Characterization of the leaf microbiome from whole-genome sequencing data of the 3000 rice genomes project.

Román-Reyna, Verónica; Pinili, Dale; Borja, Frances Nikki; Quibod, Ian Lorenzo; Groen, Simon C.; Alexandrov, Nickolai N.; Mauleon, Ramil; Oliva, Ricardo

doi:10.21203/rs.3.rs-35287/v2

Cited by 4 publications

(6 citation statements)

References 32 publications

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“…1B). This is in line with the polygenic architecture reported in GWAS conducted on microbial communities (Horton et al 2014; Walters et al 2018; Bergelson et al 2019; Roman-Reyna et al 2020; Deng et al 2021; Brachi et al 2022; VanWallendael et al 2022). Differences in the number of QTLs among the six ‘plant compartment × seasons’ were barely significant (Generalized Linear Model, GLM, F = 2.30, P = 0.0471).…”

Section: Resultssupporting

confidence: 88%

“…All GWAS performed previously on plant microbial communities were conducted on one specific plant compartment (Walters et al 2018; Roman-Reyna et al 2020; Deng et al 2021; Brachi et al 2022; VanWallendael et al 2022), with the exception of one GWAS conducted on worldwide accessions of A. thaliana at the leaf (Horton et al 2014) and root (Bergelson et al 2019) levels. Similar to our results, this latter GWAS showed a small overlap between the leaf and root compartments in candidate genes associated with descriptors of bacterial and fungal communities (Bergelson et al 2019), which is in line with the adaptive differences in microbial community diversity and composition observed among plant niches, from rhizosphere soils to plant canopies (Müller et al 2016; Cregger et al 2018).…”

Section: Resultsmentioning

confidence: 99%

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The genetic architecture of adaptation to leaf and root bacterial microbiota inArabidopsis thaliana

Roux

Frachon

Bartoli

2022

Preprint

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Understanding the role of host genome in modulating microbiota variation is a need to shed light into the holobiont theory and overcome the current limits on the description of host-microbiota interactions at the genomic and molecular levels. However, the host genetic architecture structuring microbiota is only partly described in plants. In addition, most association genetic studies on microbiota are often carried out outside the native habitats where the host evolve and the identification of signatures of local adaptation on the candidate genes has been overlooked. To fill these gaps and dissect the genetic architecture driving adaptive plant-microbiota interactions, we adopted a Genome-Environmental-Association (GEA) analysis on 141 whole-genome sequenced natural populations of Arabidopsis thaliana characterized in situ for their leaf and root bacterial communities and a large range of environmental descriptors (i.e. climate, soil and plant communities). Across 194 microbiota traits, a much higher fraction of among-population variance was explained by the host genetics than by ecology, with the plant neighborhood as the main ecological driver of microbiota variation. Importantly, the relative importance of host genetics and ecology expressed a phylogenetic signal at the family and genus level. In addition, the polygenic architecture of adaptation to bacterial communities was highly flexible between plant compartments and seasons. Relatedly, signatures of local adaptation were stronger on QTLs of the root microbiota in spring. Finally, we provide evidence that plant immunity, in particular the FLS2 gene, is a major source of adaptive genetic variation structuring bacterial assemblages in A. thaliana.

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Section: Resultssupporting

confidence: 88%

Section: Resultsmentioning

confidence: 99%

The genetic architecture of adaptation to leaf and root bacterial microbiota inArabidopsis thaliana

Roux

Frachon

Bartoli

2022

Preprint

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“…We used high-yielding commercial cultivars adapted to Northern European conditions, and thus genotypes were highly similar. Detailed studies of host genetic control of microbiome assembly has only recently been initiated [36,37]. For instance, in a recent study in wheat using cultivars having different pathogen resistance genes, it was found that genotype was important for determining the leaf-associated microbiome [38].…”

Section: Discussionmentioning

confidence: 99%

Under Attack: Fungal Landscape of Spring Barley From Seedling Emergence to Harvest During a Severe Puccinia Hordei Epidemic

