Potential of high-throughput eDNA sequencing of soil fungi and bacteria for monitoring ecological restoration in ultramafic substrates: The case study of the New Caledonian biodiversity hotspot

International audienceDue to their central role in ecosystems functioning and their ability to rapidly respond to environmental changes, soil microorganisms could potentially be used for monitoring ecosystems recovery in the context of degraded land restoration. However, these belowground organisms have been, to date, largely neglected. Here, we investigated fungal and bacterial community diversity, composition, and structure from ultramafic soils in New Caledonia, an archipelago in the southwest Pacific recognized as a priority for conservation and restoration. The emerging approach of high-throughput amplicon sequencing of environmental DNA (eDNA)-metabarcoding of eDNAwas used to compare soil microbial communities from four different native vegetation types, representing different stages of a chronosequence and defined as reference ecosystems, to five distinct post-mining sites revegetated several years ago. Our results clearly revealed changes in soil microbial phyla and functional groups along the reference chronosequence and variable responses at the different revegetated sites, with two of the five sites showing a good trajectory of recovery. We thus propose three ratios as metrics for monitoring the restoration trajectory of soil microorganisms: the Ascomycota:Basidiomycota and Saprotrophic:Ectomycorrhizal ratios for fungi, and the Cyanobacteria:Chloroflexi ratios for bacteria. Our study, combined with recent works undertaken in other geographical areas, underpins the great promise that could represent soil microbial eDNA metabarcoding for monitoring restoration progress and success. With the emergence of these new cost-effective and scalable sequencing technologies, soil microbes could, in the near future, be included in guidelines for restoration operations in complement to more conventional approaches

Improving the accuracy of genomic predictions in an outcrossing species with hybrid cultivars between heterozygote parents: a case study of oil palm (Elaeis guineensis Jacq.)

International audienceGenomic selection (GS) is a method of marker-assisted selection revolutionizing crop improvement, but it can still be optimized. For hybrid breeding between heterozygote parents of different populations or species, specific aspects can be considered to increase GS accuracy: (1) training population genotyping, i.e., only genotyping the hybrid parents or also a sample of hybrid individuals, and (2) marker effects modeling, i.e., using population-specific effects of single nucleotide polymorphism alleles model (PSAM) or across-population SNP genotype model (ASGM). Here, this was investigated empirically for the prediction of the performances of oil palm hybrids for yield traits. The GS model was trained on 352 hybrid crosses and validated on 213 independent hybrid crosses. The training and validation hybrid parents and 399 training hybrid individuals were genotyping by sequencing. Despite the small proportion of hybrid individuals genotyped and low parental heterozygosity, GS prediction accuracy increased on average by 5% (range 1.4-31.3%, depending on trait and model) when training was done using genomic data on hybrids and parents compared with only parental genomic data. With ASGM, GS prediction accuracy increased on average by 3% (- 10.2 to 40%, depending on trait and genotyping strategy) compared with PSAM. We conclude that the best GS strategy for oil palm is to aggregate genomic data of parents and hybrid individuals and to ignore the parental origin of marker alleles (ASGM). To gain a better insight into these results, future studies should examine the respective effect of capturing genetic variability within crosses and taking segregation distortion into account when genotyping hybrid individuals, and investigate the factors controlling the relative performances of ASGM and PSAM in hybrid crops

Three founding ancestral genomes involved in the origin of sugarcane

International audienceAbstract Background and Aims Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum. Methods To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus. Key Results The diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered. Conclusions This evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity

Three founding ancestral genomes involved in the origin of sugarcane.

Background and aimsModern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum.MethodsTo analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus.Key resultsThe diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered.ConclusionsThis evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity

Genomic predictions improve clonal selection in oil palm (Elaeis guineensis Jacq.) hybrids

