Microbial biomarkers of tree water status for next-generation biomonitoring of forest ecosystems

Next-generation biomonitoring proposes to combine machine-learning algorithms with environmental DNA data to automate the monitoring of the Earth's major ecosystems. In the present study, we searched for molecular biomarkers of tree water status to develop next-generation biomonitoring of forest ecosystems. Because phyllosphere microbial communities respond to both tree physiology and climate change, we investigated whether environmental DNA data from tree phyllosphere could be used as molecular biomarkers of tree water status in forest ecosystems. Using an amplicon sequencing approach, we analysed phyllosphere microbial communities of four tree species (Quercus ilex, Quercus robur, Pinus pinaster and Betula pendula) in a forest experiment composed of irrigated and non-irrigated plots. We used these microbial community data to train a machine-learning algorithm (Random Forest) to classify irrigated and non-irrigated trees. The Random Forest algorithm detected tree water status from phyllosphere microbial community composition with more than 90% accuracy for oak species, and more than 75% for pine and birch. Phyllosphere fungal communities were more informative than phyllosphere bacterial communities in all tree species. Seven fungal amplicon sequence variants were identified as candidates for the development of molecular biomarkers of water status in oak trees. Altogether, our results show that microbial community data from tree phyllosphere provides information on tree water status in forest ecosystems and could be included in next-generation biomonitoring programmes that would use in situ, real-time sequencing of environmental DNA to help monitor the health of European temperate forest ecosystems.</p

Towards microbiota-based disease management: analysis of grapevine microbiota in plots with contrasted levels of downy mildew infection

Vineyards harbor a myriad of microorganisms that interact with each other and with the grapevines. Some microorganisms are plant pathogens, such as the oomycete Plasmopara viticola that causes grapevine downy mildew. Others, such as plant growth promoting bacteria and disease biocontrol agents, have a positive influence on vine health. The present study aims to (1) investigate whether vine-based culture media increase the cultivability of the grapevine microbiota, in comparison to standard culture media and (2) identify and isolate bacterial taxa naturally present in grapevine leaves and significantly more abundant in plots showing low susceptibility to downy mildew

Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

<p>Abstract</p> <p>Background</p> <p>Single nucleotide polymorphisms (SNPs) are the most abundant source of genetic variation among individuals of a species. New genotyping technologies allow examining hundreds to thousands of SNPs in a single reaction for a wide range of applications such as genetic diversity analysis, linkage mapping, fine QTL mapping, association studies, marker-assisted or genome-wide selection. In this paper, we evaluated the potential of highly-multiplexed SNP genotyping for genetic mapping in maritime pine (<it>Pinus pinaster </it>Ait.), the main conifer used for commercial plantation in southwestern Europe.</p> <p>Results</p> <p>We designed a custom GoldenGate assay for 1,536 SNPs detected through the resequencing of gene fragments (707 <it>in vitro </it>SNPs/Indels) and from Sanger-derived Expressed Sequenced Tags assembled into a unigene set (829 <it>in silico </it>SNPs/Indels). Offspring from three-generation outbred (G2) and inbred (F2) pedigrees were genotyped. The success rate of the assay was 63.6% and 74.8% for <it>in silico </it>and <it>in vitro </it>SNPs, respectively. A genotyping error rate of 0.4% was further estimated from segregating data of SNPs belonging to the same gene. Overall, 394 SNPs were available for mapping. A total of 287 SNPs were integrated with previously mapped markers in the G2 parental maps, while 179 SNPs were localized on the map generated from the analysis of the F2 progeny. Based on 98 markers segregating in both pedigrees, we were able to generate a consensus map comprising 357 SNPs from 292 different loci. Finally, the analysis of sequence homology between mapped markers and their orthologs in a <it>Pinus taeda </it>linkage map, made it possible to align the 12 linkage groups of both species.</p> <p>Conclusions</p> <p>Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in maritime pine, a conifer species that has a genome seven times the size of the human genome. This SNP-array will be extended thanks to recent sequencing effort using new generation sequencing technologies and will include SNPs from comparative orthologous sequences that were identified in the present study, providing a wider collection of anchor points for comparative genomics among the conifers.</p

Cartographie de gènes candidats impliqués dans le débourrement, la réponse à l’hypoxie et au stress hydrique chez le chêne pédonculé

