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Results for “Plant Biology”

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bioRxiv2016

3D sorghum reconstructions from depth images enable identification of quantitative trait loci regulating shoot architecture

Dissecting the genetic basis of complex traits is aided by frequent and non-destructive measurements. Advances in range imaging technologies enable the rapid acquisition of three-dimensional (3D) data from an imaged scene. A depth camera was used to acquire images of Sorghum bicolor, an important grain, forage, and bioenergy crop, at multiple developmental timepoints from a greenhouse-grown recombinant inbred line population. A semi-automated software pipeline was developed and used to generate segmented, 3D plant reconstructions from the images. Automated measurements made from 3D plant reconstructions identified quantitative trait loci (QTL) for standard measures of shoot architecture such as shoot height, leaf angle and leaf length, and for novel composite traits such as shoot compactness. The phenotypic variability associated with some of the QTL displayed differences in temporal prevalence; for example, alleles closely linked with the sorghum Dwarf3 gene, an auxin transporter and pleiotropic regulator of both leaf inclination angle and shoot height, influence leaf angle prior to an effect on shoot height. Furthermore, variability in composite phenotypes that measure overall shoot architecture, such as shoot compactness, is regulated by loci underlying component phenotypes like leaf angle. As such, depth imaging is an economical and rapid method to acquire shoot architecture phenotypes in agriculturally important plants like sorghum to study the genetic basis of complex traits.

Plant Biology↗

bioRxiv2016

Modifications to a LATE MERISTEM IDENTITY-1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.)

Leaf shape is spectacularly diverse. As the primary source of photo-assimilate in major crops, understanding the evolutionary and environmentally induced changes in leaf morphology are critical to improving agricultural productivity. The role of leaf shape in cotton domestication is unique, as breeders have purposefully selected for entire and lobed leaf morphs resulting from a single locus, okra (L-D1). The okra locus is not only of agricultural importance in cotton (Gossypium hirsutum L.), but through pioneering chimeric and morphometric studies it has contributed to fundamental knowledge about leaf development. Here we show that the major leaf shapes of cotton at the L-D1 locus are controlled by a HD-Zip transcription factor most similar to Late Meristem Identity1 (LMI1) gene. The classical okra leaf shape gene has133-bp tandem duplication in the promoter, correlated with elevated expression, while an 8-bp deletion in the third exon of the presumed wild-type normal leaf causes a frame-shifted and truncated coding sequence. Virus-induced gene silencing (VIGS) of this LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. An intermediate leaf shape allele, sub-okra, lacks both the promoter duplication and the exonic deletion. Our results indicate that sub-okra is the ancestral leaf shape of tetraploid cotton and normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton.

Plant Biology↗

bioRxiv2016

Beyond APs and VPs: evidences of chaos and self-organized criticality in electrical signals in plants.

Studies on plant electrophysiology are mostly focused on specific traits of action potentials (APs) and/or variation potentials (VPs), often in single cells. Inspired by the complexity of the signaling network in plants and by analogies with some traits of neurons in human brains, we have sought for evidences of high complexity in the electrical dynamics of plant signaling, beyond APs and VPs responses. Thus, from EEG-like data analyses of soybean plants, we showed consistent evidences of chaotic dynamics in the electrical time series. Furthermore, we have found that the dynamic complexity of electrical signals is affected by the plant physiological conditions, decreasing when plant was stressed. Surprisingly, but not unlikely, we have observed that, after stimuli, electrical spikes arise following a power law distribution, which is indicative of self-organized criticality (SOC). Since, as far as we know, these were the first evidences of chaos and SOC in plant electrophysiology, we have asked follow-up questions and we have proposed new hypotheses, seeking for improving our understanding about these findings.

