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10 pages; International audience; Over the course of history, humans have moved crops from their regions of origin to new locations across the world. The social, cultural and economic drivers of these movements have generated differences not only between current distributions of crops and their climatic origins, but also between crop distributions and climate suitability for their production. Although these mismatches are particularly important to inform agricultural strategies on climate change adaptation, they have, to date, not been quantified consistently at the global level. Here, we show that the relationships between the distributions of 12 major food crops and climate suitability for their yields display strong variation globally. After investigating the role of biophysical, socio-economic and historical factors, we report that high-income world regions display a better match between crop distribution and climate suitability. In addition, although crops are farmed predominantly in the same climatic range as their wild progenitors, climate suitability is not necessarily higher there, a pattern that reflects the legacy of domestication history on current crop distribution. Our results reveal how far the global distribution of major crops diverges from their climatic optima and call for greater consideration of the multiple dimensions of the crop socio-ecological niche in climate change adaptive strategies.

International audience; Crop diversity is shaped by biological and social processes interacting at different spatiotemporal scales. Here we combined population genetics and ethnobotany to investigate date palm (Phoenix dactylifera L.) diversity in Siwa Oasis, Egypt. Based on interviews with farmers and observation of practices in the field, we collected 149 date palms from Siwa Oasis and 27 uncultivated date palms from abandoned oases in the surrounding desert. Using genotyping data from 18 nuclear and plastid microsatellite loci, we confirmed that some named types each constitute a clonal line, i.e. a true-to-type cultivar. We also found that others are collections of clonal lines, i.e. ethnovarieties, or even unrelated samples, i.e. local categories. This alters current assessments of agrobiodiversity, which are visibly underestimated, and uncovers the impact of low-intensity, but highly effective, farming practices on biodiversity. These hardly observable practices, hypothesized by ethnographic survey and confirmed by genetic analysis, are enabled by the way Isiwans conceive and classify living beings in their oasis, which do not quite match the way biologists do: a classic disparity of etic vs. emic categorizations. In addition, we established that Siwa date palms represent a unique and highly diverse genetic cluster, rather than a subset of North African and Middle Eastern palm diversity. As previously shown, North African date palms display evidence of introgression by the wild relative Phoenix theophrasti Greuter, and we found that the uncultivated date palms from the abandoned oases share even more alleles with this species than cultivated palms in this region. The study of Siwa date palms could hence be a key to the understanding of date palm diversification in North Africa. Integration of ethnography and population genetics promoted the understanding of the interplay between diversity management in the oasis (short-time scale), and the origins and dynamic of diversity through domestication and diversification (long-time scale).; La diversité des plantes cultivées est façonnée par des processus biologiques et sociaux qui interagissent à différentes échelles spatiotemporelles. Nous avons ici combiné la génétique des populations et l’ethnobotanique pour étudier la diversité du palmier-dattier (Phoenix dactylifera L.) dans l’oasis de Siwa, en Égypte. Sur la base d’entretiens avec des agriculteurs et de l’observation des pratiques sur le terrain, nous avons collecté 149 palmiers dattiers de l’oasis de Siwa et 27 palmiers dattiers non cultivés provenant d’oasis abandonnées dans le désert environnant. En utilisant les données de génotypage de 18 loci microsatellites nucléaires et plastidiques, nous avons confirmé que certains types nommés constituent chacun une ligne clonale, c’est-à-dire un « cultivar vrai » (true-to-type). Nous avons également constaté que d’autres sont des collections de lignes clonales, c’est-à-dire des « ethnovariétés », voire même des échantillons non apparentés, c’est-à-dire des « catégories locales ». Cela modifie les évaluations existantes de l’agrobiodiversité, qui sont visiblement sous-estimées, et révèle l’impact des pratiques agricoles de faible intensité, mais très efficaces, sur la biodiversité. Ces pratiques difficilement observables, supposées par l’enquête ethnographique et confirmées par l’analyse génétique, sont rendues possibles par la façon dont les Isiwans conçoivent et classifient les êtres vivants dans leur oasis, qui ne correspond pas tout à fait à la façon dont les biologistes le font : une disparité classique des catégorisations étiques vs. émiques. En outre, nous avons établi que les palmiers dattiers de Siwa représentent un groupe génétique unique et très diversifié, plutôt qu’un sous-ensemble de la diversité des palmiers d’Afrique du Nord et du Moyen-Orient. Comme nous l’avons montré précédemment, les palmiers dattiers d’Afrique du Nord présentent des signes d’introgression par le parent sauvage Phoenix theophrasti Greuter, et nous avons constaté que les palmiers dattiers non cultivés des oasis abandonnées partagent encore plus d’allèles avec cette espèce que les palmiers cultivés de cette région. L’étude des palmiers dattiers de Siwa pourrait donc être une clé pour la compréhension de la diversification des palmiers dattiers en Afrique du Nord. L’intégration de l’ethnographie et de la génétique des populations a permis de comprendre l’interaction entre la gestion de la diversité dans l’oasis (l’échelle du court terme) et les origines et la dynamique de la diversité au travers de la domestication et de la diversification (l’échelle du long terme).

