Biology subjects

Carrere, S.

Publications and source records attributed to Carrere, S..

18 recordsLinked to original sources

bioRxiv2026

Intraspecific variation at the free-living stage of a soil-borne pathogen is organized into an exploration syndrome associated with infectivity

Many pathogens spend a substantial portion of their life cycle outside the host tissues. During its free-living stage, the root legume-plant pathogen Aphanomyces euteiches persists in soil either as non-motile resting oospores or actively explores the environment through mycelium and motile zoospores. These two latter stages are critical for survival, dispersal and host encounter. However, the extent of intraspecific variation during these phases remains poorly explored, and it is still unknown whether they are organized into phenotypic syndromes contributing to infection success. Here, we measured eight free-living phenotypic traits associated with mycelial and zoospore stages across 23 A. euteiches strains from distinct geographic regions (USA, Europe) whose genomes were sequenced. We tested whether traits are organized into a phenotypic syndrome linked to either geographic origin, genomic diversity or infectivity. The microbial strains exhibited substantial intraspecific phenotypic variation that we proposed as an 'exploration syndrome' linked to host search. Beyond this general syndrome, we detected sub-structure according to strains' infectivity, geographic origin and genetic group. This suggests that the free-living stage of pathogens may contribute to disease potential. Our results highlight the importance of integrating functional trait approaches into plant pathology and suggest that the identified "exploration syndrome" may serve as a predictor of infectivity in soilborne oomycete pathogens.

ecology↗

bioRxiv2025

Natural variation in an NLR pair confers thermostable resistance to a devastating bacterial pathogen

Climate change reshapes host-pathogen interactions by increasing pathogen aggressiveness and weakening plant immune responses, particularly under heat stress. Nucleotide-binding leucine-rich repeat (NLR) immune receptors, key players in pathogen recognition, are altered under elevated temperatures in both plants and mammals, posing a major challenge to disease resistance. In Arabidopsis thaliana, the well-described RPS4/RRS1 NLR pair confers resistance to the worldwide devastating phytopathogenic Ralstonia pseudosolanacearum. Here, by combining the exploration of natural genetic variation with genetic mapping, polymorphism analysis, structural modeling, and functional complementation, we demonstrated that the paucity of full thermostable resistance is primarily associated with a unique RPS4/RRS1 haplotype carrying key substitutions in leucine-rich repeat domains. These findings reveal natural genetic diversity as a source of thermostable resistance, highlighting promising opportunities to engineer climate-resilient plants.

plant biology↗

bioRxiv2025

A Xanthomonas effector protein contributes quantitatively to virulence by inducing at least two minor Susceptibility genes

The transcription activator-like effector Tal12a is widely conserved among Xanthomonas campestris pv. campestris strains that cause black rot in Brassica crops. However, its role in disease remains unclear. To investigate how Tal12a contributes to pathogenesis, we combined transcriptomic profiling of cauliflower leaves infected with Tal12a-expressing strains, prediction of TALE-binding elements, and heterologous expression assays in Nicotiana benthamiana. The aim of this approach was to identify candidate susceptibility genes. Artificial TALEs were further employed to validate the contribution of these candidate targets to disease development. Tal12a enhanced both virulence and bacterial growth in cauliflower. Transcriptome analysis revealed 380 genes that were induced upon infection, nine of which were prioritised as candidates. Seven of these were confirmed as direct Tal12a targets, while the induction of the sugar transporter genes BoSWEET13 and BoSWEET14c likely occurred indirectly. Functional assays demonstrated that these two SWEET genes and the BoIAA7c gene, which encodes auxin-dependent transcriptional regulator, contribute to disease development. These findings identify the first susceptibility genes in cauliflower and reveal that Tal12a promotes disease through a complex transcriptional reprogramming, involving direct and indirect target induction, with several genes functioning as minor susceptibility factors.

plant biology↗

bioRxiv2025

New resistance to bacterial wilt in heat-stressed tomato is revealed by two-reference Genome Wide Association

