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In this chapter, we develop new indicators and statistical tests to characterize patterns of crop diversity at local scales to better understand interactions between ecological and socio-cultural functions of agroecosystems. Farms, where a large number of crops (species or landraces) is grown, are known to contribute a large part of the locally available diversity of both rare and common crops but the role of farms with low diversity remains little understood: do they grow only common varieties-following a nestedness pattern typical of mutualistic networks in ecology-or do 'crop-poor' farmers also grow rare varieties? This question is pivotal in ongoing efforts to assess the local-scale contribution of small farms to global agrobiodiversity. We develop new network-based approaches to characterize the distribution of local crop diversity (species and infra-species) at the village level and to validate these approaches using meta-datasets from 10 countries. Our results highlight the sources of heterogeneity in crop diversity at the village level. We often identify two or more groups of farms based on their different levels of diversity. In some datasets, 'crop-poor' farms significantly contribute to the local crop diversity. Generally, we find that the distribution of crop diversity is more heterogeneous at the species than at the infra-species level. This analysis reveals the absence of a general pattern of crop diversity distribution, suggesting strong dependence on local agroecological and socio-cultural contexts. These different patterns of crop diversity distribution reflect an heterogeneity in farmers' self-organized action in cultivating and maintaining local crop diversity, which ensures the adaptability of agroecosystems to global change.

agr.2011.0501 Auteur(s) : Adeline Barnaud adeline.barnaud@ird.fr, Claire Billot claire.billot@cirad.fr Voir version pdf.

International audience; Significant efforts have been undertaken in West Africa to increase biofuel production with the expectation to alleviate the dependency on fossil energies and to reduce rural poverty by diversifying cultivated crops. In this context, Jatropha curcas L., a shrub belonging to Euphorbiaceae family, has gained great interest because of its oil which can be converted to biodiesel. It is also highly adaptable to marginal soils due to its drought-tolerant characteristics. Characterisation of J. curcas germplasm in Senegal could be an important input for its better management and in identifying genotypes that could be used in breeding program. Genetic diversity of 103 accessions including 82 accessions from different agro ecological zones in Senegal and 21 exotic accessions was assessed through 33 microsatellite markers. All the markers gave amplifications at the expected band size. Only one microsatellite marker, JCT17, was polymorphic showing 3 alleles and allows distinguishing 2 accessions from Burkina Faso. The surprisingly low level of genetic variation might be because introduction of J. curcas in Senegal seems to have been done from one or a few origins and the species has not regained genetic diversity since then due to vegetative propagation. Cultivation of J. curcas at large scale may face to vulnerability to pests and require many cautions. They are necessity to widen the genetic base of J. curcas in Senegal via new introductions from its centre of origin.

INRA UMR 1334 AGAP, Equipe DAVEM = Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes; International audience; Biodiversity, phylogeography and population genetic studies will be revolutionized by access to large data sets thanks to next-generation sequencing methods. In this study, we develop an easy and cost-effective protocol for in-solution enrichment hybridization capture of complete chloroplast genomes applicable at deep-multiplexed levels. The protocol uses cheap in-house species-specific probes developed via long-range PCR of the entire chloroplast. Barcoded libraries are constructed, and in-solution enrichment of the chloroplasts is carried out using the probes. This protocol was tested and validated on six economically important West African crop species, namely African rice, pearl millet, three African yam species and fonio. For pearl millet, we also demonstrate the effectiveness of this protocol to retrieve 95% of the sequence of the whole chloroplast on 95 multiplexed individuals in a single MiSeq run at a success rate of 95%. This new protocol allows whole chloroplast genomes to be retrieved at a modest cost and will allow unprecedented resolution for closely related species in phylogeography studies using plastomes.

Les collectivités paysannes duupa, une ethnie de 5 000 personnes environ, ont pour base de leur subsistance la pratique de l’agriculture, et la production du sorgho y joue un rôle éminent. Comme beaucoup d’agriculteurs dits « traditionnels », les Duupa disposent d’un large éventail de variétés de cette céréale – plus de cinquante sont nommées dans leur langue. Toutefois, cette diversité est inégalement répartie entre les agriculteurs d’un même village ou d’un village à l’autre. Peut-on considérer que ce corpus de variétés locales, et le pool génétique qu’elles représentent, est un trait culturel de l’ensemble du groupe ethnique duupa ? Un examen croisé des principes sociologiques qui sous-tendent la circulation des semences et de l’analyse de la structure génétique du sorgho révèle que l’étendue du territoire où on les retrouve dépasse celle du terroir villageois et du groupe ethnique. Les ressources génétiques dont dépendent les Duupa pour assurer leur subsistance et leur identité culturelle sont semblables à celles de leur voisin dowayo dont ils se distinguent pourtant par leur langue et de nombreux traits de leur culture.

