Bacteria are able to sense their population's density through a cell–cell communication system, termed ‘quorum sensing’ (QS). This system regulates gene expression in response to cell density through the constant production and detection of signalling molecules. These molecules commonly act as auto-inducers through the up-regulation of their own synthesis. Many pathogenic bacteria, including those of plants, rely on this communication system for infection of their hosts. The finding that the countering of QS-disrupting mechanisms exists in many prokaryotic and eukaryotic organisms offers a promising novel method to fight disease. During the last decade, several approaches have been proposed to disrupt QS pathways of phytopathogens, and hence to reduce their virulence. Such studies have had varied success in vivo, but most lend promising support to the idea that QS manipulation could be a potentially effective method to reduce bacterial-mediated plant disease. This review discusses the various QS-disrupting mechanisms found in both bacteria and plants, as well as the different approaches applied artificially to interfere with QS pathways and thus protect plant health.
Knockout of all six alleles of a gene in the large wheat genome confers resistance to powdery mildew --- Genetic engineering to improve crops is entering a new era as conventional transgenesis technology, which involves random insertion of genes into the genome, is superseded by newer approaches that enable precise genetic alterations. A particular technological challenge in carrying out targeted genome modification in crops is that many plant genomes are polyploid, including such important species as wheat, potato and canola1. In this issue, Wang et al.2 report engineering of the hexaploid wheat genome using sequence-specific nucleases (SSNs)—the first demonstration in a polyploid crop of SSN-mediated genetic alterations that are stably transmitted to the next generation. By knocking out all six alleles encoding the MILDEW-RESISTANCE LOCUS (MLO) protein, the authors generated a mutant line that shows strong resistance to powdery mildew, a devastating fungal disease. This is a remarkable feat, given the ploidy and enormous size (17.1 Gb) of the wheat genome, and showcases the power of SSNs for engineering complex plant genomes and for creating crops with valuable traits.
Plant interactions with other organisms: molecules, ecology and evolution
Different shades of JAZ during plant growth and defense
Nutrient supply differentially alters the dynamics of co-infecting phytoviruses
From shade avoidance responses to plant performance at vegetation level: using virtual plant modelling as a tool F. J. Bongers, J. B. Evers, N. P. R. Anten & R. Pierik
Magical mystery tour: MLO proteins in plant immunity and beyond J. Acevedo-Garcia, S. Kusch & R. Panstruga
The squeeze cell hypothesis for the activation of jasmonate synthesis in response to wounding
E. E. Farmer, D. Gasperini & I. F. Acosta
Lipochitooligosaccharide recognition: an ancient story Y. Liang, K. Tóth, Y. Cao, K. Tanaka, C. Espinoza & G. Stacey
Herbivore-induced plant volatiles: targets, perception and unanswered questions M. Heil
There’s no place like home? An exploration of the mechanisms behind plant litter–decomposer affinity in terrestrial ecosystems A. T. Austin, L. Vivanco, A. González-Arzac & L. I. Pérez
Insect herbivore-associated organisms affect plant responses to herbivory F. Zhu, E. H. Poelman & M. Dicke
When mutualism goes bad: density- dependent impacts of introduced bees on plant reproduction M. A. Aizen, C. L. Morales, D. P. Vázquez, L. A. Garibaldi, A. Sáez & L. D. Harder
Insect and pathogen attack and resistance in maize and its wild ancestors, the teosintes E. S. de Lange, D. Balmer, B. Mauch-Mani & T. C. J. Turlings
Linking phytochrome to plant immunity: low red : far-red ratios increase Arabidopsis susceptibility to Botrytis cinerea by reducing the biosynthesis of indolic glucosinolates and camalexin M. D. Cargnel, P. V. Demkura & C. L. Ballaré
To grow or defend? Low red : far-red ratios reduce jasmonate sensitivity in Arabidopsis seedlings by promoting DELLA degradation and increasing JAZ10 stability M. Leone, M. M. Keller, I. Cerrudo & C. L. Ballaré
β-Glucosidase BGLU42 is a MYB72-dependent key regulator of rhizobacteria-induced systemic resistance and modulates iron deficiency responses in Arabidopsis roots C. Zamioudis, J. Hanson & C. M. J. Pieterse
Deciphering the language of plant communication: volatile chemotypes of sagebrush R. Karban, W. C. Wetzel, K. Shiojiri, S. Ishizaki, S. R. Ramirez & J. D. Blande
The context dependence of beneficiary feedback effects on benefactors in plant facilitation C. Schöb, R. M. Callaway, F. Anthelme, R. W. Brooker, L. A. Cavieres, Z. Kikvidze, C. J. Lortie, R. Michalet, F. I. Pugnaire, S. Xiao, B. H. Cranston, M-C. García, N. R. Hupp, L. D. Llambí, E. Lingua, A. M. Reid, L. Zhao & B. J. Butterfield
Herbivore-mediated material fluxes in a northern deciduous forest under elevated carbon dioxide and ozone concentrations T. D. Meehan, J. J. Couture, A. E. Bennett & R. L. Lindroth