Bacterial wilt, caused by bacterial strains of the Ralstonia solanacearum species complex, is one of the most harmful diseases striking many crops including tomato. Its spread is dependent upon temperature and humidity, which are expected to fluctuate strongly due to climate change. Previous results have highlighted that temperature elevation led to an increase in disease severity in commercial cultivars, whose resistance is quantitative and mostly relies on the Quantitative Trait Loci (QTL) bwr-6 and bwr-12. In this study, we focused on temperature-dependent quantitative disease resistance (QDR) to bacterial wilt with the aim to unravel new resistance mechanisms that remain efficient at higher temperatures. For this purpose, a new panel of 189 accessions composed of tomato wild relatives, was assembled and sequenced thus creating a unique genomic resource. Its response to the Ralstonia pseudosolanacearum strain GMI1000 from three- to ten-days post-inoculation at 28{degrees}C and 32{degrees}C was explored. To discover the genetic basis underlying the responses of the panel, Genome-Wide Association (GWA) studies were conducted using the disease symptom scores recorded daily and monitored throughout the kinetics of the infection. To improve QTL detection, we have proposed a new approach using two reference genomes from within the panel. By correcting part of a single reference genome, especially when the only reference genome is a cultivar, this approach may be considered an alternative to pangenomic studies. As panel sequencing was highly resolutive, QTL positions allowed the identification of 44 candidate genes, which seemed to follow a temporal dynamic of activation after pathogen inoculation. Interestingly, no candidate genes were found to be common between the two phenotyping temperatures, highlighting the importance of the experimental design in addressing this type of question. Most of our quantitative disease resistance candidate genes belong to gene families described as being involved in immunity. Moreover, a significant proportion appears to be expressed in roots where bacterial infection occurs. Among them, two candidates are closely linked to the genomic positions of the bwr-6 and bwr-12 QTLs, the main QTLs of bacterial wilt Quantitative Disease Resistance (QDR) studied whose mechanisms of action are still unknown. Author summaryBacterial wilt is a plant disease that affects more than 200 crop species (including tomato, potato and banana) leading to high yield losses. The most efficient way to deal with this disease is still the use of genetic resistance. However, previous studies have shown that numerous sources of resistance are negatively affected when plants face heat stress, which is alarming in a context of global warming. In this study, we have developed a new approach for discovering candidate genes in tomato capable of conferring thermostable resistance to bacterial wilt. Forty-four genes were sequentially detected over time, reflecting different temporal dynamics of induction after inoculation. Even if none were found to be common between the two temperatures, available information on their transcriptional regulation in roots and their involvement in immune processes confirms their relevance. Finally, we provide a short list of the candidate genes identified, some of which are currently undergoing functional validation and will be used in breeding programs to help overcome epidemics in future years.

genetics↗

bioRxiv2024

Comparative transcriptomics reveal a highly polymorphic Xanthomonas HrpG virulence regulon

