Medicago truncatula symbiosis mutants affected in the interaction with a biotrophic root pathogen.

Understanding how plants balance between enabling microbial symbionts and fending off pathogens has direct implications both for basic plant biology and optimal use of crop plants in agriculture. The degree to which the processes associated with these two types of interactions overlap is poorly known. Recent studies revealed that symbiotic and pathogenic filamentous microbes require common plant genetic elements to establish colonisation (Wang et al., 2012; Rey et al., 2013), supporting the long-held view that plants have evolved the ability to accommodate microbes (Parniske, 2000) and that pathogens have exploited these pathways. However, the extent to which plant genes implicated in fungal or bacterial symbioses are involved in interactions with biotrophic pathogens is unknown and research has been hampered by the lack of suitable common host experimental systems. P. palmivora, a root-infecting oomycete, is an aggressive biotrophic pathogen of M. truncatula, a model legume plant that is widely used in symbiosis research. Expression of fluorescent proteins in P. palmivora permits visualisation of infection structures in M. truncatula roots. During its initial biotrophic colonisation of M. truncatula roots which lasts until about 48 hours post infection (hpi), P. palmivora zoospores expressing tdtomato red fluorescent protein (isolate AJ-td) germinate and form appressoria to penetrate the epidermis followed by rapid colonisation of the root cortex apoplast and projection of short specialised hyphae, termed haustoria into plant cells (Fig. 1a). P. palmivora infection is accompanied by visible disease development in M. truncatula seedlings consisting of translucent tissue at the root tip at two days post inoculation (dpi) and tissue browning in upper parts of the root at three dpi. (Fig. 1b, see also supplementary material). Concomitant with a switch to a nectrophic lifestyle, the pathogen enters the vasculature (Fig. 1a).We wish to thank numerous members of the symbiosis community for providing plant material and fruitful discussions (see table S1), to S. Whisson and H. Judelson for providing fluorescent protein expression vectors and M. Smoker and T. Yunusov for help with P. palmivora culturing and transformation. We are grateful to S. Kamoun for his continued support and input into an early draft of this manuscript. This work was supported by the Gatsby Charitable Foundation [RG62472 to S.S.]; by the Royal Society (RG69135 to S.S.) and by a Marie Curie Intra-European fellowship [FP7-PEOPLE-2013-IEF, SYMUNITY- EC project 624398 to T.R.].This is the author accepted manuscript. The final published version is available from Wiley at http://onlinelibrary.wiley.com/doi/10.1111/nph.13233/abstract

The Medicago truncatula GRAS protein RAD1 supports arbuscular mycorrhiza symbiosis and Phytophthora palmivora susceptibility.

The roots of most land plants are colonized by symbiotic arbuscular mycorrhiza (AM) fungi. To facilitate this symbiosis, plant genomes encode a set of genes required for microbial perception and accommodation. However, the extent to which infection by filamentous root pathogens also relies on some of these genes remains an open question. Here, we used genome-wide association mapping to identify genes contributing to colonization of Medicago truncatula roots by the pathogenic oomycete Phytophthora palmivora. Single-nucleotide polymorphism (SNP) markers most significantly associated with plant colonization response were identified upstream of RAD1, which encodes a GRAS transcription regulator first negatively implicated in root nodule symbiosis and recently identified as a positive regulator of AM symbiosis. RAD1 transcript levels are up-regulated both in response to AM fungus and, to a lower extent, in infected tissues by P. palmivora where its expression is restricted to root cortex cells proximal to pathogen hyphae. Reverse genetics showed that reduction of RAD1 transcript levels as well as a rad1 mutant are impaired in their full colonization by AM fungi as well as by P. palmivora. Thus, the importance of RAD1 extends beyond symbiotic interactions, suggesting a general involvement in M. truncatula microbe-induced root development and interactions with unrelated beneficial and detrimental filamentous microbes

Towards increased shading potential: a combined phenotypic and genetic analysis of rice shoot architecture

Rice feeds more than half of the world’s human population. In modern rice farming, a major constraint for productivity is weed proliferation and the ecological impact of herbicide application. Increased weed competitiveness of commercial rice varieties requires enhanced shade casting to limit growth of shade-sensitive weeds and the need for herbicide. We aimed to identify traits that enhance rice shading capacity based on the canopy architecture and the underlying genetic components. We performed a phenotypic screen of a rice diversity panel comprised of 344 varieties, examining 13 canopy architecture traits linked with shading capacity in 4-week-old plants. The analysis revealed a vast range of phenotypic variation across the diversity panel. We used trait correlation and clustering to identify core traits that define shading capacity to be shoot area, number of leaves, culm and solidity (the compactness of the shoot). To simplify the complex canopy architecture, these traits were combined into a Shading Rank metric that is indicative of a plant’s ability to cast shade. Genome wide association study (GWAS) revealed genetic loci underlying canopy architecture traits, out of which five loci were substantially contributing to shading potential. Subsequent haplotype analysis further explored allelic variation and identified seven haplotypes associated with increased shading. Identification of traits contributing to shading capacity and underlying allelic variation presented in this study will serve future genomic assisted breeding programmes. The investigated diversity panel, including widely grown varieties, shows that there is big potential and genetic resources for improvement of elite breeding lines. Implementing increased shading in rice breeding will make its farming less dependent on herbicides and contribute towards more environmentally sustainable agriculture. One sentence summary Through screening a rice diversity panel for variation in shoot architecture, we identified traits corresponding to plant shading potential and their genetic constituents