International audience; Understanding the effects of actions undertaken by human societies on crop evolution processes is a major challenge for the conservation of genetic resources. This study investigated the mechanisms whereby social boundaries associated with patterns of ethnolinguistic diversity have influenced the on-farm distribution of sorghum diversity. Social boundaries limit the diffusion of planting material, practices and knowledge, thus shaping crop diversity in situ.To assess the effect of social boundaries, this study was conducted in the contact zone between the Chuka, Mbeere and Tharaka ethnolinguistic groups in eastern Kenya. Sorghum varieties were inventoried and samples collected in 130 households. In all, 297 individual plants derived from seeds collected under sixteen variety names were characterized using a set of 18 SSR molecular markers and 15 morphological descriptors. The genetic structure was investigated using both a Bayesian assignment method and distance-based clustering. Principal Coordinates Analysis was used to describe the structure of the morphological diversity of the panicles. The distribution of the varieties and the main genetic clusters across ethnolinguistic groups was described using a non-parametric MANOVA and pairwise Fisher tests.The spatial distribution of landrace names and the overall genetic spatial patterns were significantly correlated with ethnolinguistic partition. However, the genetic structure inferred from molecular makers did not discriminate the short-cycle landraces despite their morphological distinctness. The cases of two improved varieties highlighted possible fates of improved materials. The most recent one was often given the name of local landraces. The second one, that was introduced a dozen years ago, displays traces of admixture with local landraces with differential intensity among ethnic groups. The patterns of congruence or discordance between the nomenclature of farmers’ varieties and the structure of both genetic and morphological diversity highlight the effects of the social organization of communities on the diffusion of seed, practices, and variety nomenclature.

Understanding the evolutionary patterns of genetic diversity of cultivated plants and their wild relatives is a fundamental aspect of agrobiodiversity research. Documenting genetic diversity and understanding the evolutionary histories of crops will have important impacts in terms of food security in southern countries such as Africa. In this study, we develop a generalized method for sequencing full chloroplast genomes via hybridization enrichment suitable for multiplexing a large number of individuals. We will present application of the method to the study of wild pearl millet, wild and cultivated yams, fonio and to African rice. (Texte intégral)

International audience

Knowledge of the pathways of colonization is critical for risk assessment and management of weeds. In this study we adopted a landscape genetics approach to assess the impact of human disturbances and large-scale environmental features on the colonization of a global agricultural weed, Raphanus raphanistrum. We used nuclear microsatellite and chloroplast DNA sequence data to quantify the pattern of genetic diversity in 336 plants collected from 13 sites throughout the Cape Floristic Region, South Africa, one of the world's recognized global biodiversity hotspots. The lack of strong spatial genetic structure suggests that R. raphanistrum colonized throughout the Cape Floristic Region via both local diffusive spread and long-distance jump dispersal. Furthermore, 47 % of analyzed plants contained Raphanus sativus (cultivated radish) chloroplast genomes, indicating historical and/or contemporary gene flow between wild and cultivated radish populations. The prevalence of high genetic diversity and long-distance gene flow are discussed in the context of ecological risk assessment.

International audience; The circulation of seed among farmers is central to agrobiodiversity conservation and dynamics. Agrobiodiversity, the diversity of agricultural systems from genes to varieties and crop species, from farming methods to landscape composition, is part of humanity’s cultural heritage. Whereas agrobiodiversity conservation has received much attention from researchers and policy makers over the last decades, the methods available to study the role of seed exchange networks in preserving crop biodiversity have only recently begun to be considered. In this overview, we present key concepts, methods, and challenges to better understand seed exchange networks so as to improve the chances that traditional crop varieties (landraces) will be preserved and used sustainably around the world. The available literature suggests that there is insufficient knowledge about the social, cultural, and methodological dimensions of environmental change, including how seed exchange networks will cope with changes in climates, socio-economic factors, and family structures that have supported seed exchange systems to date. Methods available to study the role of seed exchange networks in the preservation and adaptation of crop specific and genetic diversity range from meta-analysis to modelling, from participatory approaches to the development of bio-indicators, from genetic to biogeographical studies, from anthropological and ethnographic research to the use of network theory. We advocate a diversity of approaches, so as to foster the creation of robust and policy-relevant knowledge. Open challenges in the study of the role of seed exchange networks in biodiversity conservation include the development of methods to (i) enhance farmers’ participation to decision-making in agro-ecosystems, (ii) integrate ex situ and in situ approaches, (iii) achieve interdisciplinary research collaboration between social and natural scientists, and (iv) use network analysis as a conceptual framework to bridge boundaries among researchers, farmers and policy makers, as well as other stakeholders.