Bacteria of the genus Xanthomonas cause economically significant diseases in various crops. Their virulence is dependent on the translocation of type III effectors (T3Es) into plant cells by the type III secretion system (T3SS), a process regulated by the master response regulator HrpG. Although HrpG has been studied for over two decades, its regulon across diverse Xanthomonas species, particularly beyond type III secretion, remains understudied. In this study, we conducted transcriptome sequencing to explore the HrpG regulons of 17 Xanthomonas strains, encompassing six species and nine pathovars, each exhibiting distinct host and tissue specificities. We employed constitutive expression of plasmid-borne hrpG*, which encodes a constitutively active form of HrpG, to induce the regulon. Our findings reveal substantial inter- and intra-specific diversity in the HrpG* regulons across the strains. Besides 21 genes directly involved in the biosynthesis of the T3SS, the core HrpG* regulon is limited to only five additional genes encoding the transcriptional activator HrpX, the two T3E proteins XopR and XopL, a major facility superfamily (MFS) transporter, and the phosphatase PhoC. Interestingly, genes involved in chemotaxis and genes encoding enzymes with carbohydrate-active and proteolytic activities are variably regulated by HrpG*. The diversity in the HrpG* regulon suggests that HrpG-dependent virulence in Xanthomonas might be achieved through several distinct strain-specific strategies, potentially reflecting adaptation to diverse ecological niches. These findings enhance our understanding of the complex role of HrpG in regulating various virulence and adaptive pathways, extending beyond T3Es and the T3SS. IMPORTANCEIn the decades since its discovery, HrpG and its role in the regulation of the type III secretion system (T3SS) and its associated type III effectors (T3Es) in Xanthomonas has been the subject of extensive research. Despite notable progress in understanding its molecular regulatory mechanisms, the full spectrum of processes under control of HrpG, particularly beyond the T3SS and T3Es, and the degree of regulatory conservation across plant-pathogenic Xanthomonas species, remained unclear. To address this knowledge gap, we systematically compared the transcriptomes of 17 Xanthomonas strains, expressing a constitutively active form of HrpG, called HrpG*. We showed that HrpG* regulates different physiological processes other than the T3SS and T3Es and that this regulation shows substantial variation across the different strains. Taken together, our results provide new insights into Xanthomonas-plant interactions through the regulation of different metabolic and virulence pathways by the master response regulator HrpG.

microbiology↗

bioRxiv2023

A fully sequenced collection of homozygous EMS mutants for forward and reverse genetic screens in Arabidopsis thaliana

Genetic screens are powerful tools for biological research and are one of the reasons for the success of the thale cress Arabidopsis thaliana as a model species. Here, we describe the whole-genome sequencing of 871 Arabidopsis lines from the Homozygous EMS Mutant (HEM) collection as a novel resource for forward and reverse genetics. With an average 576 high-confidence mutations per HEM line, over three independent mutations altering protein sequence are found on average per gene in the collection. Pilot reverse genetics experiments on reproductive, developmental and physiological traits confirmed the efficacy of the tool for identifying both null and knockdown alleles. The possibility of conducting subtle repeated phenotyping of HEM lines and the immediate availability of the mutations will empower forward genetic approaches. The sequence resource is searchable with the ATHEM web interface (https://lipm-browsers.toulouse.inra.fr/pub/ATHEM/), and the biological material is distributed by the Versailles Arabidopsis Stock Center.

plant biology↗

bioRxiv2023

A metabolic crosstalk between liposarcoma and muscle sustains tumor growth

Dedifferentiated (DD-LPS) and Well-differentiated (WD-LPS) liposarcoma are characterized by a systematic amplification of the MDM2 oncogene. We recently demonstrated that p53-independent metabolic functions of chromatin-bound MDM2 (C-MDM2) are exacerbated in LPS and mediate an addiction to serine metabolism in order to sustain tumor growth. Here, we show that metabolic cooperation between LPS and distant muscle, which raise serine and glycine blood levels, is essential for LPS tumor growth. By releasing IL-6, tumor influence distant muscle to upregulate their serine synthesis machinery. Blocking IL-6 secretion or treating LPS cells with FDA approved IL-6 inhibitor, decreased serine production and impaired tumor proliferation. These data reveal IL-6 as a central tumorkine in metabolic crosstalk between tissues and identifies IL-6 as a plausible treatment for LPS patients.

cancer biology↗

bioRxiv2022

Arabidopsis hydathodes are sites of intense auxin metabolism and nutrient scavenging

