutants, inhibition of polar auxin transport does compensate the vein-less phenotype, suggesting that the site-specific accumulation of auxin, which is likely to be mainly caused by the local auxin biosynthesis, is important for leaf vein formation. Our computational model of midvein development brings forth the interplay of cell stiffness and auxin dependent cell division. We propose that local auxin biosynthesis has the integral role in leaf vascular development.\n\nHighlightsO_LIBuilt spatially and temporally resolved auxin biosynthesis map in growing leaf primordium of Arabidopsis.\nC_LIO_LIExpression domains of auxin biosynthetic enzymes within primordia strongly correlated with leaf vein initiation.\nC_LIO_LIResults show that domains of auxin biosynthesis within primordia drive leaf vein initiation and patterning.\nC_LI\n\nHighlights and eTOC BlurbUsing modelling and a spatiotemporal analysis of auxin biosynthesis and transport, Kneuper et al. show that tissue specific auxin biosynthesis defines places of vein initiation hence underlining the importance of auxin concentration in vein initiation.

plant biology↗
bioRxiv2017

Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum

The domestication of diverse grain crops from wild grasses resulted from artificial selection for a suite of overlapping traits producing changes referred to in aggregate as \"domestication syndrome\". Parallel phenotypic change can be accomplished by either selection on orthologous genes, or selection on non-orthologous genes with parallel phenotypic effects. To determine how often artificial selection for domestication traits in the grasses targeted orthologous genes, we employed resequencing data from wild and domesticated accessions of Zea (maize) and Sorghum (sorghum). Many \"classic\" domestication genes identified through QTL mapping in populations resulting from wild/domesticated crosses indeed show signatures of parallel selection in both maize and sorghum. However, the overall number of genes showing signatures of parallel selection in both species is not significantly different from that expected by chance. This suggests that, while a small number of genes will extremely large phenotypic effects have been targeted repeatedly by artificial selection during domestication, the optimization portion of domestication targeted small and largely non-overlapping subsets of all possible genes which could produce equivalent phenotypic alterations.

plant biology↗
bioRxiv2017

Climbing Legumes: An Underutilized Resource With Significant Potential to Intensify Farming on Terrace Walls (FTW) for Smallholder Farmers

Millions of subsistence farmers cultivate crops on terraces. These farmers face unique challenges including severe shortages of arable land and remoteness leading to poor access to inputs including nitrogen fertilizer. These challenges contribute to human and livestock malnutrition. Terrace walls (risers) as a vertical surface to grow climbing or trailing legumes represents an opportunity to help overcome these challenges. These crops are rich in minerals and protein, and their associated microbes produce nitrogen fertilizer. Rice bean is already grown on terrace risers in South Asia. This paper reviews the literature concerning crops that are currently farmed on terrace walls (FTW), then surveys climbing legume species that have potential for FTW, focusing on crops that are nutritious and tolerate shade (caused by the terrace wall) and resist drought (many terrace farms experience an extended dry season). A total of 29 legume species are discussed including climbing varieties of jack bean, common bean, cowpea, winged bean, horse gram and velvet bean. The review concludes by discussing the practical challenges of farmer adoption of FTW and makes concrete recommendations. Terrace wall cultivation of legumes represents an opportunity to intensify agriculture and increase resiliency in remote mountainous areas.

plant biology↗
bioRxiv2017

Leveraging multiple datasets for deep leaf counting

The number of leaves a plant has is one of the key traits (phenotypes) describing its development and growth. Here, we propose an automated, deep learning based approach for counting leaves in model rosette plants. While state-of-the-art results on leaf counting with deep learning methods have recently been reported, they obtain the count as a result of leaf segmentation and thus require per-leaf (instance) segmentation to train the models (a rather strong annotation). Instead, our method treats leaf counting as a direct regression problem and thus only requires as annotation the total leaf count per plant. We argue that combining different datasets when training a deep neural network is beneficial and improves the results of the proposed approach. We evaluate our method on the CVPPP 2017 Leaf Counting Challenge dataset, which contains images of Arabidopsis and tobacco plants. Experimental results show that the proposed method significantly outperforms the winner of the previous CVPPP challenge, improving the results by a minimum of 50% on each of the test datasets, and can achieve this performance without knowing the experimental origin of the data (i.e. \"in the wild\" setting of the challenge). We also compare the counting accuracy of our model with that of per leaf segmentation algorithms, achieving a 20% decrease in mean absolute difference in count (|DiC|).

plant biology↗
bioRxiv2017

Functional characterization of the ABF gene family in upland cotton (Gossypium hirsutum L.)