Si l’on considere qu’un patrimoine est constitue d’entites (materielles ou non) transmises entre generations de personnes pour signifier leur appartenance a un meme groupe social et affirmer la singularite de ce groupe, les varietes traditionnelles de plantes cultivees par les communautes paysannes constituent des modeles interessants a etudier. La « mise en patrimoine » des elements d’une culture releve avant tout de mecanismes sociaux et politiques qui sous-tendent les manieres qu’ont les groupes humains de se differencier les uns des autres. Toutefois, les objets vivants, et plus particulierement les plantes domestiquees (especes et varietes), presentent aussi des caracteristiques particulieres sur lesquelles il convient de reflechir.

The invasive Mediterranean fruit fly (medfly), Ceratitis capitata, is one of the major agricultural and economical pests globally. Understanding invasion risk and mitigation of medfly in agricultural landscapes requires knowledge of its population structure and dispersal patterns. Here, estimates of dispersal ability are provided in medfly from South Africa at three spatial scales using molecular approaches. Individuals were genotyped at 11 polymorphic microsatellite loci and a subset of individuals were also sequenced for the mitochondrial cytochrome oxidase subunit I gene. Our results show that South African medfly populations are generally characterized by high levels of genetic diversity and limited population differentiation at all spatial scales. This suggests high levels of gene flow among sampling locations. However, natural dispersal in C. capitata has been shown to rarely exceed 10 km. Therefore, documented levels of high gene flow in the present study, even between distant populations (> 1600 km), are likely the result of human-mediated dispersal or at least some form of long-distance jump dispersal. These findings may have broad applicability to other global fruit production areas and have significant implications for ongoing pest management practices, such as the sterile insect technique.

Le genre Digitaria Haller (Poaceae) constitue l’un des genres les plus diversifies des Poaceae du Senegal avec 19 especes. Bien qu’il y ait une monographie mondiale du genre, la determination des especes reste difficile et repose essentiellement sur les caracteres de l’appareil reproducteur. Ce travail, qui est une revision du genre Digitaria au Senegal, est entrepris afin de rechercher des caracteres pertinents sur l’appareil vegetatif et d’ameliorer l’identification des especes. Pour ce faire, une description detaillee des differents organes des specimens etudies est realisee a l’aide d’une loupe binoculaire. Les resultats de l’etude montrent que la pubescence de l’epillet est un caractere essentiel pour l’identification des especes. De plus, les longueurs relatives de la glume superieure et de la lemma inferieure sont tres interessantes pour la discrimination d’especes affines. Toutefois, l’etude supplementaire des organes vegetatifs de la plante adulte montre que certains caracteres vegetatifs pourraient contribuer considerablement a l’amelioration de l’identification des especes. Il s’agit du cycle biologique, de la pubescence de la ligule, de la marge du limbe, des noeuds et des entre-noeuds du chaume qui sont des caracteres plus faciles a observer. Une cle de determination basee sur des caracteres vegetatifs et reproducteurs des especes est ainsi elaboree. © 2015 International Formulae Group. All rights reserved. Mots cles: Digitaria , Poaceae, revision, cle de determination, Senegal English Title: Review of Digitaria Haller (Poaceae) genus in Senegal: suggestion of a determination key for a better identification of species English Abstract The genus Digitaria Haller (Poaceae) is one of the most diversified genera of Poaceae in Senegal with 19 species. Although it has a worldwide monograph of the genus, the identification of species remains difficult and mainly based on the characteristics of the reproductive system. This work, which is a review of the genus Digitaria in Senegal, is undertaken in order to search relevant characteristics on the vegetative system and to improve the identification of species. To do this, a detailed description of the various organs of the studied specimens is carried out using a binocular microscope. The results of the study show that the pubescence of the spikelet is an essential characteristic for the identification of species. Moreover, the relative lengths of the upper glume and lower lemma are very interesting for the discrimination of species closely related. However, the additional study of vegetative organs of the adult plant shows that some vegetative characteristics could contribute considerably to the improvement of the identification of species. It is the biological cycle, the pubescence of the ligule, the margin of the leaf blade, nodes and internodes of the thatch which are characteristics easier to observe. A key of determination based on vegetative and reproductive characteristics of species is thus worked out. © 2015 International Formulae Group. All rights reserved. Mots cles: Digitaria , Poaceae, review, key of determination, Senegal

