Genetic control of plasticity of oil yield for combined abiotic stresses using a joint approach of crop modeling and genome-wide association

Understanding the genetic basis of phenotypic plasticity is crucial for predicting and managing climate change effects on wild plants and crops. Here, we combined crop modeling and quantitative genetics to study the genetic control of oil yield plasticity for multiple abiotic stresses in sunflower. First we developed stress indicators to characterize 14 environments for three abiotic stresses (cold, drought and nitrogen) using the SUNFLO crop model and phenotypic variations of three commercial varieties. The computed plant stress indicators better explain yield variation than descriptors at the climatic or crop levels. In those environments, we observed oil yield of 317 sunflower hybrids and regressed it with three selected stress indicators. The slopes of cold stress norm reaction were used as plasticity phenotypes in the following genome-wide association study. Among the 65,534 tested SNP, we identified nine QTL controlling oil yield plasticity to cold stress. Associated SNP are localized in genes previously shown to be involved in cold stress responses: oligopeptide transporters, LTP, cystatin, alternative oxidase, or root development. This novel approach opens new perspectives to identify genomic regions involved in genotype-by-environment interaction of a complex traits to multiple stresses in realistic natural or agronomical conditions.Comment: 12 pages, 5 figures, Plant, Cell and Environmen

Corrigendum: Investigating genetic diversity within the most abundant and prevalent non-pathogenic leaf-associated bacteria interacting with Arabidopsis thaliana in natural habitats

International audienc

HMW DNA extraction from diverse plants species for PacBio and Nanopore sequencing

Modified from the protocol of Baptiste Mayjonade, Jérome Gouzy, Cécile Donnadieu, Nicolas Pouilly, William Marande, Caroline Callot, Nicolas Langlade and Stéphane Munos, High molecular weight gDNA extraction, Bio Techniques, Vol. 61, No. 4, October 2016, pp. 203-205. BioTechniques 61:203-205 (October 2016) doi 10.2144/000114460 https://www.future-science.com/doi/10.2144/000114460 The original protocol failed to extract High Molecular Weight genomic DNA from orchids samples (poor yield and low purity). Therefore modifications (mainly/mostly BME addition during the lysis step and a Phenol:Chloroform purification step) were made to create a new version of this protocol. This new version allowed to successfully extract DNA from orchid samples. This DNA was then sequenced on a Nanopore PromethION platform and good results in term of total yield and read length were obtained. This protocol was also successfully applied to a wide range of plant species (See attached document/excel sheet)

Unraveling the genetic architecture of the adaptive potential of Arabidopsis thaliana to face the bacterial pathogen Pseudomonas syringae in the context of global change

ABSTRACT Phytopathogens are a continuous threat for global food production and security. Emergence or re-emergence of plant pathogens is highly dependent on the environmental conditions affecting pathogen spread and survival. Under climate change, a geographic expansion of pathogen distribution poleward has been observed, potentially resulting in disease outbreaks on crops and wild plants. Therefore, estimating the adaptive potential of plants to novel epidemics and describing its underlying genetic architecture, is a primary need to propose agricultural management strategies reducing pathogen outbreaks and to breed novel plant cultivars adapted to pathogens that might spread in novel habitats under climate change. To address this challenge, we inoculated Pseudomonas syringae strains isolated from Arabidopsis thaliana populations located in south-west of France on the highly genetically polymorphic TOU-A A. thaliana population located east-central France. While no adaptive potential was identified in response to most P. syringae strains, the TOU-A population displays a variable disease response to the P. syringae strain JACO-CL belonging to the phylogroup 7 (PG7). This strain carried a reduced T3SS characteristic of the PG7 as well as flexible genomic traits and potential novel effectors. GWA mapping on 192 TOU-A accessions inoculated with JACO-CL revealed a polygenic architecture. The main QTL region encompasses two R genes and the AT5G18310 gene encoding for ubiquitin hydrolase, a target of the AvrRpt2 P. syringae effector. Altogether, our results pave the way for a better understanding of the genetic and molecular basis of the adaptive potential in an ecologically relevant A. thaliana – P. syringae pathosystem

The genetic architecture of the adaptive potential of Arabidopsis thaliana in response to Pseudomonas syringae strains isolated from south-west France

International audiencePhytopathogens are a threat for global food production and security. Emergence or re-emergence of plant pathogens is highly dependent on the environmental conditions affecting pathogen spread and survival. Under climate change, a geographic expansion of pathogen distribution poleward has been observed, potentially resulting in disease outbreaks on crops and wild plants. Therefore, estimating the adaptive potential of plants to novel epidemics and describing the underlying genetic architecture is a primary need to propose agricultural management strategies reducing pathogen outbreaks and to breed novel plant cultivars adapted to pathogens that might spread under climate change. To address this challenge, we inoculated Pseudomonas syringae strains isolated from Arabidopsis thaliana populations from south-west of France on the highly genetically polymorphic TOU-A A. thaliana population from north-east France. While no adaptive potential was identified in response to most P. syringae strains, the TOU-A population displayed a variable disease response to the JACO-CL strain belonging to the P. syringae phylogroup 7 (PG7). This strain carried a reduced type III secretion system (T3SS) characteristic of the PG7 as well as flexible genomic traits and potential novel effectors. Genome-wide association mapping on 192 TOU-A accessions revealed a polygenic architecture of disease response to JACO-CL. The main quantitative trait locus (QTL) region encompasses two R genes and the AT5G18310 gene encoding ubiquitin hydrolase, a target of the AvrRpt2 P. syringae effector. Altogether, our results pave the way for a better understanding of the genetic and molecular basis of the adaptive potential in an ecologically relevant A. thaliana-P. syringae pathosystem

