Institute for Genetics, Environment and Plant Protection

Abstract Rapeseed (Brassica napus L.) is an oleaginous crop of great economic value but with considerable nitrogen requirement. Breeding for root systems efficiently taking up nitrogen from soil could be a lever to ensure genetic gains for producing rapeseed more sustainably. This study aims at identifying genomic regions regulating root morphology in response to nitrate availability. The natural variability offered by a set of 300 inbred lines was screened. Seedlings grew hydroponically with low or elevated nitrate levels. On average for the diversity panel, low nitrate level increased the root-to-shoot biomass ratio and stimulated the lateral root outgrowth. A large phenotypic variation was observed, along with important heritability values and genotypic effects, but poor genotype-by-nitrogen interactions. Genome-wide association study and bulk segregant analysis were employed to identify loci regulating traits of biomass production and root morphology. The first approach identified 1,305 SNPs, associated with 15 phenotypic traits. These SNPs clustered into 26 QTLs, with seven of them distributed on chromosome A07. Some 14 QTLs were stable across nitrate levels. The second approach was selecting segregant individuals from the tails of the phenotypic distribution of an experimental F2 population, deriving from two accessions with a contrasting lateral root development. Six genomic regions showed allele frequency differences between the two bulks above 0.15, including one significant QTL detected on A06. Some genes involved in root organogenesis coincided with QTL regions. This study provides selection targets for potentially redesigning root morphology in rapeseed.

Plaquette de communication

The fall armyworm (FAW; Spodoptera frugiperda) is one of the major agricultural pest insects. FAW is native to the Americas, and its invasion was first reported in West Africa in 2016. Then it quickly spread through Africa, Asia, and Oceania, becoming one of the main threats to corn production. We analyzed whole genome sequences of 177 FAW individuals from 12 locations on four continents to infer evolutionary processes of invasion. Principal component analysis from the TPI gene and whole genome sequences shows that invasive FAW populations originated from the corn strain. Ancestry coefficient and phylogenetic analyses from the nuclear genome indicate that invasive populations are derived from a single ancestry, distinct from native populations, while the mitochondrial phylogenetic tree supports the hypothesis of multiple introductions. Adaptive evolution specific to invasive populations was observed in detoxification, chemosensory, and digestion genes. We concluded that extant invasive FAW populations originated from the corn strain with potential contributions of adaptive evolution.

Until recently, genotypes of Phytophthora infestans were regionally distributed in Europe, with populations in western Europe being dominated by clonal lineages and those in northern Europe being genetically diverse because of frequent sexual reproduction. However, since 2013 a new clonal lineage (EU_41_A2) has successfully established itself and expanded in the sexually recombining P. infestans populations of northern Europe. The objective of this study was to study phenotypic traits of the new clonal lineage of P. infestans, which may explain its successful establishment and expansion within sexually recombining populations. Fungicide sensitivity, aggressiveness, and virulence profiles of isolates of EU_41_A2 were analyzed and compared with those of the local sexual populations from Denmark, Norway, and Estonia. None of the phenotypic data obtained from the isolates collected from Denmark, Estonia, and Norway independently explained the invasive success of EU_41_A2 within sexual Nordic populations. Therefore, we hypothesize that the expansion of this new genotype could result from a combination of fitness traits and more favorable environmental conditions that have emerged in response to climate change.

Promoting pest biological control within agrosystems is a way to reduce the use of pesticides. The lack of quantification tools of this ecosystem service is a major obstacle to the changes in crop protection strategies. ARENA's ambition was to build methods to observe natural pest control directly on fields, provide tools to quantify and predict natural pest control potential. An important monitoring campaign of pests (slugs and aphids) and natural enemies monitoring took place in 171 fields (wheat, barley, corn, rape). On the basis of the monitoring carried out, tools for quantifying the regulation service were developed along three lines: (1) identification of agro-environmental contexts favourable to the expression of a high level of biological control, (2) development of a statistical model for the early evaluation of pest risk taking into account the level of local biological control and (3) development of an indicator of the potential for regulation by communities of beneficials in the field.