International audience

Premise of the study: We developed nuclear microsatellite primers to explore the genetic diversity, population genetic structure, and evolutionary history of the fonio (Digitaria exilis), an understudied cereal cultivated in West Africa. o Methods and Results: We used a microsatellite-enriched library approach to isolate and characterize 38 nuclear primer pairs (31 di-, five tri-, and two tetranucleotide repeats), of which 21 were polymorphic and exhibited a clear pattern in 36 accessions from West Africa. The number of alleles per locus ranged from two to 22, with a mean of 4.71, and expected heterozygosity ranged from 0.03 to 0.93. o Conclusions: The developed set of 21 polymorphic SSR markers will provide tools for population and evolutionary genetics studies of the cultivated fonio. (Resume d'auteur)

Sorghum is the Duupa 'cultural supercrop' : it is a main subject of concern for the people and the backbone of the reproduction, on a material and a symbolic way, of the community. More than forty landraces are named and recognized, and widely exchanged between all cultivators in the community. Each year, every cultivator selects panicles from his own previous crop but often mix it with exchanged seeds. Fluxes of seeds follow the lines of kinship or affinal relations, but they can also come from commercial transactions outside the community. An outstanding feature of the Duupa seed system is the institution of free access to sorghum seeds during the collective threshing work parties. Anyone attending these parties can pick a few panicles for his own seeds on the bulk of the crop to be threshed. Strong moral values underline this safety net, which makes the diversity of landraces, seeds a common property. However, these institutionalized exchanged do not account for all the gene flux and people also rely on non-institutionalized, transfers sometimes including grains for current food use rather than properly selectionized panicles. All these transfers, public as well as private, even if difficult to quantify, should be taken into account for a proper understanding of the shaping of sorghum varietal and genetic diversity.

Selon la FAO, plus de 7 000 plantes sont cultivées ou collectées à l'état sauvage à travers le monde pour l'alimentation. Le blé, le riz et le maïs fournissent à eux seuls plus de 50 % de l'apport énergétique à base de plantes. Cet état de fait provient du potentiel agronomique de ces espèces mais aussi d'orientations fortes en matière de politique, de recherche et d'amélioration des plantes qui ont focalisé toutes les énergies sur des espèces qualifiées de " majeures ". Un grand nombre d'espèces ont été négligées. Or ces espèces présentent des caractéristiques intéressantes dans un contexte de croissance démographique et de changements environnementaux. Elles sont produites localement (bonne adaptation à leur zone de culture), elles contribuent à la sécurité alimentaire, sont facilement ou gratuitement accessibles aux populations, voire même peuvent produire de substantiels revenus, et enf n, ont une bonne résilience dans des zones marginales. C'est le cas du fonio, une céréale cultivée en Afrique de l'Ouest. L'atelier qui s'est tenu au Niger en décembre 2010, a dressé un état des lieux des connaissances scientifiques sur le sujet et des problématiques de recherche à développer pour mieux valoriser cette céréale.

Chloroplast DNA sequences are of great interest for population genetics and phylogenetic studies. However, only a small set of markers are commonly used. Most of them have been designed for amplification in a large range of Angiosperms and are located in the Large Single Copy (LSC). Here we developed a new set of 100 primer pairs optimized for amplification in Monocotyledons. Primer pairs amplify coding (exon) and non-coding regions (intron and intergenic spacer). They span the different chloroplast regions: 72 are located in the LSC, 13 in the Small Single Copy (SSC) and 15 in the Inverted Repeat region (IR). Amplification and sequencing were tested in 13 species of Monocotyledons: Dioscorea abyssinica, D. praehensilis, D. rotundata, D. dumetorum, D. bulbifera, Trichopus sempervirens (Dioscoreaceae), Phoenix canariensis, P. dactylifera, Astrocaryum scopatum, A. murumuru, Ceroxylon echinulatum (Arecaceae), Digitaria excilis and Pennisetum glaucum (Poaceae). The diversity found in Dioscorea, Digitaria and Pennisetum mainly corresponded to Single Nucleotide Polymorphism (SNP) while the diversity found in Arecaceae also comprises Variable Number Tandem Repeat (VNTR). We observed that the most variable loci (rps15-ycf1, rpl32-ccsA, ndhF-rpl32, ndhG-ndhI and ccsA) are located in the SSC. Through the analysis of the genetic structure of a wild-cultivated species complex in Dioscorea, we demonstrated that this new set of primers is of great interest for population genetics and we anticipate that it will also be useful for phylogeny and bar-coding studies.