Are plant–soil feedback responses explained by plant traits? C. Baxendale, K. H. Orwin, F. Poly, T. Pommier & R. D. Bardgett
Environmental nutrient supply alters prevalence and weakens competitive interactions among coinfecting viruses C. Lacroix, E. W. Seabloom & E. T. Borer
Scientists from the Wyss Institute, the Broad Institute, and the University of California, Berkeley, have helped develop a versatile and powerful new genome editing tool by altering a natural method of bacterial self-defense. Bacteria use a system called CRISPR to store DNA from invading viruses so they can recognize and cleave that foreign DNA later when the invader returns. CRISPR-associated (Cas) enzymes do the cutting, and one in particular, an enzyme from the bacterium Streptococcus pyogenes known as Cas9, can cut DNA at exactly the location dictated by an RNA — a snippet of RNA that can be programmed to seek out precise DNA sequences in the genome to edit. Wyss Institute scientists have shown for the first time that the Cas9 system works in cells of higher organisms, including humans. The CRISPR/Cas9 technology enables highly efficient and specific genome editing, opening the path to numerous therapeutic applications such as correcting genetic disorders and battling invading pathogens.
Millions of tons. That’s how much plastic should be floating in the world’s oceans, given our ubiquitous use of the stuff. But a new study finds that 99% of this plastic is missing. One disturbing possibility: Fish are eating it.
If that’s the case, “there is potential for this plastic to enter the global ocean food web,” says Carlos Duarte, an oceanographer at the University of Western Australia, Crawley. “And we are part of this food web.”
Humans produce almost 300 million tons of plastic each year. Most of this ends up in landfills or waste pits, but a 1970s National Academy of Sciences study estimated that 0.1% of all plastic washes into the oceans from land, carried by rivers, floods, or storms, or dumped by maritime vessels. Some of this material becomes trapped in Arctic ice and some, landing on beaches, can even turn into rocks made of plastic. But the vast majority should still be floating out there in the sea, trapped in midocean gyres—large eddies in the center of oceans, like theGreat Pacific Garbage Patch.
To figure out how much refuse is floating in those garbage patches, four ships of the Malaspina expedition, a global research project studying the oceans, fished for plastic across all five major ocean gyres in 2010 and 2011. After months of trailing fine mesh nets around the world, the vessels came up light—by a lot. Instead of the millions of tons scientists had expected, the researchers calculated the global load of ocean plastic to be about only 40,000 tons at the most, the researchers report online today in the Proceedings of the National Academy of Sciences. “We can’t account for 99% of the plastic that we have in the ocean,” says Duarte, the team’s leader.
He suspects that a lot of the missing plastic has been eaten by marine animals. When plastic is floating out on the open ocean, waves and radiation from the sun can fragment it into smaller and smaller particles, until it gets so small it begins to look like fish food—especially to small lanternfish, a widespread small marine fish known to ingest plastic.
“Yes, animals are eating it,” says oceanographer Peter Davison of the Farallon Institute for Advanced Ecosystem Research in Petaluma, California, who was not involved in the study. “That much is indisputable.”
But, he says, it’s hard to know at this time what the biological consequences are. Toxic ocean pollutants like DDT, PCBs, or mercury cling to the surface of plastics, causing them to “suck up all the pollutants in the water and concentrate them.” When animals eat the plastic, that poison could be going into the fish and traveling up the food chain to market species like tuna or swordfish. Or, Davison says, toxins in the fish “may dissolve back into the water … or for all we know they’re puking [the plastic] or pooping it out, and there’s no long-term damage. We just don’t know.”
The last several years have witnessed an explosion in the understanding and use of novel, versatile trans-acting elements. TALEs, CRISPR/Cas, and sRNAs can be easily fashioned to bind any specific sequence of DNA (TALEs, CRISPR/Cas) or RNA (sRNAs) because of the simple rules governing their interactions with nucleic acids. This unique property enables these tools to repress the expression of genes at the transcriptional or post-transcriptional levels, respectively, without prior manipulation of cis-acting and/or chromosomal target DNA sequences. These tools are now being harnessed by synthetic biologists, particularly those in the eukaryotic community, for genome-wide regulation, editing, or epigenetic studies. Here we discuss the exciting opportunities for using TALEs, CRISPR/Cas, and sRNAs as synthetic trans-acting regulators in prokaryotes.