Essential oils of aromatic plants represent an alternative to classical pest control with synthetic chemicals. They are especially promising for the alternative control of stored product pest insects. Here, we tested behavioral and electrophysiological responses of the stored product pest Tribolium confusum, to the essential oil of a Brazilian indigenous plant, Varronia globosa, collected in the Caatinga ecosystem. We analyzed the essential oil by GC-MS, tested the effects of the entire oil and its major components on the behavior of individual beetles in a four-way olfactometer, and investigated responses to these stimuli in electroantennogram recordings (EAG). We could identify 25 constituents in the essential oil of V. globosa, with anethole, caryophyllene and spathulenole as main components. The oil and its main component anethole had repellent effects already at low doses, whereas caryophyllene had only a repellent effect at a high dose. In addition, the essential oil abolished the attractive effect of the T. confusum aggregation pheromone. EAG recordings revealed dose-dependent responses to the individual components and increasing responses to the blend and even more to the entire oil. Our study reveals the potential of anethole and the essential oil of V. globosa in the management of stored product pests.

Abstract Most endogenous viruses, an important proportion of eukaryote genomes, are doomed to slowly decay. Little is known, however, on how they evolve when they confer a benefit to their host. Bracoviruses are essential for the parasitism success of parasitoid wasps, whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome, for the first time at a chromosomal scale, that symbiotic bracovirus genes spread to and colonized all the chromosomes. Moreover, large viral clusters are stably maintained suggesting strong evolutionary constraints. Genomic comparison with another wasps revealed that this organization was already established ~53 mya. Transcriptomic analyses highlight temporal synchronization of viral gene expression, leading to particle production. Immune genes are not induced, however, indicating the virus is not perceived as foreign by the wasp. This recognition suggests that no conflicts remain between symbiotic partners when benefits to them converge.

Aphids secrete proteins from their stylets that evidence indicates function similar to pathogen effectors for virulence. Here, we describe two small candidate effector gene families of the pea aphid, Acyrthosiphon pisum, that share highly conserved secretory signal peptide coding regions and divergent non-secretory coding sequences derived from miniature exons. The KQY candidate effector family contains eleven members with additional isoforms, generated by alternative splicing. Pairwise comparisons indicate possible four unique KQY families based on coding regions without the secretory signal region. KQY1a, a representative of the family, is encoded by a 968 bp mRNA and a gene that spans 45.7 kbp of the genome. The locus consists of 37 exons, 33 of which are 15 bp or smaller. Additional KQY members, as well as members of the KHI family, share similar features. Differential expression analyses indicate that the genes are expressed preferentially in salivary glands. Proteomic analysis on salivary glands and saliva revealed 11 KQY members in salivary proteins, and KQY1a was detected in an artificial diet solution after aphid feeding. A single KQY locus and two KHI loci were identified in Myzus persicae, the peach aphid. Of the genes that can be anchored to chromosomes, loci are mostly scattered throughout the genome, except a two-gene region (KQY4/KQY6). We propose that the KQY family expanded in A. pisum through combinatorial assemblies of a common secretory signal cassette and novel coding regions, followed by classical gene duplication and divergence.

Cette etude contribue a evaluer les pertes alimentaires en France au sein des filieres de fruits, legumes et pomme de terre. Compte tenu du nombre de produits, de la variete des systemes de production et des multiples destinations, l’analyse s’appuie sur 9 productions illustrant la diversite existant au sein de ces trois filieres. Des pertes alimentaires potentielles apparaissent tout au long de ces filieres, de la parcelle du producteur a l’etal du distributeur, et peuvent etre plus ou moins importantes selon les produits (d’environ 5% a plus de 20%). Elles representent globalement pour l’ensemble des fruits et des legumes 12% de la production disponible au champ. Les trois quarts de ces pertes sont constates aux premieres etapes de la filiere, de la recolte a la mise en marche. Leurs principales causes sont la sensibilite des produits aux aleas sanitaires et climatiques, leur perissabilite, l’application de normes reglementaires ou de cahiers des charges exigeants. Les pertes aux stades de la distribution (grossistes et detaillants) representent le quart restant ; elles sont principalement dues a la manipulation de produits tres perissables et surtout a des problemes de surmaturite lies en partie a une gestion inappropriee des stocks. Ces produits ecartes de ces filieres sont en majorite epandus dans les parcelles agricoles, et plus occasionnellement orientes vers des plateformes de methanisation. Pour reduire ou mieux valoriser ces pertes alimentaires, plusieurs leviers d’action peuvent etre envisages a differents niveaux de ces filieres, avec pour certaines d’entre elles l’appui de la Recherche et/ou un soutien des politiques publiques.