The AREB/ABF bZIP transcription factors play a pivotal role in abscisic acid-dependent abiotic stress-responsive gene expression. Despite the perennial damage and reduced productivity that result from water-deficit and unpredictable early season temperature fluctuations, these critical genes have not been previously examined in upland cotton (Gossypium hirsutum). Here, we report the isolation of the G. hirsutum ABF homologs, characterization of their expression patterns in response to abiotic stress treatments, and examination of their functions through heterologous ectopic expression in Arabidopsis. As expected for an allotetraploid, G. hirsutum ABF homologs are present in the genome as homeologous pairs. These genes are differentially expressed, both among the homologs and within the homeologous pairs, in response to exogenous abscisic acid (ABA) application, dehydration, and chilling temperatures. Furthermore, heterologous ectopic expression of many of the G. hirsutum ABF genes in Arabidopsis conferred increased tolerance to water deficit and osmotic stress, as well as cold tolerance, in a gene specific manner. These results indicate the G. hirsutum ABF homologs are functional in Arabidopsis and, as in other species, are likely to play an essential role in the abiotic stress response.\n\nHighlightThe Gossypium hirsutum ABF homeologs are differentially expressed in response to abiotic stress, and their ectopic expression in Arabidopsis can confer increased water deficit tolerance.

plant biology↗
bioRxiv2017

Parallels between artificial selection in temperate maize and natural selection in the cold-adapted crop-wild relative Tripsacum

Artificial selection has produced varieties of domesticated maize which thrive in temperate climates around the world. However, the direct progenitor of maize, teosinte, is indigenous only to a relatively small range of tropical and sub-tropical latitudes and grows poorly or not at all outside of this region. Tripsacum, a sister genus to maize and teosinte, is naturally endemic to the majority of areas in the western hemisphere where maize is cultivated. A full-length reference transcriptome for Tripsacum dactyloides generated using long-read isoseq data was used to characterize independent adaptation to temperate climates in this clade. Genes related to phospholipid biosynthesis, a critical component of cold acclimation on other cold adapted plant lineages, were enriched among those genes experiencing more rapid rates of protein sequence evolution in T. dactyloides. In contrast with previous studies of parallel selection, we find that there is a significant overlap between the genes which were targets of artificial selection during the adaptation of maize to temperate climates and those which were targets of natural selection in temperate adapted T. dactyloides. This overlap between the targets of natural and artificial selection suggests genetic changes in crop-wild relatives associated with adaptation to new environments may be useful guides for identifying genetic targets for breeding efforts aimed at adapting crops to a changing climate.

plant biology↗
bioRxiv2017

The FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis

The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1), subunit of the chromatin remodeler FAcilitates Chromatin Transactions (FACT), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We find that FACT co-localizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.

plant biology↗
bioRxiv2017

Comparison of gene expression patterns of Kappaphycus alvarezii (Rhodophyta, Solieriaceae) under different light wavelengths and CO2 enrichment

Transcriptomes associated with the process of photosynthesis and carbon fixation have offered insights into the mechanism of gene regulation in terrestrial plants, however limited information is available as far as macroalgae are concerned. Intertidal red alga, Kappaphycus alvarezii is exposed to different wavelengths of light in their lives as light quantity and quality changes at different depths in seawater. This investigation aims to study the underlying mechanisms associated with photosynthesis and carbon fixation under specific light qualities and CO2 enrichment. Light regulation of gene expression has not been previously described for red algae. By using next generation sequencing, transcriptome profiling of K. alvarezii generated 76,871 qualified transcripts with a mean length of 979bp and a N50 length of 1,707bp and 55.83% transcripts were annotated on the basis of function. Blue, green and red light all have demonstrated roles in modulating light responses, such as changes in gene expression. Here we analysed the effects of light regulation on four selected photosynthesis aspects (light-harvesting complex, phycobilisomes, photosystems and photoreceptors). We observed that light-regulated gene expression in this species is not a single light response and different light qualities are transduced to regulate the same metabolic pattern. The carbon fixation pathway was analysed and key genes encoding enzymes involved in the carbon fixation pathway such as ppc, pepc, prk, pgk, ppdk, provided that unequivocal molecular evidence that most of the C3 and C4 pathway genes were actively transcribed in K. alvarezii. In addition to this the CO2 induced transcriptome suggested the possibility of shifting carbon metabolism pathway after acclimation to increased level of CO2. Impact of CO2 enrichment on the cultures has provided new insight into the response to rising CO2.

plant biology↗
bioRxiv2017

Phytophthora palmivora establishes tissue-specific intracellular infection structures in the earliest divergent land plant lineage

The expansion of plants onto land was a formative event that brought forth profound changes to the Earths geochemistry and biota. Filamentous eukaryotic microbes developed the ability to colonize plant tissues early during the evolution of land plants, as demonstrated by intimate symbiosis-like associations in >400 million-year-old fossils. However, the degree to which filamentous microbes establish pathogenic interactions with early divergent land plants is unclear. Here, we demonstrate that the broad host-range oomycete pathogen Phytophthora palmivora colonizes liverworts, the earliest divergent land plant lineage. We show that P. palmivora establishes a complex tissue-specific interaction with Marchantia polymorpha, where it completes a full infection cycle within air chambers of the dorsal photosynthetic layer. Remarkably, P. palmivora invaginates M. polymorpha cells with haustoria-like structures that accumulate host cellular trafficking machinery and the membrane-syntaxin MpSYP13B but not the related MpSYP13A. Our results indicate that the intracellular accommodation of filamentous microbes is an ancient plant trait that is successfully exploited by pathogens like P. palmivora.