Towards increased shading capacity: A combined phenotypic and genetic analysis of rice shoot architecture

Societal Impact Statement: Rice farming is transitioning from transplanting rice seedlings towards the less labour-intensive and less water-demanding method of directly seeding rice. This, however, is accompanied by increased weed proliferation. To tackle this issue, this study seeks to identify how the crop itself can better suppress weeds, with a focus on light competition via shading. Using a rice diversity panel, traits were identified that contribute to enhanced shading capacity, and these traits were encapsulated into a single shading capacity metric. This was followed by the identification of the genetic loci underpinning variation in the core traits. The identified haplotypes can be used in breeding programmes to improve weed suppression by rice, thus contributing to sustainable agriculture. Summary: In modern rice farming, one of the major constraints is weed proliferation and the entailed ecological impact of herbicide application. This requires increased weed competitiveness in current rice varieties, achieved via enhanced shade casting to limit the growth of shade-sensitive weeds. To identify traits that increase rice shading capacity, we exhaustively phenotyped a rice diversity panel of 344 varieties at an early vegetative stage. A genome-wide association study (GWAS) revealed genetic loci underlying variation in canopy architecture traits linked with shading capacity. The screen shows considerable natural variation in shoot architecture for 13 examined traits, of which shading potential is mostly determined by projected shoot area, number of leaves, culm height and canopy solidity. The shading rank, a metric based on these core traits, identifies varieties with the highest shading potential. Five genetic loci were found to be associated with canopy architecture, shading potential and early vigour. Identification of traits contributing to shading capacity and underlying allelic variation will serve future genomic-assisted breeding programmes. Implementing the presented genetic resources for increased shading and weed competitiveness in rice breeding will make its farming less dependent on herbicides and contribute towards more environmentally sustainable agriculture

Flooding tolerance in the major rice weed Echinochloa crus-galli

Unlike most crops, rice is flooding tolerant and this feature has been exploited for weed management in rice fields. Flooding of rice fields prevents weed establishment, while rice remains unaffected. However, the recent emergence of certain endemic weed species adapted to submergence has decreased the effectiveness of this weeding method. Studying these weeds is important both for devising alternative weed management strategies and to better understand plant flood adaptation, to uncover associated genetic mechanisms. For our study, Echinochloa crus-galli, often referred to as one of the worst weeds worldwide and highly submergence tolerant, was selected together with an intolerant maize cultivar and two rice varieties (one tolerant and one intolerant). Flooding resilience in the tolerant weed and in the tolerant rice is achieved by different means. Time-course transcriptomics analyses indicated many commonly regulated genes but also revealed crucial mechanisms associated with differential growth and metabolic responses to both underwater stress (hypoxia and reduction of light) and post-submergence stress (reoxygenation and re-illumination). A comparative analysis of the weed genome composition to 17 other grass species revealed a conservation of flooding responses in the grass family, as well as species-specific flooding tolerance responses in the weed. This could have been acquired by a relatively recent exposure to flooded conditions. Greenhouse and field experiments showed that weed management protocols using early flooding followed by natural shade from high shade-casting rice cultivars might be the most efficient way to both naturally suppress weed growth in rice fields and preserve fresh water resources

Flooding tolerance in the major rice weed Echinochloa crus-galli

Unlike most crops, rice is flooding tolerant and this feature has been exploited for weed management in rice fields. Flooding of rice fields prevents weed establishment, while rice remains unaffected. However, the recent emergence of certain endemic weed species adapted to submergence has decreased the effectiveness of this weeding method. Studying these weeds is important both for devising alternative weed management strategies and to better understand plant flood adaptation, to uncover associated genetic mechanisms. For our study, Echinochloa crus-galli, often referred to as one of the worst weeds worldwide and highly submergence tolerant, was selected together with an intolerant maize cultivar and two rice varieties (one tolerant and one intolerant). Flooding resilience in the tolerant weed and in the tolerant rice is achieved by different means. Time-course transcriptomics analyses indicated many commonly regulated genes but also revealed crucial mechanisms associated with differential growth and metabolic responses to both underwater stress (hypoxia and reduction of light) and post-submergence stress (reoxygenation and re-illumination). A comparative analysis of the weed genome composition to 17 other grass species revealed a conservation of flooding responses in the grass family, as well as species-specific flooding tolerance responses in the weed. This could have been acquired by a relatively recent exposure to flooded conditions. Greenhouse and field experiments showed that weed management protocols using early flooding followed by natural shade from high shade-casting rice cultivars might be the most efficient way to both naturally suppress weed growth in rice fields and preserve fresh water resources

