Search

PremiseIn-solution based capture is becoming a method of choice for sequencing targeted sequence.Methods and resultsWe assessed and optimized a capture protocol in 20 different species from 6 different plant genus using kits from 20,000 to 200,000 baits targeting from 300 to 32,000 genes. We evaluated both the effectiveness of the capture protocol and the fold enrichment in targeted sequences. We proposed a protocol with multiplexing up to 96 samples in a single hybridization and showed it was an efficient and cost-effective strategy. We also extended the use of capture to pools of 100 samples and proved the efficiency of the method to assess allele frequency. Using a set of various organisms with different genome sizes, we demonstrated a correlation between the percentage of on-target reads vs. the relative size of the targeted sequences.ConclusionAltogether, we proposed methods, strategies, cost-efficient protocols and statistics to better evaluate and more effectively use hybridization capture.

Collaborative research practices in the field of plant genetic resources must follow the principles of fairness and equity as defined in the Convention on Biological Diversity (CBD) and in the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA). In this context the concepts of fairness and equity generally refer to the substantive and procedural dimensions associated with sharing the benefits of this research. But neither term is clearly defined by these international treaties, and the meanings attributed to the concepts vary among different societies. This paper looks at the question of how to account for the diversity among value systems when conducting research that implicates diverse stakeholders and respects the requirements of fairness and equity. We incorporated an auto-ethnography method developed as part of a multi-stakeholder network involved in research projects on plant genetic resources in West Africa. A theatrical device was used as a framework for testing the principles of fairness and equity, helping us to collectively identify feelings of injustice, and explore the conditions for making collaborative research practices more ethical in ways that respect the perspectives of different stakeholders. In an environment of extensive political and socio-cognitive inequality, this approach makes it possible to explain the criteria relating to interactional justice and expectations in terms of socio-political and socio-emotional benefits. It also invites us to consider the principles of fairness and equity in a framework of ethical competence that goes beyond international directives.

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.

Climate change is already affecting agro-ecosystems and threatening food security by reducing crop productivity and increasing harvest uncertainty. Mobilizing crop diversity could be an efficient way to mitigate its impact. We test this hypothesis in pearl millet, a nutritious staple cereal cultivated in arid and low-fertility soils in sub-Saharan Africa. We analyze the genomic diversity of 173 landraces collected in West Africa together with an extensive climate dataset composed of metrics of agronomic importance. Mapping the pearl millet genomic vulnerability at the 2050 horizon based on the current genomic-climate relationships, we identify the northern edge of the current areas of cultivation of both early and late flowering varieties as being the most vulnerable to climate change. We predict that the most vulnerable areas will benefit from using landraces that already grow in equivalent climate conditions today. However, such seed-exchange scenarios will require long distance and trans-frontier assisted migrations. Leveraging genetic diversity as a climate mitigation strategy in West Africa will thus require regional collaboration., Replacement of local crops with alternative varieties adapted to future conditions may improve food security under climate change. Here the authors apply landscape genomics and ensemble climate modelling to pearl millet in West Africa, supporting the potential of transfrontier assisted seed exchange.

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.

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; Sub-Saharan agriculture has been identified as vulnerable to ongoing climate change. Adaptation of agriculture has been suggested as a way to maintain productivity. Better knowledge of intra-specific diversity of varieties is prerequisites for the successful management of such adaptation. Among crops, root and tubers play important roles in food security and economic growth for the most vulnerable populations in Africa. Here, we focus on the sweet potato. The Sweet potato (Ipomoea batatas) was domesticated in Central and South America and was later introduced into Africa and is now cultivated throughout tropical Africa. We evaluated its diversity in West Africa by sampling a region extending from the coastal area of Togo to the northern Sahelian region of Senegal that represents a range of climatic conditions. Using 12 microsatellite markers, we evaluated 132 varieties along this gradient. Phenotypic data from field trials conducted in three seasons was also obtained. Genetic diversity in West Africa was found to be 18% lower than in America. Genetic diversity in West Africa is structured into five groups, with some groups found in very specific climatic areas, e.g. under a tropical humid climate, or under a Sahelian climate. We also observed genetic groups that occur in a wider range of climates. The genetic groups were also associated with morphological differentiation, mainly the shape of the leaves and the color of the stem or root. This particular structure of diversity along a climatic gradient with association to phenotypic variability can be used for conservation strategies. If such structure is proved to be associated with specific climatic adaptation, it will also allow developing strategies to adapt agriculture to ongoing climate variation in West Africa.

The human diet depends on very few crops. Current diversity in these crops is the result of a long interaction between farmers and cultivated plants, and their environment. Man largely shaped crop biodiversity from the domestication period 12,000 B.P. to the development of improved varieties during the last century. We illustrate this process through a detailed analysis of the domestication and early diffusion of maize. In smallholder agricultural systems, farmers still have a major impact on crop diversity today. We review several examples of the major impact of man on current diversity. Finally, biodiversity is considered to be an asset for adaptation to current environmental changes. We describe the evolution of pearl millet in West Africa, where average rainfall has decreased over the last forty years. Diversity in cultivated varieties has certainly helped this crop to adapt to climate variation.

Le système de diffusion des semences a un impact direct sur la structure génétique des populations de plantes domestiquées et sur son évolution. Ce système peut être caractérisé par ses acteurs, mais aussi par la nature, le sens et l'intensité des échanges. En décrivant les pratiques de sélection et la circulation des semences de sorgho dans la société duupa au Nord Cameroun, notre étude vise à comprendre la dynamique de la diversité génétique. Les agriculteurs duupa maintiennent une importante diversité variétale (40 variétés) qu'ils cultivent en mélange polyvariétal. Chaque année, ils sélectionnent des panicules pour reconduire leur culture, mais peuvent également utiliser des graines non sélectionnées. Les échanges de semences sont importants, et 56 % des agriculteurs se pourvoient auprès de leur famille ou de leurs voisins. Le battage est le moment privilégié des échanges de semences en panicules, mais les agriculteurs duupa introduisent également dans leurs semences des graines à vocation alimentaire échangées à l'occasion de visites et de cérémonies. Les liens sociaux qu'entretiennent les Duupa influencent directement la circulation des semences et sont au coeur de la dynamique de la diversité génétique.

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 agro-ecological 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.

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.

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.

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.

Underutilized crops do not benefit from the same research effort as major crops even if they are locally essential for food security. Knowledge and resources developed on major crops could be transferred to the lesser studied ones in order to analyze and exploit the genetic and agronomical potential of these crops. Fonio, so-called by farmers and consumers, includes Digitaria exilis Stapf. and D. iburua Stapf. as well as wild related species (D. ternata and D. longiflora) and Brachiaria or Panicum genera. It is an indigenous staple crop in western Africa regarded as a valuable source of income, especially for small scale farmers. Recent progress in post-harvest technologies, which has long hampered the development of fonio cultivation, has 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. We shall discuss how the study, conservation and uses of fonio genetic resources can take advantage of methodological advances in other plant genetic research. Several issues are addressed, which are not only related to biotechnologies but also to the combination of biological and social science approaches. The genetic structure of crop on-farm diversity results from the interplay between numerous factors, including historical, social, cultural, economic, biological and environmental factors. 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. (Resume d'auteur)