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Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments., Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.

The genus Digitaria Haller is one of the most important of grass flora of Senegal by both its specific richness and the socio-economic value of its species. Despite this importance, no studies have been done specifically on these species. This study aims, therefore, to document the diversity, distribution, ecology and usefulness of the genus of such species for raising public awareness about botanical, ecological distribution, and status of such species and their uses in Senegal. Data collection approach was based on field work conducted in Senegal that has allowed the preparation of distribution maps of species related to ecological factors such as climate, vegetation and soil coupled with a literature review used to determine the use of species. Consequently, literature accessed has revealed that various species of Digitaria exist and they consist mainly of weeds, forage or food crops. Digitaria spp. has a wider distribution with some species having a broader distribution whereas others are restricted to some African regions. They are generally encountered throughout the tropics including in rainforests, savannas and steppes; wherein soils are sandy and acidic types. In Senegal, most of the species are found in the south under a Sudano-Sahelian zone, growing on almost all vegetation and soil types. This study, which is a contribution to the improvement and preservation of the living environment of these species, is an important step for the facilitation of any conservation action. It also encourages a greater appreciation of the value of these species, which are potential sources of genes from Digitaria exilis, the cultivated species. Key words: Digitaria, climatic zones, vegetation types, soil types, conservation, Senegal.

International audience; Fonio is an ancient orphan cereal, cultivated by resource-poor farmers in arid and semi-arid regions of West Africa, who conserved and used the cereal for nutrition and income generation. However, the extent and patterns of phenotypic variation within the fonio germplasm remain scarcely evaluated to inform breeding decisions. In this study, we used alpha lattice design to assess the phenotypic variability of 180 fonio accessions using 20 agro morphological descriptors, including both qualitative and quantitative traits at Bengou research station in 2018 and 2019. Descriptive statistics, combined analysis and multivariate analyses, including principal components analysis (PCA), hierarchical clustering, and multiple factor analysis (MFA) were performed. As results, we found significant differences among fonio accessions and among agro ecological zones of provenance for most of the quantitative traits. Furthermore, highly significant positive correlations were found between grain yield and other yield-related attributes such as harvest index and thousand seeds weight, whereas significant negative correlations were found between grain yield and flowering and maturity times. Clusters analysis revealed three phenotypic groups. Group 1 was characterized by early maturing fonio accessions with higher grain yield. Groups 2 and 3 were characterized by late maturing accessions with intermediate to moderate grain yield. The accessions from Group 1 are candidate for yield improvement and development of fonio lines with enhanced lodging resistance. Accessions from Group 2 and 3 can be improved for yield through marker-assisted selection of best thousand seed weight. This study highlights how traits are correlated within the major phenotypic groups of fonio in West Africa, and we discussed how these groups could be further exploited for improving traits of economic importance. Furthermore, this study exhibited agro morphological descriptors that discriminate fonio accessions and provide useful information for parental selection with economically important agronomic traits.

International audience; Ethnicity Differences in Use Values and Management Practices of Bitter Kola (Garcinia kola) in Cameroon. Bitter kola (Garcinia kola) is an indigenous multipurpose tree species in West and Central Africa, threatened by overexploitation and classified by the IUCN as vulnerable. Understanding local knowledge and management patterns in different socioecological contexts could contribute to designing strategies for conservation and long-term use of the species. In order to characterize the parts of the plant and the harvesting techniques that are used by different ethnic groups in Cameroon, we conducted surveys through the use of semi-structured questionnaires (N = 182) in six different sites covering different agro-ecological zones where the species is present (forest and savanna). Ethnic groups from the savanna agro-ecological zone shared similar patterns in G. kola organs/parts used and harvesting techniques, but these patterns differed among ethnic groups from the savanna and forest zones and within the forest zone. Ethnic groups from the savanna zone mainly harvest the species for its seeds that are used as stimulants. Conversely ethnic groups from the forest zone mainly collect bark and roots, and uses differ between agriculturalists (Fang and Bassa) and hunter-gatherers (Baka). These patterns have direct consequences on species management practices. Savanna farmers applied sustainable harvesting as they extract fruits and seeds and planting more trees in order to increase the species’ contribution to their livelihood. People in the forest zone destructively felled standing trees, threatening the species in its natural environment. The influence of these results on the conservation status of the species in the region are discussed.

Digitaria exilis is an important indigenous cereal in West Africa. The first fonio reference transcriptome was released and became a key tool for developing new molecular markers contributing to a better understanding of its genetic diversity. A total of 126 new putative primer pairs were successfully designed in 37,327 unigenes from the D. exilis transcriptome. Thirty-seven primer pairs were randomly selected and tested for their ability to cross-amplify to related species. Clear amplification patterns were observed on 24 primer pairs. Of these, 71, 74 and 35% showed polymorphism in three species: D. exilis, D. longiflora and D. iburua. The transferability from D. exilis was 96% to D. longiflora and 71% to D. iburua. The new SSR markers confirmed the close genetic proximity of D. exilis with D. longiflora and its stronger genetic difference of D. exilis from D. iburua. These markers will be valuable for completing future knowledge on Digitaria evolutionary history, and for testing gene flows between related species.