Aujourd'hui, près d'un tiers de la population mondiale dépend des zones arides pour son alimentation. La compréhension des facteurs d'organisation de l'agrobiodiversité dans ces zones est un enjeu majeur pour la conservation et l'amélioration des systèmes agricoles. Parmi les facteurs d'organisation, les facteurs sociaux ont été peu étudiés. L'influence des facteurs sociaux sur l'organisation de l'agrobiodiversité a été abordée dans cette étude à travers l'exemple des Tharaka, une communauté d'agriculteurs qui exploitent les plaines semi-arides à l'Est du Mont Kenya. Les espèces et les variétés de sorgho cultivées par 95 agriculteurs ont été inventoriées. Les Tharaka présentent une organisation sociale en groupes de voisinages (ntora), en clans et en classes d'âge. L'effet de ces facteurs sociaux sur le nombre moyen d'espèces cultivées et de variétés de sorgho par foyer a été testé par une analyse de variance (ANOVA). La différenciation des portefeuilles variétaux et spécifiques entre groupes sociaux a ensuite été vérifiée par une analyse inter classes sur tableau de distance suivie d'un test de Monte-Carlo. L'appartenance des agriculteurs à des clans et à des classes d'âge n'est pas un facteur significatif d'organisation de la diversité. En revanche, les groupes de voisinage sont des facteurs d'organisation significatifs, tant au niveau intra qu'interspécifique. L'autoproduction des semences est généralisée sur la zone d'étude et les barrières sociales entre groupes de voisinage limitent les échanges de semences. Les variétés sont donc sélectionnées, reproduites et préférentiellement échangées à ce niveau. Ces travaux soulignent l'intérêt d'approfondir l'étude des facteurs sociaux d'organisation de l'agrobiodiversité, en décrivant le lien entre l'organisation sociale des communautés et les systèmes d'échanges de semences.

While over 7000 species are cultivated as agricultural or horticultural crops, food safety and nutrition worldwide are based on few crops. Wheat, rice and maize alone provide more than 50 % of plant energy. Agricultural research has mainly concentrated on these few "major" crops, neglecting the vast majority of cultivated species. Until now, despite the call for an increased use of underutilized crops to diversify alimentation and provide sustainable agriculture, those crops remain a largely untapped reservoir of agrobiodiversity. Are they really crops for the future? Fonio represents a promising crop. It is an indigenous staple cereal in Western Africa regarded as a valuable source of income, especially for small scale farmers. Fonio includes Digitaria exilis Stapf and D. iburua Stapf as well as wild related species (D. ternata and D. longiflora). Recent progresses in post-harvest technologies, which have long hampered the development of fonio cultivation, have increased its economic potential. The need to characterize its genetic resources and adaptive potential to the changing climate, and more generally fast evolving environmental pressures, is therefore more important. So far, fonio remains largely under-studied compared to other African cereals such as sorghum, millet and rice. Here, we discuss how the study, conservation and uses of fonio genetic resources can take advantage of methodological advances in other plant genetic research. Molecular resources can now be developed rapidly. Combined with innovative and multidisciplinary approaches, this will lead to an accurate estimation of fonio evolutionary history (including domestication), as well as an evaluation of the genetic resources and their dynamics. These approaches will allow a better understanding of on-farm diversity of fonio, the development of sound collecting and ex situ conservation strategies and appropriate crop improvement to ensure food security. This project benefits from the financial supports of Agropolis Resource Center for Crop Conservation, Adaptation and Diversity (www.arcad-project.org), Agropolis Fondation (www.agropolis-fondation.fr), IRD and Cirad (Action Incitative Stratégique 3-2010). (Texte intégral)