Phyllosphere Colonization by a Soil Streptomyces sp. Promotes Plant Defense Responses Against Fungal Infection

International audienceStreptomycetes are soil-dwelling, filamentous actinobacteria and represent a prominent bacterial clade inside the plant root microbiota. The ability of streptomycetes to produce a broad spectrum of antifungal metabolites suggests that these bacteria could be used to manage plant diseases. Here, we describe the identification of a soil Streptomyces strain named AgN23 which strongly activates a large array of defense responses when applied on Arabidopsis thaliana leaves. AgN23 increased the biosynthesis of salicylic acid, leading to the development of salicylic acid induction deficient 2 (SID2)-dependent necrotic lesions. Size exclusion fractionation of plant elicitors secreted by AgN23 showed that these signals are tethered into high molecular weight complexes. AgN23 mycelium was able to colonize the leaf surface, leading to plant resistance against Alternaria brassicicola infection in wild-type Arabidopsis plants. AgN23-induced resistance was found partially compromised in salicylate, jasmonate, and ethylene mutants. Our data show that Streptomyces soil bacteria can develop at the surface of plant leaves to induce defense responses and protection against foliar fungal pathogens, extending their potential use to manage plant diseases

Towards increased shading potential: a combined phenotypic and genetic analysis of rice shoot architecture

Rice feeds more than half of the world’s human population. In modern rice farming, a major constraint for productivity is weed proliferation and the ecological impact of herbicide application. Increased weed competitiveness of commercial rice varieties requires enhanced shade casting to limit growth of shade-sensitive weeds and the need for herbicide. We aimed to identify traits that enhance rice shading capacity based on the canopy architecture and the underlying genetic components. We performed a phenotypic screen of a rice diversity panel comprised of 344 varieties, examining 13 canopy architecture traits linked with shading capacity in 4-week-old plants. The analysis revealed a vast range of phenotypic variation across the diversity panel. We used trait correlation and clustering to identify core traits that define shading capacity to be shoot area, number of leaves, culm and solidity (the compactness of the shoot). To simplify the complex canopy architecture, these traits were combined into a Shading Rank metric that is indicative of a plant’s ability to cast shade. Genome wide association study (GWAS) revealed genetic loci underlying canopy architecture traits, out of which five loci were substantially contributing to shading potential. Subsequent haplotype analysis further explored allelic variation and identified seven haplotypes associated with increased shading. Identification of traits contributing to shading capacity and underlying allelic variation presented in this study will serve future genomic assisted breeding programmes. The investigated diversity panel, including widely grown varieties, shows that there is big potential and genetic resources for improvement of elite breeding lines. Implementing increased shading in rice breeding will make its farming less dependent on herbicides and contribute towards more environmentally sustainable agriculture. One sentence summary Through screening a rice diversity panel for variation in shoot architecture, we identified traits corresponding to plant shading potential and their genetic constituents

Developmental Modulation of Root Cell Wall Architecture Confers Resistance to an Oomycete Pathogen.

The cell wall is the primary interface between plant cells and their immediate environment and must balance multiple functionalities, including the regulation of growth, the entry of beneficial microbes, and protection against pathogens. Here, we demonstrate how API, a SCAR2 protein component of the SCAR/WAVE complex, controls the root cell wall architecture important for pathogenic oomycete and symbiotic bacterial interactions in legumes. A mutation in API results in root resistance to the pathogen Phytophthora palmivora and colonization defects by symbiotic rhizobia. Although api mutant plants do not exhibit significant overall growth and development defects, their root cells display delayed actin and endomembrane trafficking dynamics and selectively secrete less of the cell wall polysaccharide xyloglucan. Changes associated with a loss of API establish a cell wall architecture with altered biochemical properties that hinder P. palmivora infection progress. Thus, developmental stage-dependent modifications of the cell wall, driven by SCAR/WAVE, are important in balancing cell wall developmental functions and microbial invasion.The Gatsby Foundation (GAT3395/GLD), European Research Council (ERC-2014-STG, H2020, 637537) Royal Society (UF110073, UF160413). TR was funded by The European Research Council (FP7-PEOPLE-2013-IEF, FP7, 624398). SB was funded by the University of California, Los Angeles (403976-SB-69313), Gatsby Charitable Foundation (GAT3396/PR4), and Biotechnology and Biological Sciences Research Council (BB.L002884.1). JLK was funded by the George and Lillian Schiff Foundation. DR, E-PJ, FD, and FdeCN were funded by TULIP (no. ANR-10-LABX-41). V.C. is a recipient of a Thailand Research Fund grant (MRG6080235) and also supported by Faculty of Science, Mahidol University, Thailand