The prediction of clonal genetic value for yield is challenging in oil palm (Elaeis guineensis Jacq.). Currently, clonal selection involves two stages of phenotypic selection (PS): ortet preselection on traits with sufficient heritability among a small number of individuals in the best crosses in progeny tests, and final selection on performance in clonal trials. The present study evaluated the efficiency of genomic selection (GS) for clonal selection. The training set comprised almost 300 Deli x La Me crosses phenotyped for eight palm oil yield components and the validation set 42 Deli x La Me ortets. Genotyping-by-sequencing (GBS) revealed 15,054 single nucleotide polymorphisms (SNP). The effects of the SNP dataset (density and percentage of missing data) and two GS modeling approaches, ignoring (ASGM) and considering (PSAM) the parental origin of alleles, were assessed. The results showed prediction accuracies ranging from 0.08 to 0.70 for ortet candidates without data records, depending on trait, SNP dataset and modeling. ASGM was better (on average slightly more accurate, less sensitive to SNP dataset and simpler), although PSAM appeared interesting for a few traits. With ASGM, the number of SNPs had to reach 7,000, while the percentage of missing data per SNP was of secondary importance, and GS prediction accuracies were higher than those of PS for most of the traits. Finally, this makes possible two practical applications of GS, that will increase genetic progress by improving ortet preselection before clonal trials: (1) preselection at the mature stage on all yield components jointly using ortet genotypes and phenotypes, and (2) genomic preselection on more yield components than PS, among a large population of the best possible crosses at nursery stage

Multivariate genomic model improves analysis of oil palm (Elaeis guineensis Jacq.) progeny tests

International audienceGenomic selection is promising for plant breeding, particularly for perennial crops. Multivariate analysis, which considers several traits jointly, takes advantage of the genetic correlations to increase accuracy. The aim of this study was to empirically evaluate the potential of a univariate and multivariate genomic mixed model (G-BLUP) compared to the traditional univariate pedigree-based BLUP (T-BLUP) when analyzing progeny tests of oil palm, the world’s major oil crop. The dataset comprised 478 crosses between two heterotic groups, A and B, with 140 and 131 parents, respectively, genotyped with 313 simple sequence repeat markers. The traits were bunch number and average bunch weight. We found that G-BLUP with a genomic matrix based on a similarity index gave a higher likelihood than T-BLUP. In addition, multivariate G-BLUP improved the accuracy of additive effects (breeding values or general combining abilities, GCAs), in particular for the less heritable trait, and of dominance effects (specific combining abilities, SCAs). The average increase in accuracy was 22.5 % for GCAs and 18.7 % for SCAs. Using 160 markers in group A and 90 in group B was enough to reach maximum GCA prediction accuracy. The contrasted history of the parental groups likely explained the higher benefit of G-BLUP over T-BLUP for group A than for group B. Finally, G-BLUP should be used instead of T-BLUP to analyze oil palm progeny tests, with a multivariate approach for correlated traits. G-BLUP will allow breeders to consider SCAs in addition to GCAs when selecting between the progeny-tested parents

Vers un capitalisme de plateforme ?