Face aux changements climatiques annoncés, l’étude de la variabilité génétique existante au sein des espèces forestières est devenue un enjeu important. Pour anticiper l’impact de ces changements sur les espèces à longue durée de vie comme les chênes, il est nécessaire d’étudier les facteurs génétiques impliqués dans l’adaptation à ces nouvelles contraintes. Dans ce cadre, des études sont menées chez le chêne pédonculé pour trois caractères déterminants : le débourrement, la réponse aux stress hydrique et hypoxique. Mon travail vise à étudier la relation gènephénotype entre des gènes candidats et ces caractères. Cette étude a été menée sur une famille de pleins frères issue d’un croisement intraspécifique du chêne pédonculé. Une centaine de gènes candidats expressionnels ou fonctionnels pour les 3 caractères adaptatifs précédents a été proposée. Après la conception des amorces et la recherche de polymorphisme par séquençage chez les parents du croisement, le génotypage des EST polymorphes (par extension d’amorces ou SSCP) a permis de les positionner sur les cartes génétiques du croisement. La recherche de co-localisations entre les gènes polymorphes et des QTL impliqués dans la variation des trois caractères adaptatifs a été menée après reconstruction des cartes parentales à l’aide du logiciel JoinMap. Sur les 9 EST cartographiées, 3 colocalisent avec des QTL impliqués dans la réponse au stress hydrique et hypoxique dont la pertinence biologique et génétique est discutée.The study of genetic diversity in forest tree species is becoming an important issue in the context of global change. In order to anticipate the impact of climatic changes on long lived species such as oak trees, it is of main importance to study the genetic factors involved in the adaptation to these new constraints. In this context, genetic researches are being conducted in Pedunculate oaks on three traits: bud bursting, and response to drought and hypoxia. My work aims at studying the gene to phenotype relationships for selected candidate genes potentially involved in the genetic control of these traits. We use a full-sib mapping pedigree obtained from an intra-specific cross of Quercus robur. A list of candidate genes was proposed, including about 100 accessions for the three above mentioned traits. Once primer pairs were designed and polymorphisms tested by sequencing parental trees, the genotyping of informative ESTs (by primer extension or SSCP) made it possible to localise these genes on the linkage map constructed with JoinMap. A total of three interesting co-localizations between mapped genes and QTLs for the three adaptive traits were observed. These coincidences are discussed according to their genetic and biological relevances

Cartographie de gènes candidats impliqués dans le débourrement, la réponse à l’hypoxie et au stress hydrique chez le chêne pédonculé

Face aux changements climatiques annoncés, l’étude de la variabilité génétique existante au sein des espèces forestières est devenue un enjeu important. Pour anticiper l’impact de ces changements sur les espèces à longue durée de vie comme les chênes, il est nécessaire d’étudier les facteurs génétiques impliqués dans l’adaptation à ces nouvelles contraintes. Dans ce cadre, des études sont menées chez le chêne pédonculé pour trois caractères déterminants : le débourrement, la réponse aux stress hydrique et hypoxique. Mon travail vise à étudier la relation gènephénotype entre des gènes candidats et ces caractères. Cette étude a été menée sur une famille de pleins frères issue d’un croisement intraspécifique du chêne pédonculé. Une centaine de gènes candidats expressionnels ou fonctionnels pour les 3 caractères adaptatifs précédents a été proposée. Après la conception des amorces et la recherche de polymorphisme par séquençage chez les parents du croisement, le génotypage des EST polymorphes (par extension d’amorces ou SSCP) a permis de les positionner sur les cartes génétiques du croisement. La recherche de co-localisations entre les gènes polymorphes et des QTL impliqués dans la variation des trois caractères adaptatifs a été menée après reconstruction des cartes parentales à l’aide du logiciel JoinMap. Sur les 9 EST cartographiées, 3 colocalisent avec des QTL impliqués dans la réponse au stress hydrique et hypoxique dont la pertinence biologique et génétique est discutée.The study of genetic diversity in forest tree species is becoming an important issue in the context of global change. In order to anticipate the impact of climatic changes on long lived species such as oak trees, it is of main importance to study the genetic factors involved in the adaptation to these new constraints. In this context, genetic researches are being conducted in Pedunculate oaks on three traits: bud bursting, and response to drought and hypoxia. My work aims at studying the gene to phenotype relationships for selected candidate genes potentially involved in the genetic control of these traits. We use a full-sib mapping pedigree obtained from an intra-specific cross of Quercus robur. A list of candidate genes was proposed, including about 100 accessions for the three above mentioned traits. Once primer pairs were designed and polymorphisms tested by sequencing parental trees, the genotyping of informative ESTs (by primer extension or SSCP) made it possible to localise these genes on the linkage map constructed with JoinMap. A total of three interesting co-localizations between mapped genes and QTLs for the three adaptive traits were observed. These coincidences are discussed according to their genetic and biological relevances

Species-level identification of the critically endangered European sturgeon Acipencer sturio using DNA-based approaches

The native European sturgeon Acipenser sturio is the focus of restoration programs. However, A. sturio identification by direct observation is not always obvious for non-specialists. We aimed to develop a quick and easy genetic tool applicable to identify the species at risk in case of incidental capture or monitoring either at sea or in the watershed. We showed that primers and probe developed allow specific amplification for A. sturio by PCR, qPCR and Real-Time Loop-mediated isothermal amplification (LAMP) techniques. We determine benefits and limits of each method and highlight perspectives for field applications within the frame of conservation programs

Establishment of a composite SNP linkage map for maritime pine

International audienc

Intégration des approches génétiques au programme de conservation d'une espèce menacée, l'esturgeon européen (Acipenser sturio) : passé, présent et futur

Extrait de documen