Hydathodes are small organs located on the leaf margins of all vascular plants. They release excess xylem sap through guttation when stomata are closed or when the humidity level is high. Many promoter analyses have suggested other hydathode functions in metabolite transport and auxin metabolism, but experimental demonstration is still lacking. Here, we compared the transcriptomic and metabolomic features of mature Arabidopsis hydathodes to the leaf blade. 1460 differentially-expressed genes were identified revealing that genes related to auxin metabolism, transport, stress, DNA, plant cell wall, RNA or wax were on average more expressed in hydathodes. On the other hand, genes involved in glucosinolate metabolism, sulfation pathway, metal handling or photosynthesis were downregulated in hydathodes. In hydathodes, there are an increased expression of auxin transcriptional regulators and biosynthetic genes, a lower expression of auxin transport genes and a differential expression of genes related to its vacuolar storage that is consistent with increased contents of free and conjugated auxin. We also found that ca. 78% of the total content of 52 xylem sap metabolites were removed from guttation fluid at the hydathode level. Using reverse genetics, we showed that the capture of nitrate and phosphate in the guttation fluid relies on the NRT2.1 and PHT1;4 transporters, respectively. Thus, hydathodes absorb a significant part of xylem sap nutrients, limiting the loss of valuable chemicals during guttation. Our transcriptomic and metabolomic analyses reveal an organ with its own transcriptomic and physiological identity and highlight hydathode biological processes that may impact the whole plant. One sentence summaryTranscriptome and physiological analysis of mature and healthy hydathodes of Arabidopsis demonstrates that those organs are sites of intense auxin metabolism and nutrient scavenging

plant biology↗

bioRxiv2022

Comparative phylotranscriptomics reveals a 110 million years-old symbiotic program

Symbiotic interactions have structured past and present ecosystems and shaped the evolution of life. As any trait, the symbiotic state observed in extant species builds on ancestral and conserved features, and lineage-specific innovations. From these mixed origins, defining the ancestral state of symbiotic associations is challenging although it is instrumental for understanding how symbiotic abilities emerge from non-symbiotic states. Here we aimed at reconstructing the intermediate steps leading to the root-nodule nitrogen-fixing symbiosis (RNS) observed in some extant flowering plants. For this, we compared the transcriptomic responses of nine host plants in response to symbiotic bacteria. We included the mimosoid legume Mimosa pudica for which we assembled a chromosome-level genome and generated the transcriptomic response to experimentally evolved bacterial symbionts. With this dataset, we reconstructed the ancestral RNS transcriptome, composed of most already described symbiotic genes together with hundreds of novel candidates. We found that the response to the chemical signals produced by the symbiont, nodule organogenesis and nitrogen-fixation are predominantly linked to ancestral responses, although these traits have diversified in the different nitrogen-fixing lineages. We detected a clear signature of recent and convergent evolution for the ability to release intracellular symbiosomes in two legume lineages, exemplified by the expression of different classes of small proteins in each group, potentially leading to the convergent gain of symbiotic evolutionary stability. Our findings demonstrate that most of the novelties for RNS were mostly in place in the most recent common ancestor of the RNS-forming species that lived on Earth 110 million years ago. Graphical abstractA little graphical/nice phylogeny with nodes of interest HighlightsO_LIWe sequenced a high-quality genome of the Mimosoideae Mimosa pudica C_LIO_LIThe nitrogen-fixing root-nodule symbiosis relies on an ancestral transcriptomic response C_LIO_LIAll symbiotic traits involve genes of the ancestral symbiotic program C_LIO_LISymbiont perception, nodule organogenesis and nitrogen-fixation are essentially ancestral processes C_LIO_LIConvergent evolution of intracellular accommodation of symbionts additionally involves lineage-specific genes C_LI