Crop species are characterised by their intimate association with human populations, their history and their practices and needs. In long domesticated crops, migration can have expanded gradually within continents and jumped between continents, shaping global patterns of diversity and adaptation. Sorghum (Sorghum bicolor bicolor) is one such case of very successful crop, which was domesticated in Subsahelian Africa and is now grown throughout the world. Here we review conclusions of recent studies conducted at various geographical scales (field, village, region, country, continent), sometimes including temporal variation, and practised at the level of morpho-agronomic traits, whole-genome molecular markers as well as selected candidate genes. Local diversity in the area of sorghum origin is almost as large as whole-species diversity, with peripheral regions displaying specific genotypic combinations corresponding to distinct races, but very limited specific genic diversity. This pattern of diversity is accompanied with a generally low level of linkage disequilibrium, which is confined to genome segments within the Mb range. A focus on certain genes involved in cereal grain quality revealed cases of novel alleles that appeared during the course of migration outside the centre of origin, being likely selected by the action of the farmers, highlighted the potential of neo-diversity for crop diversification. The diversity of human groups acts together with the agro-ecological factors to shape the structure of sorghum genetic diversity. As detailed in a village in Cameroon, introgression occurs among weedy types and cultivated types, yielding an array of intermediates; farmers identify and name them, and actively select against certain morphotypes, but several practices unconsciously favour gene flow. Based on a study covering 79 villages in Niger, no genetic erosion occurred over a 26 year period; farmers' management can preserve the diversity despite recurrent and severe drought periods and major social changes. The tremendous diversity maintained by farmers in traditional agroecosystems of Western Africa supports the development of crop improvement approaches making broad use of local germplasm in decentralized breeding programs.(Texte intégral)

Despite the major ecological and economic impacts of gene fl ow between domesticated plants and their wild relatives, many aspects of the process, particularly the relative roles of natural and human selection in facilitating or constraining gene fl ow, are still poorly understood. We developed a multidisciplinary approach, involving both biologists and social scientists, to investigate the dynamics of genetic diversity of a sorghum weed - crop complex in a village of Duupa farmers in northern Cameroon. Farmers distinguish a gradient from weedy morphotypes ( naa baa see , haariya , and genkiya ) to domesticated morphotypes; haariya and genkiya have intermediate morphological traits. We investigated the pattern of diversity in this complex using both morphological and genetic data. Our biological results are interpreted in the light of data on farmers ' taxonomy and practices such as spatial pattern of planting and plant selection. Both morphological and genetic data are congruent with farmers ' taxonomy and confi rm the introgressed status of intermediate weedy morphotypes. Farmers actively select against weedy morphotypes, but several practices unconsciously favor gene fl ow. Furthermore, haariya and genkiya may facilitate introgression between naa baa see and domesticated morphotypes by virtue of their intermediate fl owering period and their mode of management by farmers.

The effect of mating system on genetic diversity is a major theme in plant evolutionary genetics, because gene flow plays a large role in structuring the genetic variability within and among populations. Understanding crop mating systems and their consequences for gene flow can aid in managing agricultural systems and conserving genetic resources. We evaluated the extent of pollen flow, its links with farming practices and its impact on the dynamics of diversity of sorghum in fields of Duupa farmers in Cameroon. Duupa farmers grow numerous landraces mixed in a field, a practice that favours extensive pollen flow. We estimated parameters of the mating system of five landraces representative of the genetic diversity cultivated in the study site, using a direct method based on progeny array. The multilocus outcrossing rate calculated from all progenies was 18% and ranged from 0 to 73% among progenies. Outcrossing rates varied greatly among landraces, from 5 to 40%. Our results also showed that individual maternal plants were usually pollinated by more than eight pollen donors, except for one landrace (three pollen donors). Although the biological traits of sorghum (inflorescence morphology, floral traits, phenology) and the spatial planting practices of Duupa farmers led to extensive pollen flow among landraces, selection exerted by farmers appears to be a key parameter affecting the fate of new genetic combinations from outcrossing events. Because both natural and human-mediated factors shape evolution in crop populations, understanding evolutionary processes and designing in situ conservation measures requires that biologists and anthropologists work together.