Plant Biology↗

bioRxiv2016

CRISPR-Cas9 mediated mutagenesis of a DMR6 ortholog in tomato confers broad-spectrum disease resistance

Pathogenic microbes are responsible for severe production losses in crops worldwide. The use of disease resistant crop varieties can be a sustainable approach to meet the food demand of the worlds growing population. However, classical plant breeding is usually laborious and time-consuming, thus hampering efficient improvement of many crops. With the advent of genome editing technologies, in particular the CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-Cas9) system, we are now able to introduce improved crop traits in a rapid and efficient manner. In this work, we genome edited durable disease resistance in tomato by modifying a specific gene associated with disease resistance. Recently, it was demonstrated that inactivation of a single gene called DMR6 (downy mildew resistance 6) confers resistance to several pathogens in Arabidopsis thaliana. This gene is specifically up-regulated during pathogen infection, and mutations in the dmr6 gene results in increased salicylic acid levels. The tomato SlDMR6-1 orthologue Solyc03g080190 is also up-regulated during infection by Pseudomonas syringae pv. tomato and Phytophthora capsici. Using the CRISPR-Cas9 system, we generated tomato plants with small deletions in the SlDMR6-1 gene that result in frameshift and premature truncation of the protein. Remarkably, these mutants do not have significant detrimental effects in terms of growth and development under greenhouse conditions and show disease resistance against different pathogens, including P. syringae, P. capsici and Xanthomonas spp.

Plant Biology↗

bioRxiv2016

Quantitative, image-based phenotyping methods provide insight into spatial and temporal dimensions of plant disease

Plant disease symptoms exhibit complex spatial and temporal patterns that are challenging to quantify. Image-based phenotyping approaches enable multi-dimensional characterization of host-microbe interactions and are well suited to capture spatial and temporal data that are key to understanding disease progression. We applied image-based methods to investigate cassava bacterial blight, which is caused by the pathogen Xanthomonas axonopodis pv. manihotis (Xam). We generated Xam strains in which individual predicted type III effector (T3E) genes were mutated and applied multiple imaging approaches to investigate the role of these proteins in bacterial virulence. Specifically, we quantified bacterial populations, water-soaking disease symptoms, and pathogen spread from the site of inoculation over time for strains with mutations in avrBs2, xopX, and xopK as compared to wild-type Xam. {Delta}avrBs2 and {Delta}xopX both showed reduced growth in planta and delayed spread through the vasculature system of cassava. {Delta}avrBs2 exhibited reduced water-soaking symptoms at the site of inoculation. In contrast, {Delta}xopK exhibited enhanced induction of disease symptoms at the site of inoculation but reduced spread through the vasculature. Our results highlight the importance of adopting a multi-pronged approach to plant disease phenotyping to more fully understand the roles of T3Es in virulence. Finally, we demonstrate that the approaches used in this study can be extended to many host-microbe systems and increase the dimensions of phenotype that can be explored.\n\nSummaryNovel, image-based phenotyping methods enhance characterization of plant-pathogen interactions.

Plant Biology↗

bioRxiv2016

NUCLEAR FACTOR Y, subunit A (NF-YA) proteins positively regulate flowering and act through FLOWERING LOCUS T

Photoperiod dependent flowering is one of several mechanisms used by plants to initiate the developmental transition from vegetative growth to reproductive growth. The NUCLEAR FACTOR Y (NF-Y) transcription factors are heterotrimeric complexes composed of NF-YA and histone-fold domain (HFD) containing NF-YB/NF-YC, that initiate photoperiod-dependent flowering by cooperatively interacting with CONSTANS (CO) to drive the expression of FLOWERING LOCUS T (FT). This involves NF-Y and CO binding at distal CCAAT and proximal \"CORE\" elements, respectively, in the FT promoter. While this is well established for the HFD subunits, there remains some question over the potential role of NF-YA as either positive or negative regulators of this process. Here we provide strong support, in the form of genetic and biochemical analyses, that NF-YA, in complex with NF-YB/NF-YC proteins, can directly bind the distal CCAAT box in the FT promoter and are positive regulators of flowering in an FT-dependent manner.\n\nAuthor SummaryFor plants to have reproductive success, they must time their flowering with the most beneficial biotic and abiotic environmental conditions - after all, reproductive success would likely be low if flowers developed when pollinators were not present or freezing temperatures were on the horizon. Proper timing mechanisms for flowering vary significantly between different species, but can be connected to a variety of environmental cues, including water availability, temperature, and day length. Numerous labs have studied the molecular aspects of these timing mechanisms and discovered that many of these pathways converge on the gene FLOWERING LOCUS T (FT). This means that understanding precisely how this gene is regulated can teach us a lot about many plant species in both natural and agricultural settings. In the current study, we focus on day length as an essential cue for flowering in the plant species Arabidopsis thaliana. We further unravel the complexity of FT regulation by clarifying the roles of NUCLEAR FACTOR Y genes in day length perception.