plant biology↗

bioRxiv2022

The genomics of linkage drag in sunflower

Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases. However, introgressions from wild relatives might have deleterious effects on desirable traits, including yield, due to linkage drag. Here we comprehensively analyzed the genomic and phenotypic impacts of wild introgressions into cultivated sunflower to estimate the impacts of linkage drag. First, we generated new reference sequences for seven cultivated and one wild sunflower genotype, as well as improved assemblies for two additional cultivars. Next, relying on previously generated sequences from wild donor species, we identified introgressions in the cultivated reference sequences, as well as the sequence and structural variants they contain. We then used a ridge regression model to test the effects of the introgressions on phenotypic traits in the cultivated sunflower association mapping population. We found that introgression has introduced substantial sequence and structural variation into the cultivated sunflower gene pool, including > 3,000 new genes. While introgressions reduced genetic load at protein-coding sequences and positively affected traits associated with abiotic stress resistance, they mostly had negative impacts on yield and quality traits. Introgressions found at high frequency in the cultivated gene pool had larger effects than low frequency introgressions, suggesting that the former likely were targeted by artificial selection. Also, introgressions from more distantly related species were more likely to be maladaptive than those from the wild progenitor of cultivated sunflower. Thus, pre-breeding efforts should focus, as far as possible, on closely related and fully compatible wild relatives.

genomics↗

bioRxiv2022

Genome-wide identification of fitness determinants in the Xanthomonas campestris bacterial pathogen during early stages of plant infection

Plant diseases are an important threat to food production. While major pathogenicity determinants required for disease have been extensively studied, less is known on how pathogens thrive during host colonization especially at early infection stages. Here, we used randomly barcoded-transposon insertion site sequencing (RB-TnSeq) to perform a genome-wide screen and identify key bacterial fitness determinants of the vascular pathogen Xanthomonas campestris pv. campestris (Xcc) during infection of the cauliflower host plant (Brassica oleracea). This high-throughput analysis was conducted in hydathodes, the natural entry site of Xcc, in xylem sap and in synthetic media. Xcc did not face a strong bottleneck during hydathode infection. 183 genes important for fitness were identified in plant-associated environments with functional enrichment in genes involved in metabolism when only few genes known to be involved in virulence were found to be affected. The biological relevance of 13 genes was independently confirmed by phenotyping single mutants. Notably, we show that the XC_3388, a protein with no known function (DUF1631), plays a key role in the adaptation and virulence of Xcc possibly through c-di-GMP-mediated regulation. This study thus revealed yet unsuspected social behaviors adopted by Xcc individuals when confined inside hydathodes at early infection stages.

microbiology↗

bioRxiv2021

MtExpress, a Comprehensive and Curated RNAseq-based Gene Expression Atlas for the Model Legume Medicago truncatula

Although RNA sequencing has been becoming the main transcriptomic approach in the model legume Medicago truncatula, there is currently no genome-wide gene expression atlas covering the whole set of RNAseq data published for this species. Nowadays, such tool is highly valuable to provide a global view of gene expression in a wide range of conditions and tissues/organs. Here, we present MtExpress, a gene expression atlas that compiles an exhaustive set of published M. truncatula RNAseq data (https://medicago.toulouse.inrae.fr/MtExpress). MtExpress makes use of recent releases of M. truncatula genome sequence and annotation, as well as up-to-date tools to perform mapping, quality control, statistical analysis and normalization of RNAseq data. MtExpress combines semi-automated pipelines with manual re-labelling and organization of samples, to produce an attractive and user-friendly interface, fully integrated with other available Medicago genomic resources. Importantly, MtExpress is highly flexible, in terms of both queries, e.g. allowing searches with gene names and orthologous gene IDs from Arabidopsis and other legume species, and outputs, to customize visualization and redirect gene study to relevant Medicago webservers. Thanks to its semi-automated pipeline, MtExpress will be frequently updated to follow the rapid pace of M. truncatula RNAseq data publications, as well as the constant improvement of genome annotation.

plant biology↗

bioRxiv2021

Xanthomonas transcriptome inside cauliflower hydathodes reveals bacterial virulencestrategies and physiological adaptation at early infection stages