High-throughput phenotyping is emerging as an important technology to dissect phenotypic components in plants. Efficient image processing and feature extraction are prerequisites to quantify plant growth and performance based on phenotypic traits. Issues include data management, image analysis, and result visualization of large-scale phenotypic data sets. Here, we present Integrated Analysis Platform (IAP), an open-source framework for high-throughput plant phenotyping. IAP provides user-friendly interfaces, and its core functions are highly adaptable. Our system supports image data transfer from different acquisition environments and large-scale image analysis for different plant species based on real-time imaging data obtained from different spectra. Due to the huge amount of data to manage, we utilized a common data structure for efficient storage and organization of data for both input data and result data. We implemented a block-based method for automated image processing to extract a representative list of plant phenotypic traits. We also provide tools for build-in data plotting and result export. For validation of IAP, we performed an example experiment that contains 33 maize (Zea mays ‘Fernandez’) plants, which were grown for 9 weeks in an automated greenhouse with nondestructive imaging. Subsequently, the image data were subjected to automated analysis with the maize pipeline implemented in our system. We found that the computed digital volume and number of leaves correlate with our manually measured data in high accuracy up to 0.98 and 0.95, respectively. In summary, IAP provides a multiple set of functionalities for import/export, management, and automated analysis of high-throughput plant phenotyping data, and its analysis results are highly reliable.
Cloud computing offers some great opportunities for science, but most cloud computing platforms are I/O and memory limited, and hence are poor matches for data-intensive computing. After 4 years of research software development we are now instrumenting and benchmarking our analysis pipelines; numbers, lessons learned, and future plans will be discussed. Everything is open source.
Plant stature and development are governed by cell proliferation and directed cell growth. These parameters are determined largely by cell wall characteristics. Cellulose microfibrils, composed of hydrogen-bonded β-1,4 glucans, are key components for anisotropic growth in plants. Cellulose is synthesized by plasma membrane–localized cellulose synthase complexes. In higher plants, these complexes are assembled into hexagonal rosettes in intracellular compartments and secreted to the plasma membrane. Here, the complexes typically track along cortical microtubules, which may guide cellulose synthesis, until the complexes are inactivated or internalized. Determining the regulatory aspects that control the behavior of cellulose synthase complexes is vital to understanding directed cell and plant growth and to tailoring cell wall content for industrial products, including paper, textiles, and fuel. In this review, we summarize and discuss cellulose synthesis and regulatory aspects of the cellulose synthase complex, focusing on Arabidopsis thaliana.
Drought is one of the most important environmental stresses affecting the productivity of most field crops. Elucidation of the complex mechanisms underlying drought resistance in crops will accelerate the development of new varieties with enhanced drought resistance. Here, we provide a brief review on the progress in genetic, genomic, and molecular studies of drought resistance in major crops. Drought resistance is regulated by numerous small-effect loci and hundreds of genes that control various morphological and physiological responses to drought. This review focuses on recent studies of genes that have been well characterized as affecting drought resistance and genes that have been successfully engineered in staple crops. We propose that one significant challenge will be to unravel the complex mechanisms of drought resistance in crops through more intensive and integrative studies in order to find key functional components or machineries that can be used as tools for engineering and breeding drought-resistant crops.
Plant microbiomes are critical to host adaptation and impact plant productivity and health. Root-associated microbiomes vary by soil and host genotype, but the contribution of these factors to community structure and metabolic potential has not been fully addressed. Here we characterize root microbial communities of two disparate agricultural crops grown in the same natural soil in a controlled and replicated experimental system. Metagenomic (genetic potential) analysis identifies a core set of functional genes associated with root colonization in both plant hosts, and metatranscriptomic (functional expression) analysis revealed that most genes enriched in the root zones are expressed. Root colonization requires multiple functional capabilities, and these capabilities are enriched at the community level. Differences between the root-associated microbial communities from different plants are observed at the genus or species level, and are related to root-zone environmental factors.