Plant Biology↗

bioRxiv2016

NUCLEAR FACTOR Y, subunit C (NF-YC) transcription factors are positive regulators of photomorphogenesis in Arabidopsis thaliana

Recent reports suggested that NF-Y transcription factors are positive regulators of skotomorphogenesis in Arabidopsis thaliana. Three NF-YC genes (NF-YC3, NF-YC4, and NF-YC9) are known to have overlapping functions in photoperiod dependent flowering and previous studies demonstrated that they interact with basic leucine zipper (bZIP) transcription factors. This included ELONGATED HYPOCOTYL 5 (HY5), which has well-demonstrated roles in photomorphogenesis. Similar to hy5 mutants, we report that nf-yc3 nf-yc4 nf-yc9 triple mutants failed to inhibit hypocotyl elongation in all tested light wavelengths. Surprisingly, nf-yc3 nf-yc4 nf-yc9 hy5 mutants had synergistic defects in light perception, suggesting that NF-Ys represent a parallel light signaling pathway. As with other photomorphogenic transcription factors, nf-yc3 nf-yc4 nf-yc9 triple mutants also partially suppress the short hypocotyl and dwarf rosette phenotypes of CONSTITUTIVE PHOTOMORPHOGENIC 1 (cop1) mutants. Thus, our data strongly suggest that NF-Y transcription factors have important roles as positive regulators of photomorphogenesis, and in conjunction with other recent reports implies that the NF-Y are multifaceted regulators of early seedling development.\n\nAuthor SummaryLight perception is critically important for the fitness of plants in both natural and agricultural settings. Plants not only use light for photosynthesis, but also as a cue for proper development. As a seedling emerges from soil it must determine the light environment and adopt an appropriate growth habit. When blue and red wavelengths are the dominant sources of light, plants will undergo photomorphogenesis. Photomorphogenesis describes a number of developmental responses initiated by light in a seedling, and includes shortened stems and establishing the ability to photosynthesize. The genes regulating photomorphogenesis have been studied extensively, but a complete picture remains elusive. Here we describe the finding that NUCLEAR FACTOR-Y (NF-Y) genes are positive regulators of photomorphogenesis - i.e., in plants where NF-Y genes are mutated, they display some characteristics of dark grown plants, even though they are in the light. Our data suggests that the roles of NF-Y genes in light perception do not fit in easily with those of other described pathways. Thus, studying these genes promises to help develop a more complete picture of how light drives plant development.

Plant Biology↗

bioRxiv2016

Morphometric analysis of Passiflora leaves I: the relationship between landmarks of the vasculature and elliptical Fourier descriptors of the blade

BACKGROUNDLeaf shape among Passiflora species is spectacularly diverse. Underlying this diversity in leaf shape are profound changes in the patterning of the primary vasculature and laminar outgrowth. Each of these aspects of leaf morphology--vasculature and blade--provides different insights into leaf patterning.\n\nRESULTSHere, we morphometrically analyze >3,300 leaves from 40 different Passiflora species collected sequentially across the vine. Each leaf is measured in two different ways: using 1) 15 homologous Procrustes-adjusted landmarks of the vasculature, sinuses, and lobes and 2) Elliptical Fourier Descriptors (EFDs), which quantify the outline of the leaf. The ability of landmarks, EFDs, and both datasets together are compared to determine their relative ability to predict species and node position within the vine. Pairwise correlation of x and y landmark coordinates and EFD harmonic coefficients reveals close associations between traits and insights into the relationship between vasculature and blade patterning.\n\nCONCLUSIONSLandmarks, more reflective of the vasculature, and EFDs, more reflective of the blade contour, describe both similar and distinct features of leaf morphology. Landmarks and EFDs vary in ability to predict species identity and node position in the vine and exhibit a correlational structure (both within landmark or EFD traits and between the two data types) revealing constraints between vascular and blade patterning underlying natural variation in leaf morphology among Passiflora species.