Au Burkina Faso, au Mali, au Niger et a Wante, 1 518 echantillons de sorgho ont ete collectes et analyses a l’aide de marqueurs microsatellites. Les parametres de diversite et de differenciation genetique ont ete estimes a differentes echelles spatiales, depuis celle de la variete locale a celle du pays, pour determiner l’effet des principales forces evolutives sur la diversite genetique du sorgho. Il existe une diversite intra-varietale principalement determinee par la biologie de la reproduction du sorgho et par les derives genetiques engendrees par les effectifs limites d’individus lors de l’introduction d’une variete ou de la selection paysanne de la semence. A l’echelle d’un village, la correlation entre la diversite des noms vernaculaires et la diversite genetique mesuree par les marqueurs microsatellites est faible. Aucune structuration spatiale n’est observee dans des villages distants de plus de 30 kilometres soulignant le caractere tres local des systemes semenciers traditionnels. Au Mali et au Niger, une proportion equivalente et superieure, respectivement, de la diversite genetique du sorgho est observee sur un transect longitudinal qui recoupe essentiellement des divisions ethnolinguistiques, par rapport au transect latitudinal qui recoupe une variabilite agro-ecologique plus grande. La diversite des groupes humains explique donc, en interaction avec les conditions environnementales, la diversite genetique du sorgho in situ. Une grande partie de la diversite presente dans la core collection sorgho du Centre de cooperation internationale en recherche agronomique pour le developpement (Cirad) se retrouve a l’echelle de pays comme le Niger ou le Mali. L’importance de la diversite genetique cultivee par les paysans dans des systemes agricoles restes traditionnels souligne l’utilite des approches de conservation in situ des ressources genetiques. La conciliation des enjeux de conservation et d’amelioration varietale pourrait etre realisee par un recours plus important au germoplasme local dans des programmes de selection decentralises.

We present the first study of patterns of genetic diversity of sorghum landraces at the local scale. Understanding landrace diversity aids in deciphering evolutionary forces under domestication, and has applications in the conservation of genetic resources and their use in breeding programs. Duupa farmers in a village in Northern Cameroon distinguished 59 named sorghum taxa, representing 46 landraces. In each field, seeds are sown as a mixture of landraces (mean of 12 landraces per field), giving the potential for extensive gene flow. What level of genetic diversity underlies the great morphological diversity observed among landraces? Given the potential for gene flow, how well defined genetically is each landrace? To answer these questions, we recorded spatial patterns of planting and farmers' perceptions of landraces, and characterized 21 landraces using SSR markers. Analysis using distance and clustering methods grouped the 21 landraces studied into four clusters. These clusters correspond to functionally and ecologically distinct groups of landraces. Within-landrace genetic variation accounted for 30% of total variation. The average F(is) over landraces was 0.68, suggesting high inbreeding within landraces. Differentiation among landraces was substantial and significant (F(st) = 0.36). Historical factors, variation in breeding systems, and farmers' practices all affected patterns of genetic variation. Farmers' practices are key to the maintenance, despite gene flow, of landraces with different combinations of agronomically and ecologically pertinent traits. They must be taken into account in strategies of conservation and use of genetic resources.

Nous avons étudié la gestion et la dynamique de la diversité variétale du sorgho cultivé par les Duupa du nord Cameroun à l'échelle d'un village. Les agriculteurs Duupa maintiennent une quarantaine de variétés semées en mélange polyvariétal (11 variétés en moyenne par champ). Pour caractériser les semences, leur flux et l'impact sur la structuration de la diversité génétique, nous avons eu une approche interdisciplinaire reposant sur des outils disciplinaires empruntés à l'anthropologie, l'agronomie et la génétique des populations. Si les agriculteur duupa maintiennent une grande diversité variétale, ces variétés n'ont pas toutes le même statut et peuvent être classées en trois catégories suivant leur abondance en champs et leur fréquence dans le village. Chaque année les agriculteurs reconduisent la culture du sorgho via des semences sélectionnées sous forme de panicules ou bien des grains en vrac. En 2005, 56% des agriculteurs ont introduit de la semence venant d'une source extérieure à leur champ. Quel est le cadre social de ces flux et quel est la nature des flux (semence ou panicule). Le sorgho est au coeur de la société duupa. Ainsi, les Duupa échangent très régulièrement du sorgho sous forme de panicules ou de grains. Si le plus souvent ces échanges ont une vocation alimentaire, ils peuvent également rentrer dans la constitution des lots de semences. La plus grande partie des flux a lieu au moment du battage qui constitue pour les Duupa un moment clé du cycle agricole. C'est un moment particulièrement festif. Les Duupa parcourent de longues distances pour y participer. A cette occasion, chacun peut prélever des panicules pour sa semence. De même les femmes, qui assurent le vannage, reçoivent des petits cadeaux (grains). Les visites, les cérémonies constituent également des moments privilégiés de l'échange. D'autre part, la présence de variétés nommées par leur origine géographique extérieure au Duupa atteste également d'échange avec d'autres sociétés mais l'échelle de temps est dans ce cas plus importante. Seuls deux agriculteurs ont rapporté avoir acheté de la semence au marché. Une étude génétique de la structuration de la diversité génétique entre 5 villages duupa soulignent les résultats de nos enquêtes. La différentiation génétique est faible entre les villages duupa. En conclusion, la gestion de la diversité variétale est particulièrement dynamique et repose sur une dimension sociale importante. Ce dynamisme favorise le maintien des variétés, notamment les variétés rares et peu abondantes qui sont régulièrement perdues et réintroduites.