International audience; Doubled haploids (DH) have become a powerful tool to assist in different basic research studies, and also in applied research. The principal (but not the only) and routine use of DH by breeding companies is to produce pure lines for hybrid seed production in different crop species. Several decades after the discovery of haploid inducer lines in maize and of anther culture as a method to produce haploid plants from pollen precursors, the biotechnological revolution of the last decades allowed to the development of a variety of approaches to pursue the goal of doubled haploid production. Now, it is possible to produce haploids and DHs in many different species, because when a method does not work properly, there are several others to test. In this chapter, we overview the currently available approaches used to produce haploids and DHs by using methods based on in vitro culture, or involving the in vivo induction of haploid embryo development, or a combination of both.

International audience; Doubled haploid (DH) technology produces strictly homozygous fertile plant thanks to doubling the chromosomes of a haploid embryo/seedling. Haploid embryos are derived from either male or female germ line cells and hold only half the number of chromosomes found in somatic plant tissues, albeit in a recombinant form due to meiotic genetic shuffling. DH production allows to rapidly fix these recombinant haploid genomes in the form of perfectly homozygous plants (inbred lines), which are produced in two rather than six or more generations. Thus, DH breeding enables fast evaluation of phenotypic traits on homogenous progeny. While for most crops haploid embryos are produced by costly and often genotype-dependent in vitro methods, for maize, two unique in planta systems are available to induce haploid embryos directly in the seed. Two "haploid inducer lines", identified from spontaneous maize mutants, are able to induce embryos of paternal or maternal origin. Although effortless crosses with lines of interest are sufficient to trigger haploid embryos, substantial improvements were necessary to bring DH technology to large scale production. They include the development of modern haploid inducer lines with high induction rates (8-12%), and methods to sort kernels with haploid embryos from the normal ones. Chromosome doubling represents also a crucial step in the DH process. Recent identification of genomic loci involved in spontaneous doubling opens up perspectives for a fully in planta DH pipeline in maize. Although discovered more than 60 years ago, maize haploid inducer lines still make headlines thanks to novel applications and findings. Indeed, maternal haploid induction was elegantly diverted to deliver genome editing machinery in germplasm recalcitrant to transformation techniques. The recent discovery of two molecular players controlling haploid induction allowed to revisit the mechanistic basis of maize maternal haploid induction and to successfully translate haploid induction ability to other crops.