Plant Biology↗

bioRxiv2016

Morphometric analysis of Passiflora leaves II: divergent heteroblastic trajectories underlie the disparate leaf shapes among Passiflora species

PREMISE OF THE STUDYNot only does leaf shape vary between Passiflora species, but between sequential nodes of the vine. The profound changes in leaf shape within Passiflora vines reflect the temporal development of the shoot apical meristem from which leaves are derived and patterned, a phenomenon known as heteroblasty.\n\nMETHODSWe perform a morphometric analysis of more than 3,300 leaves from 40 different Passiflora species using two different methods: homologous landmarks and Elliptical Fourier Descriptors (EFDs).\n\nKEY RESULTSChanges in leaf shape across the vine are first quantified in allometric terms; that is, changes in the relative area of leaf sub-regions expressed in terms of overall leaf area. Shape is constrained to strict linear relationships as a function of size that vary between species. Statistical analysis of leaf shape, using landmarks and EFDs, reveals that species effects are the strongest, followed by interaction effects, and negligible heteroblasty effects. The ability of different nodes to predictively discriminate species and the variability of landmark and EFD traits at each node is then analyzed. Heteroblastic trajectories, the changes in leaf shape between the first and last measured leaves in a vine, are then compared between species in a multivariate space.\n\nCONCLUSIONLeaf shape diversity among Passiflora species is expressed in a heteroblastic-dependent manner. Leaf shape is constrained by linear, allometric relationships related to leaf size that vary between species. There is a strong species x heteroblasty interaction effect for leaf shape, suggesting that different leaf shapes between species arise through changes in shape across nodes. The first leaves in the series are not only more like each other, but are also less variable across species. From this similar, shared leaf shape, subsequent leaves in the heteroblastic series follow divergent morphological trajectories. The disparate leaf shapes characteristic of Passiflora species arise from a shared, juvenile morphology.

Plant Biology↗

bioRxiv2016

Into the Evening: Complex Interactions in the Arabidopsis circadian clock.

In Arabidopsis thaliana, an assembly of proteins named the evening complex (EC) has been established as an essential component of the circadian clock with conserved functions in regulating plant growth and development. Recent studies identifying EC-regulated genes and EC-interacting proteins have expanded our understanding of EC function. In this review, we focus on new progress uncovering how the EC contributes to the circadian network through the integration of environmental inputs and the direct regulation of key clock genes. We also summarize new findings of how the EC directly regulates clock outputs, such as day-length dependent and thermoresponsive growth, and provide new perspectives on future experiments to address unsolved questions related to the EC.

Plant Biology↗

bioRxiv2016

Low-pH induced reversible reorganizations of chloroplast thylakoid membranes - as revealed by small-angle neutron scattering

Energization of thylakoid membranes brings about the acidification of the lumenal aqueous phase, which activates important regulatory mechanisms. Earlier Jajoo and coworkers (2014 FEBS Lett. 588:970) have shown that low pH in isolated plant thylakoid membranes induces changes in the excitation energy distribution between the two photosystems. In order to elucidate the structural background of these changes, we used small-angle neutron scattering on thylakoid membranes exposed to low p2H and show that gradually lowering the p2H from 8.0 to 5.0 causes small but well discernible reversible diminishment of the periodic order and the lamellar repeat distance and an increased mosaicity - similar to the effects elicited by light-induced acidification of the lumen. Our data strongly suggest that thylakoids dynamically respond to the membrane energization and actively participate in different regulatory mechanisms.\n\nHighlightsO_LIThylakoid membranes exposed to low p2H studied by small-angle neutron scattering\nC_LIO_LIAcidification causes reversible shrinkage and diminished lamellar order\nC_LIO_LISANS changes induced by low pH resemble those due to light-induced lumenal acidification\nC_LI\n\nAbbreviations

Plant Biology↗

bioRxiv2016

Targeted re-sequencing reveals the genetic signatures and the reticulate history of barley domestication