Sapkota

Jørgensen

Boeglin

et al. 2021

Preprint

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All plant tissues from leaves, stems and roots are hosting a wide diversity of fungal species. Our understanding of the assembly of this diversity of fungi during the plant growth cycle is limited. Here, we characterized the mycobiome of three spring barley cultivars at weekly intervals from seedling emergence to senescence and seed maturity. A notable proportion of members of the fungal communities were shared among different plant organs, but community dynamics were tissue specific. A severe attack of Puccinia hordei occurring during the vegetative stage had profound effects on the mycobiome, and P. hordei biomass displaced that of other taxa. Plant tissue type was the most important factor determining the mycobiome, but also plant age was contributing significantly. Using a random forest model, we found that specific members of the mycobiome were responding differently to plant age. A co-occurrence network analysis revealed complex interactions among fungal OTUs, and network connectivity was changing as per plant growth stage and plant tissue type. This study contributes to the understanding of assembly of fungal communities in cereals by providing a detailed atlas of fungal communities associated with barley. This knowledge will be vital for microbiome assisted plant health management and our study will serve as an important baseline for future efforts to harness microbiota in cereal health.

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“…So far, the five GWAS [83][84][85][86] and the single genome-environment association study (GEAS) (Roux et al 2022) conducted on the leaf compartment and using bacterial community descriptors as phenotypic traits, revealed a polygenic architecture controlling microbiota assembly, which is in line with the small percentage of variance explained by the phenotyping of individual mutant lines [87]. In agreement with those association genetic studies and the two GWAS conducted on A. thaliana in response to a PGPB strain [47,49], we identified a complex genetic architecture for the response of A. thaliana to 13 non-pathogenic bacterial strains.…”

Section: A Complex and Highly Flexible Genetic Architecture Underlies...mentioning

confidence: 99%

The genetic architecture ofArabidopsis thalianain response to native non-pathogenic leaf bacterial species revealed by GWA mapping in field conditions

Ramírez-Sánchez

Duflos

Gibelin-Viala

et al. 2022

Preprint

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Non-pathogenic bacteria can largely contribute to plant health by mobilizing and supplying nutrients and by providing protection against pathogens and resistance to abiotic stresses. Yet, the number of GWAS reporting the genetic architecture of the response to individual members of the beneficial microbiota remains limited. In this study, we established a GWAS under field conditions to estimate the level of genetic variation and the underlying genetic architecture, among 162 accessions of Arabidopsis thaliana originating from 54 natural populations located south-west of France, in response to 13 strains of seven of the most abundant and prevalent non-pathogenic bacterial species isolated from the leaf compartment of A. thaliana in the same geographical region. Using a high-throughput phenotyping methodology to score vegetative growth-related traits, extensive genetic variation was detected within our local set of A. thaliana accessions in response to these leaf bacteria, both at the species and strain levels. The presence of crossing reaction norms among strains indicates that declaring a strain as a plant-growth promoting bacterium is highly dependent on the host genotype tested. In line with the strong genotype-by-genotype interactions, we detected a complex and highly flexible genetic architecture between the 13 strains. Finally, the candidate genes underlying the QTLs revealed a significant enrichment in several biological pathways, including cell, secondary metabolism, signalling and transport. Altogether, plant innate immunity appears as a significant source of natural genetic variation in plant-microbiota interactions and opens new avenues for better understanding the ecologically relevant molecular dialog during plant-microbiota interactions.

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Characterization of the leaf microbiome from whole-genome sequencing data of the 3000 rice genomes project.

Cited by 4 publications

References 32 publications

The genetic architecture of adaptation to leaf and root bacterial microbiota inArabidopsis thaliana

The genetic architecture of adaptation to leaf and root bacterial microbiota inArabidopsis thaliana

Under Attack: Fungal Landscape of Spring Barley From Seedling Emergence to Harvest During a Severe Puccinia Hordei Epidemic

The genetic architecture ofArabidopsis thalianain response to native non-pathogenic leaf bacterial species revealed by GWA mapping in field conditions

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