International audience; Crop diversity is shaped by biological and social processes interacting at different spatiotemporal scales. Here we combined population genetics and ethnobotany to investigate date palm (Phoenix dactylifera L.) diversity in Siwa Oasis, Egypt. Based on interviews with farmers and observation of practices in the field, we collected 149 date palms from Siwa Oasis and 27 uncultivated date palms from abandoned oases in the surrounding desert. Using genotyping data from 18 nuclear and plastid microsatellite loci, we confirmed that some named types each constitute a clonal line, i.e. a true-to-type cultivar. We also found that others are collections of clonal lines, i.e. ethnovarieties, or even unrelated samples, i.e. local categories. This alters current assessments of agrobiodiversity, which are visibly underestimated, and uncovers the impact of low-intensity, but highly effective, farming practices on biodiversity. These hardly observable practices, hypothesized by ethnographic survey and confirmed by genetic analysis, are enabled by the way Isiwans conceive and classify living beings in their oasis, which do not quite match the way biologists do: a classic disparity of etic vs. emic categorizations. In addition, we established that Siwa date palms represent a unique and highly diverse genetic cluster, rather than a subset of North African and Middle Eastern palm diversity. As previously shown, North African date palms display evidence of introgression by the wild relative Phoenix theophrasti Greuter, and we found that the uncultivated date palms from the abandoned oases share even more alleles with this species than cultivated palms in this region. The study of Siwa date palms could hence be a key to the understanding of date palm diversification in North Africa. Integration of ethnography and population genetics promoted the understanding of the interplay between diversity management in the oasis (short-time scale), and the origins and dynamic of diversity through domestication and diversification (long-time scale).; La diversité des plantes cultivées est façonnée par des processus biologiques et sociaux qui interagissent à différentes échelles spatiotemporelles. Nous avons ici combiné la génétique des populations et l’ethnobotanique pour étudier la diversité du palmier-dattier (Phoenix dactylifera L.) dans l’oasis de Siwa, en Égypte. Sur la base d’entretiens avec des agriculteurs et de l’observation des pratiques sur le terrain, nous avons collecté 149 palmiers dattiers de l’oasis de Siwa et 27 palmiers dattiers non cultivés provenant d’oasis abandonnées dans le désert environnant. En utilisant les données de génotypage de 18 loci microsatellites nucléaires et plastidiques, nous avons confirmé que certains types nommés constituent chacun une ligne clonale, c’est-à-dire un « cultivar vrai » (true-to-type). Nous avons également constaté que d’autres sont des collections de lignes clonales, c’est-à-dire des « ethnovariétés », voire même des échantillons non apparentés, c’est-à-dire des « catégories locales ». Cela modifie les évaluations existantes de l’agrobiodiversité, qui sont visiblement sous-estimées, et révèle l’impact des pratiques agricoles de faible intensité, mais très efficaces, sur la biodiversité. Ces pratiques difficilement observables, supposées par l’enquête ethnographique et confirmées par l’analyse génétique, sont rendues possibles par la façon dont les Isiwans conçoivent et classifient les êtres vivants dans leur oasis, qui ne correspond pas tout à fait à la façon dont les biologistes le font : une disparité classique des catégorisations étiques vs. émiques. En outre, nous avons établi que les palmiers dattiers de Siwa représentent un groupe génétique unique et très diversifié, plutôt qu’un sous-ensemble de la diversité des palmiers d’Afrique du Nord et du Moyen-Orient. Comme nous l’avons montré précédemment, les palmiers dattiers d’Afrique du Nord présentent des signes d’introgression par le parent sauvage Phoenix theophrasti Greuter, et nous avons constaté que les palmiers dattiers non cultivés des oasis abandonnées partagent encore plus d’allèles avec cette espèce que les palmiers cultivés de cette région. L’étude des palmiers dattiers de Siwa pourrait donc être une clé pour la compréhension de la diversification des palmiers dattiers en Afrique du Nord. L’intégration de l’ethnographie et de la génétique des populations a permis de comprendre l’interaction entre la gestion de la diversité dans l’oasis (l’échelle du court terme) et les origines et la dynamique de la diversité au travers de la domestication et de la diversification (l’échelle du long terme).

International audience; A large group of 38 strains of saprophytic bacteria was isolated from soil and the rhizosphere of agricultural plants. The novel organisms were Gram-negative, aerobic, rod-shaped bacteria that produced a green fluorescent pigment, a red-orange diffusible pigment and a complex mixture of phloroglucinol derivates with antimicrobial activity. The latter have not been found in other bacteria, but are peculiar to ferns. The bacteria were vigorous denitrifiers that synthesized levan from sucrose and liquefied gelatin, but were found not to degrade aesculin, starch, agar, Tween 80 or DNA. Bacterial growth was found to occur at 4 degrees C but not at 40 degrees C. The predominant cellular fatty acids were 16 : 0, 16 : 1(n-7), 18 : 1(n-7) and 17 : 0 cyclo. The G+C content of the novel bacteria was 61.0-62.9 mol%. 16S rRNA gene sequence analysis indicated that the representative strain CIP 109457(T) had a clear affiliation with Pseudomonas sensu stricto groups, with the nearest relatives being Pseudomonas brassicacearum, P. thivervalensis, P. corrugata, P. mediterranea and P. kilonensis. DNA-DNA hybridization experiments showed that the group of isolated strains exhibited high levels of genetic relatedness (81-100 %), confirming that they are representatives of the same species. At the same time, they bound at low levels (4-46 %) with DNA of the type strains of their nearest relatives with the exception of P. brassicacearum; DNA binding of 90 % with the DNA of P. brassicacearum CIP 107059(T) suggested that the bacteria studied belong to this species. Analysis of taxonomic data indicated that the group of novel bacteria maintain a distinct phenotypic profile, allowing the description of novel subspecies within P. brassicacearum, for which the following names are proposed: Pseudomonas brassicacearum subsp. brassicacearum subsp. nov. (type strain DBK11(T) =CFBP 11706(T) =CIP 107059(T) =DSM 13227(T) =JCM 11938(T)) and Pseudomonas brassicacearum subsp. neoaurantiaca subsp. nov., with the type strain CIP 109457(T) (=ATCC 49054(T) =IMV 387(T) =VKM B-1524(T)).