plant biology↗
bioRxiv2017

The ERA-related GTPase AtERG2 associated with mitochondria 18S RNA is essential for early embryo development in Arabidopsis

The ERA (E. coli RAS-like protein)-related GTPase (ERG) is a nuclear-encoded GTPase with two conserved domains: a GTPase domain and a K Homology domain. ERG plays a vital role in early seed development in Antirrhinum majus. However, the mechanism that regulates seed development remains unclear. Blasting the genome sequence revealed two homologies of ERG, AtERG1, and AtERG2 in Arabidopsis. In this study, we found that AtERG2 is localised in the mitochondria and binds mitochondrial 18S RNA. Promoter and transcript analyses indicated that AtERG2 was mainly expressed in the leaf vein, trichome, mature pollen, and ovule. The mutants of AtERG2 showed recessive lethal, gametophytic maternal effects, silique shortage, and early seed abortion, in which some seeds arrested in the zygotic stage at 1.5 days after pollination (DAP) and aborted at 2.0 DAP in aterg2-1 +/-. Reactive oxygen species (ROS) accumulated at 1.5 DAP in the arrested seeds, and the transcription of several ROS-responsible genes, WRKY40, ANAC017, and AOXla, was up-regulated in the aterg2-1 +/- seeds which were arrested 1.5 and 2.0 DAP but not in wild-type (WT) and aterg2-1 +/- seeds. The cell death-related gene BAG6 was also transcriptionally activated in aterg2-1 +/- seeds arrested at 2.0 DAP. Chloramphenicol treatment during pollination induced a similar phenotype and gene expression pattern but showed no transcriptional changes of ANAC017 in WT. These results suggested that AtERG2 promotes early seed development by affecting the maturation of the mitochondria ribosome small subunit and mitochondrial protein translation in Arabidopsis.

plant biology↗
bioRxiv2017

The partial duplication of an E3-ligase gene in Triticeaespecies mediates resistance to powdery mildew fungi

In plant-pathogen interactions, components of the plant ubiquitination machinery are preferred targets of pathogen-encoded effectors suppressing defense responses or co-opting host cellular functions for accommodation. Here, we employed transient and stable gene silencing-and over-expression systems in Hordeum vulgare (barley) to study the function of HvARM1 (for H. vulgare Armadillo 1), a partial gene duplicate of the U-box/armadillo-repeat E3 ligase HvPUB15 (for H. vulgare Plant U-Box 15). The partial ARM1 gene was derived from an ancient gene-duplication event in a common ancestor of the Triticeae tribe of grasses comprising the major crop species H. vulgare, Triticum aestivum and Secale cereale. The barley gene HvARM1 contributed to quantitative host as well as nonhost resistance to the biotrophic powdery mildew fungus Blumeria graminis, and allelic variants were found to be associated with powdery mildew-disease severity. Both HvPUB15 and HvARM1 proteins interacted in yeast and plant cells with the susceptibility-related, plastid-localized barley homologs of THF1 (for Thylakoid formation 1) and of ClpS1 (for Clp-protease adaptor S1) of Arabidopsis thaliana. The results suggest a neo-functionalization HvARM1 to increase resistance against powdery mildew and provide a link to plastid function in susceptibility to biotrophic pathogen attack.

plant biology↗
bioRxiv2017

CRISPR/Cas9-mediated resistance to cauliflower mosaic virus

Viral diseases are a leading cause of worldwide yield losses in crop production. Breeding of resistance genes (R gene) into elite crop cultivars has been the standard and most cost-effective practice. However, R gene-mediated resistance is limited by the available R genes within genetic resources and in many cases, by strain specificity. Therefore, it is important to generate new and broad-spectrum antiviral strategies. The CRISPR-Cas9 (clustered regularly interspaced palindromic repeat, CRISPR-associated) editing system has been employed to confer resistance to human viruses and several plant single-stranded DNA geminiviruses, pointing out the possible application of the CRISPR-Cas9 system for virus control. Here we demonstrate that strong viral resistance to cauliflower mosaic virus (CaMV), a pararetrovirus with a double-stranded DNA genome, can be achieved through Cas9-mediated multiplex targeting of the viral coat protein sequence. We further show that small interfering RNAs (siRNA) are produced and mostly map to the 3' end of guide RNAs (gRNA), although very low levels of siRNAs map to the spacer region as well. However, these siRNAs are not responsible for the inhibited CaMV infection because there is no resistance if Cas9 is not present. We have also observed edited viruses in systematically infected leaves in some transgenic plants, with short deletions or insertions consistent with Cas9-induced DNA breaks at the gRNA target sites in coat protein coding sequence. These edited coat proteins, in most cases, led to earlier translation stop and thus, non-functional coat proteins. We also recovered wild-type CP sequence in these infected transgenic plants, suggesting these edited viral genomes were packaged by wild-type coat proteins. Our data demonstrate that the CRISPR-Cas9 system can be used for virus control against plant pararetroviruses with further modifications.

plant biology↗