Adaptation to plant communities across the genome of Arabidopsis thaliana

Associate Editor: Stephen WrightInternational audienceDespite the importance of plant-plant interactions on plant community dynamics and crop yield, our understanding of the adaptive genetics underlying these interactions is still limited and deserves to be investigated in the context of complex and diffuse interactions occurring in plant assemblages. Here, based on 145 natural populations of Arabidopsis thaliana located in south-west of France and characterized for plant communities, we conducted a Genome-Environment Association analysis to finely map adaptive genomic regions of A. thaliana associated with plant community descriptors. To control for correlated abiotic environment effects, we also characterized the populations for a set of biologically meaningful climate and soil variables. A nonnegligible fraction of top single nucleotide polymorphisms was associated with both plant community descriptors and abiotic variables, highlighting the importance of considering the actual abiotic drivers of plant communities to disentangle genetic variants for biotic adaptation from genetic variants for abiotic adaptation. The adaptive loci associated with species abundance were highly dependent on the identity of the neighboring species suggesting a high degree of biotic specialization of A. thaliana to members of its plant interaction network. Moreover, the identification of adaptive loci associated with a-diversity and composition of plant communities supports the ability of A. thaliana to interact simultaneously with multiple plant neighbors, which in turn can help to understand the role of community-wide selection. Altogether, our study highlights that dissecting the genetic basis underlying plant-plant interactions at a regional scale while controlling for abiotic confounding factors can help understanding the adaptive mechanisms modulating natural plant assemblages

First whole genome assembly and annotation of a European common bean cultivar using PacBio HiFi and Iso-Seq data

Common bean (Phaseolus vulgaris L.) is the most important grain legume for direct human consumption worldwide. Flageolet bean originates from France and presents typical organoleptic properties, including the remarkable feature of having small pale green colored seeds. Here, we report the whole-genome data, assembly and annotation of the flageolet bean accession ‘Flavert’. High molecular weight DNA and RNA were extracted and subjected to long-read sequencing using PacBio Sequel II platform. The genome consisted of 566,238,753 bp assembled in 13 molecules, including 11 chromosomes plus the mitochondrial and chloroplastic genomes. Annotation predicted 29,549 protein coding genes and 6,958 non-coding RNA. This high-quality genome (99.2% BUSCO completeness) represents a valuable data set for further genomic and genetic studies on common bean and more generally on legumes. To our knowledge, this is the first whole-genome sequence of a common bean accession originating from Europe

A genomic map of local adaptation in Arabidopsis thaliana to native non-pathogenic bacteria: from mono-infections to complex communities

National audienceThere is growing interest in the potential of harnessing the microbiome towards the improvement of plant health to achieve agricultural goals. To do so through plant breeding, requires a better understanding of the role of the host genome in modulating microbiota variation. In particular, there is a need to 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. To dissect the genetic architecture driving adaptive plant-microbiota interactions, I will present the results of complementary approaches in association genetics applied on Arabidopsis thaliana: (i) a Genome-Environment Association (GEA) analysis on 141 whole-genome sequenced natural populations of A. thaliana characterized in situ for their leaf and root bacterial communities and a large set of non-microbial ecological factors (i.e., climate, soil, and plant communities), and (ii) a Genome-Wide Association study conducted in field conditions on 162 whole-genome sequenced accessions of A. thaliana inoculated with 13 native Plant Growth-Promoting Bacteria (PGPB) isolated from these populations. By combining these two approaches, we established a genomic map of local adaptation in A. thaliana to its native bacterial microbiota. Plant immunity appears as a major source of adaptive genetic variation structuring beneficial interactions between A. thaliana and the main members of its microbiota

A genomic map of local adaptation in Arabidopsis thaliana to native non-pathogenic bacteria: from mono-infections to complex communities

National audienceThere is growing interest in the potential of harnessing the microbiome towards the improvement of plant health to achieve agricultural goals. To do so through plant breeding, requires a better understanding of the role of the host genome in modulating microbiota variation. In particular, there is a need to 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. To dissect the genetic architecture driving adaptive plant-microbiota interactions, I will present the results of complementary approaches in association genetics applied on Arabidopsis thaliana: (i) a Genome-Environment Association (GEA) analysis on 141 whole-genome sequenced natural populations of A. thaliana characterized in situ for their leaf and root bacterial communities and a large set of non-microbial ecological factors (i.e., climate, soil, and plant communities), and (ii) a Genome-Wide Association study conducted in field conditions on 162 whole-genome sequenced accessions of A. thaliana inoculated with 13 native Plant Growth-Promoting Bacteria (PGPB) isolated from these populations. By combining these two approaches, we established a genomic map of local adaptation in A. thaliana to its native bacterial microbiota. Plant immunity appears as a major source of adaptive genetic variation structuring beneficial interactions between A. thaliana and the main members of its microbiota