Global environmental changes strongly impact wild and domesticated species biology and their associated ecosystem services. For crops, global warming has led to significant changes in terms of phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong need for harnessing the genetic variability of crops and adapting them to new conditions. Gene flow, from either the same species or a different species, may be an immediate primary source to widen genetic diversity and adaptions to various environments. When the incorporation of a foreign variant leads to an increase of the fitness of the recipient pool, it is referred to as “adaptive introgression”. Crop species are excellent case studies of this phenomenon since their genetic variability has been considerably reduced over space and time but most of them continue exchanging genetic material with their wild relatives. In this paper, we review studies of adaptive introgression, presenting methodological approaches and challenges to detecting it. We pay particular attention to the potential of this evolutionary mechanism for the adaptation of crops. Furthermore, we discuss the importance of farmers’ knowledge and practices in shaping wild-to-crop gene flow. Finally, we argue that screening the wild introgression already existing in the cultivated gene pool may be an effective strategy for uncovering wild diversity relevant for crop adaptation to current environmental changes and for informing new breeding directions.

International audience; Phenotypic changes in plants can be observed along many environmental gradients and are determined by both environmental and genetic factors. The identification of alleles associated with phenotypic variations is a rapidly developing area of research.We studied the genetic basis of phenotypic variations in 11 populations of wild pearl millet (Pennisetum glaucum) on two NorthSouth aridity gradients, one in Niger and one in Mali. Most of the 11 phenotypic traits assessed in a common garden experimentvaried between the populations studied. Moreover, the size of the inflorescence, the number of flowers and aboveground dry mass co-varied positively with a decrease in rainfall. To decipher the genetic basis of these phenotypes, we used an associationmapping strategy with a mixed model. We found two SNPs on the same myosin XI contig significantly associated with variations in the average number of flowers. Both the allele frequency of the two SNPs and the average number of flowers co-varied withthe rainfall gradient on the two gradients. Interestingly, this gene was also a target of selection during domestication. The Myosin XI gene is thus a good candidate for fitness-related adaptation in wild populations.

We produced a unique large data set of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose, we validated a RNA-Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared the quality of de novo Illumina short-read assemblies using data from two crops for which an annotated reference genome was available, namely grapevine and sorghum. We used the same protocol for the release of 26 new transcriptomes of crop plants and wild relatives, including still understudied crops such as yam, pearl millet and fonio. The species list has a wide taxonomic representation with the inclusion of 15 monocots and 11 eudicots. All contigs were annotated using BLAST, prot4EST and Blast2GO. A strong originality of the data set is that each crop is associated with close relative species, which will permit whole-genome comparative evolutionary studies between crops and their wild-related species. This large resource will thus serve research communities working on both crops and model organisms. All the data are available at http://arcad-bioinformatics.southgreen.fr/.

International audience; Pearl millet (Pennisetum glaucum (L.) R. Br.) is a staple food and a drought-tolerant cereal well adapted to Sub-Saharan Africa agro-ecosystems. An important diversity of pearl millet landraces has been widely conserved by farmers and therefore could help copping with climate changes and contribute to future food security. Hence, characterizing its genetic diversity and population structure can contribute to better assist breeding programs for a sustainable agricultural productivity enhancement. Toward this goal, a comprehensive panel of 404 accessions were used that correspond to 12 improved varieties, 306 early flowering and 86 late-flowering cultivated landraces from Senegal. Twelve highly polymorphic SSR markers were used to study diversity and population structure. Two genes, PgMADS11 and PgPHYC, were genotyped to assess their association to flowering phenotypic difference in landraces. Results indicate a large diversity and untapped potential of Senegalese pearl millet germplasm as well as a genetic differentiation between early-and late-flowering landraces. Further, a fine-scale genetic difference of PgPHYC and PgMADS11 (SNP and indel, respectively) and co-variation of their alleles with flowering time were found among landraces. These findings highlight new genetic insights of pearl millet useful to define heterotic populations for breeding, genomic association panel, or crosses for trait-specific mapping.

International audience; In a context of the global major changes, it is mandatory to enlarge the range of crops supporting food security and pay great attention to neglected and underutilized species. However, basic knowledge of the biology of many neglected and underutilized species is still lacking to increase their yields. In this study, the mating system of white fonio [Digitaria exilis (Kippist.) Stapf], a West African minor and promising cereal, is assessed. Progenies arrays from both homozygous and heterozygous mothers were genotyped with microsatellites markers. The rate of genotyping errors in the experiments was assessed and a likelihood framework was used to determine the probability of different mating systems: outcrossing, self-fertilization and apomixis. The results suggested that white fonio has a highly selfing reproductive system with a possible outcrossing rate of 1.7%. Understanding the reproduction system of white fonio opens up opportunities for more effective breeding programs and a wider use of this cereal for food security improvement.

Objectives: Digitaria exilis Stapf (white fonio) is a staple crop in West Africa, mainly consumed during food shortage and highly associated to cultural events. The aim of this study was to test the transferability of microsatellite loci developed for D. exilis to other species of the genus Digitaria in order to further investigate the diversity of species for which there is little genomic resources available. Methodology and Results : Eight (8) microsatellite loci on 119 accessions from 39 Digitaria species were tested. With an average amplification percentage of 62.8% ranging from 25% to 100 %, these SSR markers are transferable to other species of the genus Digitaria. The transferability was higher for D. argyrothrica, D. fuscescens, D. longiflora, D. milanjiana and D. ternata. In some species such as D. abyssinica, D. nuda, D. pennata, D. pseudodiagonalis and D. tisserantii, the very low percentage of cross-amplification confirmed their distance from D. exilis. D. longiflora , thought as the most related wild species to D. exilis , exhibited 100% level of transferable polymorphic loci. Conclusion and application of findings : This set of markers will be useful for breeding and studying relationships between Digitaria species. Keywords : Cross-species amplification, Digitaria, genetic diversity, microsatellite loci.

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.

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.

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

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)

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.

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.

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.

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