Le Corpus « Vers un capitalisme de plateforme ? » situe d’emblée les transformations radicales qu’introduisent les plateformes numériques dans le capitalisme contemporain ; en plusieurs endroits on pourrait d’ailleurs parler de rupture tant ces plateformes transforment le travail en lui-même, ses conditions d’exercice et surtout l’emploi. Ce Corpus présente les résultats des premières enquêtes réalisées dans divers domaines de l’économie de plateforme, enquêtes largement centrées sur les transformations induites par cette dernière. Derrière ce modèle économique jugé innovant, une particularité fondamentale caractérise ce nouveau type de transaction économique : les offreurs de travail sur les plateformes numériques sont bien souvent des particuliers, c’est-à-dire qu’ils ne sont pas salariés, ni même nécessairement des professionnels. Ce sont eux qui possèdent l’outil de production et la force de travail qu’ils vendent en qualité d’indépendants, soit directement aux consommateurs, soit à un intermédiaire. Les travailleurs de ces plateformes assument les risques liés à l’activité (investissement, clientèle, risque physique) tout en étant peu autonomes dans l’organisation de l’activité (processus calibrés, prix fixés par la plateforme, contrôles par cette dernière et par les consommateurs). Les mutations des statuts d’emploi et des formes d’organisation du travail, ainsi que les déplacements des responsabilités dans l’exercice de l’activité apparaissent comme majeurs et justifient l’usage du terme de « capitalisme de plateforme ». En effet, cette notion met l’accent sur la création de valeur et son partage, inégalitaire, entre, d’une part, les détenteurs des algorithmes, sites et applications que sont les plateformes et, d’autre part, les travailleurs présents sur celles-ci qui doivent fournir les moyens de travail. En mettant au travail des indépendants, le capitalisme de plateforme, loin de leur conférer de l’autonomie, participe de l’émergence de formes renouvelées, voire exacerbées, de sujétion des travailleurs, visant à les mobiliser, et cela à l’écart des régulations actuelles des mondes du travail. Ainsi le capitalisme de plateforme se situe à la conjonction de l’utilisation d’innovations technologiques (l’Internet combiné à la puissance des algorithmes) et de décisions politiques allant dans le sens d’un affaiblissement du salariat stable à travers la promotion du travail indépendant, de courte durée, supposément inscrit dans une logique de projets et de collaborations sans cesse renouvelées. L’étude de ces transformations pose trois questions majeures : comment (re)penser les frontières du travail et du hors-travail ? Les processus de fuite du salariat constituent-ils une innovation ou un retour en arrière ? Qu’est-ce qui (re)fonde la relation et le contrat de travail ? Les quatre articles du Corpus répondent, chacun à leur manière à ces questionnements. Avec un titre provocateur (« Le salariat : mort ou vif ? »), la rubrique Controverses fait débattre cinq spécialistes du travail et de l’emploi autour des questions suivantes : face à l’omniprésence d’une rhétorique annonçant un déclin du salariat au profit de l’emploi indépendant, comment évaluer et interpréter la reconfiguration des conditions de mobilisation du travail ? Faut-il se féliciter de la fragilisation d’une institution salariale archaïque ? Regretter un âge d’or révolu ? Relativiser ce déclin ? Ou encore questionner plus largement le fait salarial, au-delà de sa forme juridique ? Varia publie un article qui se concentre sur une catégorie de chômeurs fortement stigmatisée et parfois désignée comme « chômeurs volontaires ». Les personnes rencontrées se déclarant ouvertement « en non-recherche active d’emploi » ont pour point commun des expériences négatives du salariat et des sensibilités politiques contestataires de l’ordre socio-économique présent. Mais en même temps, l’auteur montre combien, selon les origines sociales et le capital scolaire/universitaire acquis, les uns et les autres font face de manière différenciée à la précarité et affichent des discours divergents quant à l’emploi stable. Autrement dit, au-delà d’apparentes similitudes sur le refus du travail, s’impose une diversité de situations et de conceptions qui ouvrent de nouvelles interrogations sur le futur du travail. La rubrique Champs et contrechamps interroge Sophie Audier sur son dernier documentaire Les Chèvres de ma mère, sorti en salle en 2018. Le film traite de la transmission et de la rupture lorsqu’approche la fin d’une activité professionnelle qui a structuré le temps long d’une vie ? Sophie Audier mêle le social et l’intime, l’économique, le politique et le local. Elle filme le moment où sa mère va se séparer de ses terres et de ses animaux et sa rencontre avec les normes européennes incarnées par la jeune fille qui lui succédera. L’entretien conduit avec la réalisatrice montre en quoi la préparation détaillée et l’anticipation très précise de ce que veut dire l’auteur, conditionnent la qualité du documentaire : une évidence du temps long pour certains, mais aussi des principes insupportables là où règnent les exigences d’accélération du tournage et de la réalisation filmique. Sophie Audier fait partager ses questionnements sur le montage et sur les rapports entre réalisateur et monteur. La rubrique Matériaux entre directement en résonance avec le Corpus, puisqu’elle propose le récit de Nathan, livreur à vélo, à travers plusieurs extraits d’un entretien réalisé à Paris en mars 2017. Nathan, agent administratif de l’Éducation nationale, exerce une seconde activité de livraison de repas pour une plateforme numérique. L’entretien trace le portrait d’une figure des travailleurs des plateformes : ni étudiant trouvant là un moyen relativement facile d’obtenir un revenu jugé correct ni pseudo-indépendant aspirant au statut salarial, le cas de Nathan est celui d’une bi-activité, qui exacerbe la logique du cumul d’activités permise par le statut de micro-entrepreneur. Par sa singularité, ce cas permet d’éclairer certains ressorts de l’engagement de ces jeunes hommes dans la course urbaine et de faire ressortir l’ambivalence d’une situation poussée à son extrême, juxtaposant un discours clairvoyant et critique sur les conditions de travail et d’emploi et un engagement à la fois important, résolu et relativement durable dans l’activité au service de la plateforme. Au nombre de onze, les Recensions et notes de lectures font état des approches différenciées des objets qui sont au centre des préoccupations de la revue : les auteurs avancent des commentaires critiques et ouvrent des débats qui appellent des réponses..