Xanthomonas campestris pv. campestris (Xcc) bacterium is a seed-transmitted vascular pathogen causing black rot disease on cultivated and wild Brassicaceae. Xcc enters the plant tissues preferentially via hydathodes which are organs localized at leaf margins. In order to decipher both physiological and virulence strategies deployed by Xcc during early stages of infection, the transcriptomic profile of Xcc was analyzed three days after entry into cauliflower hydathodes. Despite the absence of visible plant tissue alterations and a bacterial biotrophic lifestyle, 18% of Xcc genes undergo a transcriptional reprogramming, including a striking repression of chemotaxis and motility functions. Xcc full repertoire of virulence factors was not yet activated but the expression of the 95-gene HrpG regulon, including genes coding for the type three secretion machinery important for suppression of plant immunity, was induced. The expression of genes involved in metabolic adaptations such as catabolism of plant compounds, transport functions, sulfur and phosphate metabolism was upregulated while limited stress responses were observed three days post infection. These transcriptomic observations give information about the nutritional and stress status of bacteria during the early biotrophic infection stages and help to decipher the adaptive strategy of Xcc to the hydathode environment.

microbiology↗

bioRxiv2019

EffectorK, a comprehensive resource to mine for pathogen effector targets in the Arabidopsis proteome

Pathogens deploy effector proteins that interact with host proteins to manipulate the host physiology to the pathogens own benefit. However, effectors can also be recognized by host immune proteins leading to the activation of defense responses. Effectors are thus essential components in determining the outcome of plant-pathogen interactions. Despite major efforts to decipher effector functions, our current knowledge on effector biology is scattered and often limited. In this study, we conducted two systematic large-scale yeast two-hybrid screenings to detect interactions between Arabidopsis thaliana proteins and effectors from two vascular bacterial pathogens: Ralstonia pseudosolanacearum and Xanthomonas campestris. We then constructed an interactomic network focused on Arabidopsis and effector proteins from a wide variety of bacterial, oomycete, fungal and animal pathogens. This network contains our experimental data and protein-protein interactions from 2,035 peer-reviewed publications (48,200 Arabidopsis-Arabidopsis and 1,300 Arabidopsis-effector protein interactions). Our results show that effectors from different species interact with both common and specific Arabidopsis targets suggesting dual roles as modulators of generic and adaptive host processes. Network analyses revealed that effector targets, particularly effector hubs and bacterial core effector targets, occupy important positions for network organization as shown by their larger number of protein interactions and centrality. These interactomic data were incorporated in EffectorK, a new graph-oriented knowledge database that allows users to navigate the network, search for homology or find possible paths between host and/or effector proteins. EffectorK is available at www.effectork.org and allows users to submit their own interactomic data. Author summaryPlant pests and diseases caused by bacteria, oomycetes, fungi or animals are threatening food security worldwide. Understanding how these pathogens infect and manipulate the host is key to develop sustainable crop resistance in the long term. Effector proteins are secreted by pathogens to subvert the host immune responses. The roles of several effector proteins have been described; however, it is yet poorly understood how effectors interact with host proteins at a global level. To address this issue, we have generated EffectorK, an interactive database focused on the model plant species Arabidopsis thaliana. This database contains manually curated Arabidopsis-effector protein interactions from the available literature on a wide variety of pathogens. It also contains new experimental data on effectors from two vascular pathogens: Ralstonia pseudosolanacearum and Xanthomonas campestris. This work integrates all the gathered knowledge over the last decades and allows to identify general patterns of how effectors interact with the host proteome. This knowledge is easily accessible and searchable at www.effectork.org.

plant biology↗

bioRxiv2019

Genome sequence of the cluster root forming white lupin

White lupin (Lupinus albus L.) is a legume that produces seeds recognized for their high protein content and good nutritional value (lowest glycemic index of all grains, high dietary fiber content, and zero gluten or starch)1-5. White lupin can form nitrogen-fixing nodules but has lost the ability to form mycorrhizal symbiosis with fungi6. Nevertheless, its root system is well adapted to poor soils: it produces cluster roots, constituted of dozens of determinate lateral roots that improve soil exploration and phosphate remobilization7. As phosphate is a limited resource that comes from rock reserves8, the production of cluster roots is a trait of interest to improve fertilizers efficiency. Using long reads sequencing technologies, we provide a high-quality genome sequence of a modern variety of white lupin (2n=50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe how domestication impacted soil exploration capacity through the early establishment of lateral and cluster roots. We identify the APETALA2 transcription factor LaPUCHI-1, homolog of the Arabidopsis morphogenesis coordinator9, as a potential regulator of this trait. Our high-quality genome and companion genomic and transcriptomic resources enable the development of modern breeding strategies to increase and stabilize yield and to develop new varieties with reduced allergenic properties (caused by conglutins10), which would favor the deployment of this promising culture.