O_LIBarley (Hordeum vulgare L.) is an established model to study domestication of the Fertile Crescent cereals. Recent molecular data suggested that domesticated barley genomes consist of the ancestral blocks descending from multiple wild barley populations. However, the relationship between the mosaic ancestry patterns and the process of domestication itself remained unclear.\nC_LIO_LITo address this knowledge gap, we identified candidate domestication genes using selection scans based on targeted resequencing of 433 wild and domesticated barley accessions. We conducted phylogenetic, population structure, and ancestry analyses to investigate the origin of the domesticated barley haplotypes separately at the neutral and candidate domestication loci.\nC_LIO_LIWe discovered multiple selective sweeps that occurred on all barley chromosomes during domestication in the background of several ancestral wild populations. The ancestry analyses demonstrated that, although the ancestral blocks of the domesticated barley genomes descended from all over the Fertile Crescent, the candidate domestication loci originated specifically in its eastern and western parts.\nC_LIO_LIThese findings provided first molecular evidence in favor of multiple barley domestications in the Levantine and Zagros clusters of the origin of agriculture.\nC_LI

Plant Biology↗

bioRxiv2016

Paleochronic reversion in Psophocarpus, the decompression function in floral anatomic fields

Paleochronic reversion (an atavism) in Psophocarpus presents a basic floral phylloid ground state. That ground state can quickly change as permutation transformation (Tx) begins. The form of permutation can vary as phyllotactic phylloid (TPhyld) and/or floral axial decompression (TAxl) presenting linear elongation (TLong), rotational (TRtn) and/or lateral (TLat) components. Research with 70 reverted floral specimens documented varying degrees of phyllotactic permutation at the bracts (Bt) region and inter-bracts (IBS) sub-region of the pre-whorls pedicel-bracts anatomic zone. Permutation further yielded an inter-zonal pericladial stalk (PCL). It continued at the floral whorls zone: the calyx (Cl), corolla (Crla), androecium (Andr), and gynoecium (Gynec) with components therein. These organ regions present a continuum as an axial dynamic vector space {pound}Taxi of floral permutation dominated by axial expansion (AE) so that an anatomic sequence of permutation activity runs from the bracts (Bt) region to the carpel (Crpl) inclusive with components therein, summarized by the formula:\n\n [Formula]stamen fltn [Formula] Andr spiral [Formula] Crpl {+/-}(Crpl web {+/-} VASCARP {+/-} Crpl diadn {+/-} Crpl fltn {+/-} [fltn no] {+/-} Crpl Rtn) = Tx. The flower reverts from a system of determinate growth to one of indeterminate growth.

Plant Biology↗

bioRxiv2016

Strigolactone regulates shoot development through a core signalling pathway

Strigolactones are a recently identified class of hormone that regulate multiple aspects of plant development. The DWARF14 (D14) /{beta} fold protein has been identified as a strigolactone receptor, which can act through the SCFMAX2 ubiquitin ligase, but the universality of this mechanism is not clear. Multiple proteins have been suggested as targets for strigolactone signalling, including both direct proteolytic targets of SCFMAX2, and downstream targets. However, the relevance and importance of these proteins to strigolactone signalling in many cases has not been fully established. Here we assess the contribution of these targets to strigolactone signalling in adult shoot developmental responses. We find that all examined strigolactone responses are regulated by SCFMAX2 and D14, and not by other D14-like proteins. We further show that all examined strigolactone responses likely depend on degradation of SMXL proteins in the SMXL6 clade, and not on other proposed proteolytic targets. Taken together, our results suggest that in the adult shoot, the dominant mode of strigolactone signalling is D14-initiated, MAX2-mediated degradation of SMXL6-related proteins. We confirm that the BRANCHED1 transcription factor and the PIN-FORMED1 auxin efflux carrier are plausible downstream targets of this pathway in the regulation of shoot branching, and show that BRC1 likely acts in parallel to PIN1.\n\nAUTHOR SUMMARYStrigolactones are a recently discovered family plant hormones with diverse roles in development, most strikingly in the regulation shoot branching. Our understanding of the mechanism(s) by which plants perceive and respond to strigolactones is growing rapidly. It is likely that the strigolactone signaling pathway has evolved by duplication and diversification of specific components of a pre-existing pathway, involved in perception and response to an as yet unknown hormone. Several of these components have been identified and several new candidate components have been implicated in the pathway. We have adopted a genetic approach to assess systematically the contributions of all these players to strigolactone signaling in the shoot. We exclude some of the candidate proteins from involvement in strigolactone-mediated shoot branching control and define a core pathway for strigolactone action in the shoot. We provide evidence that downstream of this core, the strigolactone signaling pathway branches, with different effectors mediating different shoot responses.