In crop improvement, the isolation, cloning and transfer of disease resistance genes (R-genes) is an ultimate goal usually starting from tentative R-gene analogs (RGAs) that are identified on the basis of their structure. For bread wheat, recent advances in genome sequencing are supporting the efforts of wheat geneticists worldwide. Among wheat R-genes, nucleotide-binding site (NBS)-encoding ones represent a major class. In this study, we have used a polymerase chain reaction-based approach to amplify and clone NBS-type RGAs from a bread wheat cultivar, ‘Salambo 80.’ Four novel complete ORF sequences showing similarities to previously reported R-genes/RGAs were used for in silico analyses. In a first step, where analyses were focused on the NBS domain, these sequences were phylogenetically assigned to two distinct groups: a first group close to leaf rust Lr21 resistance proteins; and a second one similar to cyst nematode resistance proteins. In a second step, sequences were used as initial seeds to walk up and downstream the NBS domain. This procedure enabled identifying 8 loci ranging in size between 2,115 and 7,653 bp. Ab initio gene prediction identified 8 gene models, among which two had complete ORFs. While GenBank survey confirmed the belonging of sequences to two groups, subsequent characterization using IWGSC genomic and proteomic data showed that the 8 gene models, reported in this study, were unique and their loci matched scaffolds on chromosome arms 1AS, 1BS, 4BS and 1DS. The gene model located on 1DS is a pseudo-Lr21 that was shown to have an NBS-LRR domain structure, while the potential association of the RGAs, here reported, is discussed. This study has produced novel R-gene-like loci and models in the wheat genome and provides the first steps toward further elucidation of their role in wheat disease resistance.
Genome sequencing projects were long confined to biomedical model organisms and required the concerted effort of large consortia. Rapid progress in high-throughput sequencing technology and the simultaneous development of bioinformatic tools have democratized the field. It is now within reach for individual research groups in the eco-evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice. Because of the cost and considerable effort involved in such an endeavour, the important first step is to thoroughly consider whether a genome sequence is necessary for addressing the biological question at hand. Once this decision is taken, a genome project requires careful planning with respect to the organism involved and the intended quality of the genome draft. Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to large and complex genomes. This tutorial is targeted at scientists with a background in conservation genetics, but more generally, provides useful practical guidance for researchers engaging in whole-genome sequencing projects.
Scott Jackson, Jeremy Schmutz, Phillip McClean and colleagues report the genome sequence of the common bean (Phaseolus vulgaris) and resequenced wild individuals and landraces from Mesoamerican and Andean gene pools, showing that common bean underwent two independent domestications.
Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus.
To feed the world's rapidly-expanding population in the coming decades, agriculture must produce more. Big data holds one of the keys for farmers, but it's also a weapon that could be used against them.
Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol is currently being applied in numerous species by a large number of researchers. Herein we describe a bioinformatics pipeline, tassel-gbs, designed for the efficient processing of raw GBS sequence data into SNP genotypes. The tassel-gbs pipeline successfully fulfills the following key design criteria: (1) Ability to run on the modest computing resources that are typically available to small breeding or ecological research programs, including desktop or laptop machines with only 8–16 GB of RAM, (2) Scalability from small to extremely large studies, where hundreds of thousands or even millions of SNPs can be scored in up to 100,000 individuals (e.g., for large breeding programs or genetic surveys), and (3) Applicability in an accelerated breeding context, requiring rapid turnover from tissue collection to genotypes. Although a reference genome is required, the pipeline can also be run with an unfinished “pseudo-reference” consisting of numerous contigs. We describe the tassel-gbs pipeline in detail and benchmark it based upon a large scale, species wide analysis in maize (Zea mays), where the average error rate was reduced to 0.0042 through application of population genetic-based SNP filters. Overall, the GBS assay and the tassel-gbs pipeline provide robust tools for studying genomic diversity.
Synthetic biology is an emerging field uniting scientists from all disciplines with the aim of designing or re-designing biological processes. Initially, synthetic biology breakthroughs came from microbiology, chemistry, physics, computer science, materials science, mathematics, and engineering disciplines. A transition to multicellular systems is the next logical step for synthetic biologists and plants will provide an ideal platform for this new phase of research. This meeting report highlights some of the exciting plant synthetic biology projects, and tools and resources, presented and discussed at the 2013 GARNet workshop on plant synthetic biology.
Natural variants of crops are generated from wild progenitor plants under both natural and human selection. Diverse crops that are able to adapt to various environmental conditions are valuable resources for crop improvements to meet the food demands of the increasing human population. With the completion of reference genome sequences, the advent of high-throughput sequencing technology now enables rapid and accurate resequencing of a large number of crop genomes to detect the genetic basis of phenotypic variations in crops. Comprehensive maps of genome variations facilitate genome-wide association studies of complex traits and functional investigations of evolutionary changes in crops. These advances will greatly accelerate studies on crop designs via genomics-assisted breeding. Here, we first discuss crop genome studies and describe the development of sequencingbased genotyping and genome-wide association studies in crops. We then review sequencing-based crop domestication studies and offer a perspective on genomics-driven crop designs.
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