La variablite morphologique de 67 accessions de fonio [Digitaria exilis (Kippist.) Stapf.] collectees au Niger a ete evaluee au cours de deux annees (2011 et 2012). Seize (16) caracteres agro morphologiques (dont 14 caracteres quantitatifs et 2 caracteres qualitatifs) ont ete evalues en station dans deux zones agroecologiques differentes (Tarna en zone sahelo-saharienne et Tara en zone soudanienne). La classification acsendante hierarchique (CAH) et l’analyse factorielle discriminante (AFD) ont mis en evidence quatre groupes (GI, GII, GIII et GIV). Les accessions du groupe GIV ont en moyenne un cycle de maturite compris entre 85 et 90 jours tandis que les autres groupes presentent un cycle de maturite superieur a 90 jours dans nos conditions experimentales. Les resultats montrent que les variables les plus discriminantes qui permettent de decrire la variabilite entre les groupes identifies sont la biomasse seche (tige et feuille) par hectare, la longueur des entrenoeuds, le rendement en graine par hectare et dans une certaine mesure le cycle de la plante. L’observation des caracteres qualitatifs a montre que cinq accessions (representant 7% du total) ont des graines non decortiquees de couleur rouge et quatre accessions (6% du total), une tige de couleur rouge. Les caracteres analyses peuvent ainsi constituer des criteres de base pour differencier les accessions des autres regions de l’Afrique de l’Ouest et servir pour une etude de variabilite entre les restes des accessions de fonio collectees au Niger. Des possiblites d’amelioration peuvent egalement etre envisagees une fois que le regime de reproduction de l’espece est bien identifie. Mots cles : Digitaria exilis, variabilite morphologique, accessions, diversite, fonio, Niger.

International audience; We present here the first study of linkage disequilibrium (LD) in cultivated grapevine, Vitis vinifera L. subsp. vinifera (sativa), an outcrossing highly heterozygous perennial species. Our goal was to characterize the amount and pattern of LD at the scale of a few centiMorgans (cM) between 38 microsatellite loci located on five linkage groups, in order to assess its origin and potential applications. We used a core collection of 141 cultivars representing the diversity of the cultivated compartment. LD was evaluated with both independence tests and multilocus r2, both on raw genotypic and reconstructed haplotypic data. Significant genotypic LD was found only within linkage groups, extending up to 16.8 cM. It appeared not to be influenced by the weak structure of the sample and seemed to be mainly of haplotypic origin. Significant haplotypic LD was found over 30 cM. Both genotypic and haplotypic r2 values declined to around 0.1 within 5–10 cM, suggesting a rather narrow genetic base of the cultivated compartment and limited recombination since domestication events. These first results open up a few application opportunities for association mapping of QTLs and marker assisted selection

Sous gestion dynamique, où les agriculteurs produisent leurs propres semences à partir de leur récolte, les pratiques agricoles modifient les forces évolutives agissant sur les plantes domestiquées. Cependant, les connections entre pratiques et évolution restent une "boîte noire". Pour trois modèles, nous montrons comment les pratiques agricoles influencent les forces évolutives agissant sur les plantes et, dans un cas, sur un insecte phytophage associé. Les pratiques et savoirs sont à leur tour tributaires de la dynamique sociale des agriculteurs. L'élaboration des stratégies de gestion des ressources génétiques demande donc une approche intégrant la biologie évolutive et l'ethnobiologie.