Plant Biology↗

bioRxiv2016

Deep learning based root-soil segmentation from X-ray tomography

One of the most challenging computer vision problem in plant sciences is the segmentation of root and soil from X-ray tomography. So far, this has been addressed from classical image analysis methods. In this paper, we address this root/soil segmentation problem from X-ray tomography using a new deep learning classification technique. The robustness of this technique, tested for the first time on this plant science problem, is established with root/soil presenting a very low contrast in X-ray tomography. We also demonstrate the possibility to segment efficiently root from soil while learning on purely synthetic soil and root.

Plant Biology↗

bioRxiv2016

An immuno-suppressive aphid saliva protein is delivered into the cytosol of plant mesophyll cells during feeding.

Herbivore selection of plant hosts and plant responses to insect colonization have been subjects of intense investigations. A growing body of evidence suggests that for successful colonization to occur, (effector/virulence) proteins in insect saliva must modulate plant defense responses to the benefit of the insect. A range of insect saliva proteins that modulate plant defense responses have been identified, but there is no direct evidence that these proteins are delivered into specific plant tissues and enter plant cells. Aphids and other sap-sucking insects of the order Hemiptera use their specialized mouthparts (stylets) to probe plant mesophyll cells, until they reach the phloem cells for long-term feeding. Here we show by immunogold-labeling of ultrathin sections of aphid feeding sites that an immuno-suppressive aphid effector localizes in the cytoplasm of mesophyll cells near aphid stylets, but not in cells further away from aphid feeding sites. In contrast, another aphid effector protein localizes in the sheaths composed of gelling saliva that surround the aphid stylets. Thus, insects deliver effectors directly into plant tissue. Moreover, different aphid effectors locate extracellularly in the sheath saliva or are introduced into the cytoplasm of plant cells.

Plant Biology↗

bioRxiv2016

Natural Variation in Arabidopsis Cvi-0 Accession Uncovers Regulation of Guard Cell CO2 Signaling by MPK12

Plant gas exchange is regulated by guard cells that form stomatal pores. Stomatal adjustments are crucial for plant survival; they regulate uptake of CO2 for photosynthesis, loss of water and entrance of air pollutants such as ozone. We mapped ozone hypersensitivity, more open stomata and stomatal CO2-insensitivity phenotypes of the Arabidopsis thaliana accession Cvi-0 to a single amino acid substitution in MAP kinase 12 (MPK12). In parallel we showed that stomatal CO2-insensitivity phenotypes of a mutant cis (CO2-insensitive) were caused by a deletion of MPK12. Lack of MPK12 impaired bicarbonate-induced activation of S-type anion channels. We demonstrated that MPK12 interacted with the protein kinase HT1, a central node in guard cell CO2 signaling, and that MPK12 can function as an inhibitor of HT1. These data provide a new function for plant MPKs as protein kinase inhibitors and suggest a mechanism through which guard cell CO2 signaling controls plant water management.

Plant Biology↗

bioRxiv2016

Gene expression analysis provides insight into the physiology of the important staple food crop cassava

O_LICassava (Manihot esculenta) feeds approximately 800 million people worldwide. Although this crop displays high productivity under drought and poor soil conditions, it is susceptible to disease, postharvest deterioration and the roots contain low nutritional content.\nC_LIO_LIHere, we provide molecular identities for eleven cassava tissue types through RNA-sequencing and develop an open access, web-based interface for further interrogation of the data.\nC_LIO_LIThrough this dataset, we report novel insight into the physiology of cassava and identify promoters able to drive specified tissue expression profiles. Specifically, we focus on identification of the transcriptional signatures that define the massive, underground storage roots used as a food source and the favored target tissue for transgene integration and genome editing, friable embryogenic callus (FEC).\nC_LIO_LIThe information gained from this study is of value for both conventional and biotechnological improvement programs.\nC_LI

Plant Biology↗