International audience

The culture of transgenic Lotus corniculatus plants producing opines, which are bacterial growth substrates, leads to the selection of rhizospheric bacteria able to utilize these substrates. We have investigated the fate of the opine-utilizing community over time under different experimental conditions following elimination of selective pressure exerted by the transgenic plants. These plants were removed from the soil, which was either left unplanted or replanted with wild-type L. corniculatus or wheat plants. The density of opine-utilizing bacteria in the fallow soils remained essentially unchanged throughout the experiment, regardless of the soil of origin (soil planted with wild-type or transgenic plants). When wild-type Lotus plants were used to replace their transgenic counterparts, only the bacterial populations able to utilize the opines were affected. Long-term changes affecting the opine-utilizing bacterial community on Lotus roots was dependent upon the opine studied. The concentration of nopaline utilizers decreased, upon replacement of the transgenic plants, to a level similar to that of normal plants, while the concentration of mannopine utilizers decreased to levels intermediate between transgenic and normal plants. These data indicate that: (i) the opine-utilizing bacterial populations can be controlled in the rhizosphere via plant-exudate engineering; (ii) the interaction between the engineered plants and their root-associated micro-organisms is transgene specific; and (iii) alterations induced by the cultivation of transgenic plants may sometimes be persistent. Furthermore, opine-utilizing bacterial populations can be controlled by crop rotation. Therefore, favouring the growth of a rhizobacterium of agronomic interest via an opine-based strategy appears feasible.

International audience; Practically all human populations are environmentally exposed to cadmium (Cd), mostly through plant-derived food. A growing body of epidemiological evidence suggests that there is no margin of safety between current Cd exposure levels and the threshold for adverse health effects and, hence, there is an urgent need to lower human Cd intake. Here we review recent studies on rice (Oryza sativa) and Cd-hyperaccumulating plants that have led to important insights into the processes controlling the passage of Cd from the soil to edible plant organs. The emerging molecular understanding of Cd uptake, root retention, root-to-shoot translocation and grain loading will enable the development of low Cd-accumulating crops.

In this review, after giving some figures on the economic impact of aphids on agricultural production, we describe the different mechanisms leading to yield losses (direct damage due to sieve drain and plant reaction, indirect damage, often the most important, due to virus transmission). Then, after a history of chemical control and of its limits, the main control strategies (chemical control with decision rules, plant resistance, biological control, farming practices) are reviewed in the light of an integrated pest management approach. Several topics tackled in this article are exemplified for cereal aphids, which are among the most important in Europe as direct feeders and virus vectors.

A-Maize-ing Maize is one of our oldest and most important crops, having been domesticated approximately 9000 years ago in central Mexico. Schnable et al. (p. 1112 ; see the cover) present the results of sequencing the B73 inbred maize line. The findings elucidate how maize became diploid after an ancestral doubling of its chromosomes and reveals transposable element movement and activity and recombination. Vielle-Calzada et al. (p. 1078 ) have sequenced the Palomero Toluqueño ( Palomero ) landrace, a highland popcorn from Mexico, which, when compared to the B73 line, reveals multiple loci impacted by domestication. Swanson-Wagner et al. (p. 1118 ) exploit possession of the genome to analyze expression differences occurring between lines. The identification of single nucleotide polymorphisms and copy number variations among lines was used by Gore et al. (p. 1115 ) to generate a Haplotype map of maize. While chromosomal diversity in maize is high, it is likely that recombination is the major force affecting the levels of heterozygosity in maize. The availability of the maize genome will help to guide future agricultural and biofuel applications (see the Perspective by Feuillet and Eversole ).

In most production areas, Alternaria leaf blight (ALB) is recognized as the most common and destructive foliage disease in carrot. To assess the genetic architecture of carrot ALB resistance, two parental coupling maps were developed with similar number of dominant markers (around 70), sizes (around 650 cM), densities (around 9.5 cM), and marker composition. The F(2:3) progenies were evaluated in field and tunnel for two scoring dates. The continuous distribution of the disease severity value indicated that ALB resistance is under polygenic control. Three QTLs regions were found on three linkage groups. Two of them were tunnel or field specific and were detected only at the second screening date suggesting that the expression of these two QTLs regions involved in resistance to Alternaria dauci might depend on environment and delay after infection.

International audience; Prostate cancer is the most frequent cancer affecting men in most Western countries. Certain risk factors have been identified (age, family history, ethnic origin), but the aetiology of this cancer remains largely unknown. However, a role for environmental factors is strongly suspected. Questions have been raised concerning the role of the chemical substances generated by human activities in the occurrence of this disease. Diverse studies have consistently demonstrated a higher risk of prostate cancer in agricultural populations than in the general population. The hypothesis that this higher risk is linked to the use of pesticides has been tested in a number of studies, mostly in North America and Europe. However, to date, with a few possible exceptions, it has been impossible to demonstrate a significant association between exposure to pesticides or a chemical family of pesticides and prostate cancer. In the face of these uncertainties, rigorous studies are required, with objective measurements of exposure, taking into account confounding factors and individual risk factors, making it possible to assess gene-environment interactions.