genomics↗

bioRxiv2018

Family-Companion: analyse, visualise, browse, query and share your homology clusters

Identifying homology groups in predicted proteomes from different biological sources allows biologists to address questions as diverse as inferring species-specific proteins or retracing the phylogeny of gene families. Nowadays, command-line software exists to infer homology clusters. However, computing and interpreting homology groups with this software remains challenging for biologists and requires computational skills.\n\nWe propose Family-Companion, a web server dedicated to the computation, the analysis and the exploration of homology clusters. Family-Companion aims to fill the gap between analytic software and databases presenting orthologous groups based on a set of public data. It offers a user-friendly interface to launch or upload precomputed homology cluster analysis, to explore and share the results with other users. The exploration of the results is highly facilitated by interactive solutions to visualize proteome intersections via Venn diagrams, phylogenetic trees, multiple alignments, and also by querying the results by blast or by keywords.\n\nFamily-Companion is available at http://family-companion.toulouse.inra.fr with a demo dataset and a set of video tutorials. Source code and installation protocol can be found at https://framagit.org/BBRIC/family-companion/. A container-based package simplifies the installation of the web-suite.

bioinformatics↗

bioRxiv2018

In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana

A current challenge in microbial pathogenesis is to identify biological control agents that may prevent and/or limit host invasion by microbial pathogens. In natura, hosts are often infected by multiple pathogens. However, most of the current studies have been performed under laboratory controlled conditions and by taking into account the interaction between a single commensal species and a single pathogenic species. The next step is therefore to explore the relationships between host-microbial communities (microbiota) and microbial members with potential pathogenic behavior (pathobiota) in a realistic ecological context. In the present study, we investigated such relationships within root and leaf associated bacterial communities of 163 ecologically contrasted Arabidopsis thaliana populations sampled across two seasons in South-West of France. In agreement with the theory of the invasion paradox, we observed a significant humped-back relationship between microbiota and pathobiota -diversity that was robust between both seasons and plant organs. In most populations, we also observed a strong dynamics of microbiota composition between seasons. Accordingly, the potential pathobiota composition was explained by combinations of season-specific microbiota OTUs. This result suggests that the potential biomarkers controlling pathogens invasion are highly dynamic.

microbiology↗

bioRxiv2017

Comparison of GWAS models to identify non-additive genetic control of flowering time in sunflower hybrids

Genome-wide association studies are a powerful and widely used tool to decipher the genetic control of complex traits. One of the main challenges for hybrid crops, such as maize or sunflower, is to model the hybrid vigor in the linear mixed models, considering the relatedness between individuals. Here, we compared two additive and three non-additive association models for their ability to identify genomic regions associated with flowering time in sunflower hybrids. A panel of 452 sunflower hybrids, corresponding to incomplete crossing between 36 male lines and 36 female lines, was phenotyped in five environments and genotyped for 2,204,423 SNPs. Intra-locus effects were estimated in multi-locus models to detect genomic regions associated with flowering time using the different models. Thirteen quantitative trait loci were identified in total, two with both model categories and one with only non-additive models. A quantitative trait loci on LG09, detected by both the additive and non-additive models, is located near a GAI homolog and is presented in detail. Overall, this study shows the added value of non-additive modeling of allelic effects for identifying genomic regions that control traits of interest and that could participate in the heterosis observed in hybrids.

genetics↗