Genetic structure of farmer-managed varieties in clonally-propagated crops.

The relative role of sexual reproduction and mutation in shaping the diversity of clonally propagated crops is largely unknown. We analyzed the genetic diversity of yam-a vegetatively-propagated crop-to gain insight into how these two factors shape its diversity in relation with farmers' classifications. Using 15 microsatellite loci, we analyzed 485 samples of 10 different yam varieties. We identified 33 different genotypes organized in lineages supported by high bootstrap values. We computed the probability that these genotypes appeared by sexual reproduction or mutation within and between each lineage. This allowed us to interpret each lineage as a product of sexual reproduction that has evolved by mutation. Moreover, we clearly noted a similarity between the genetic structure and farmers' classifications. Each variety could thus be interpreted as being the product of sexual reproduction having evolved by mutation. This highly structured diversity of farmer-managed varieties has consequences for the preservation of yam diversity.

Genetic diversity and population differentiation of traditional fonio millet (Digitaria spp.) landraces from different agro-ecological zones of West Africa.

Fonio millets (Digitaria exilis Stapf, D. iburua Stapf) are valuable indigenous staple food crops in West Africa. In order to investigate the genetic diversity and population differentiation in these millets, a total of 122 accessions from five countries (Benin, Burkina Faso, Guinea, Mali and Togo) were analysed by Amplified Fragment Length Polymorphisms (AFLPs). Genetic distance-based UPGMA clustering and principal coordinate analysis revealed a clear-cut differentiation between the two species and a clustering of D. exilis accessions in three major genetic groups fitting to their geographical origins. Shannon's diversity index detected in D. iburua was low (H = 0.02). In D. exilis, the most widespread cultivated species, moderate levels of genetic diversity (Shannon's diversity H = 0.267; Nei's gene diversity H' = 0.355) were detected. This genetic diversity is unequally distributed with the essential part observed in the Upper Niger River basin while a very low diversity is present in the Atacora mountain zone. Analysis of molecular variance (AMOVA) revealed that a large part of the genetic variation resides among the genetic groups (70%) and the country of origin (56%), indicating a clear genetic differentiation within D. exilis. Influence of mating system (inbreeding or apomixis), agricultural selection and ecological adaptations as well as founding effects in the genetic make-up of the landraces were visible and seemed to jointly contribute to the genetic structure detected in this species. The genetic variability found between the analysed accessions was weakly correlated with their phenotypic attributes. However, the genetic groups identified differed significantly in their mean performance for some agro-morphologic traits. The results obtained are relevant for fonio millets breeding, conservation and management of their genetic resources in West Africa.

Farmers' use of wild relative and sexual reproduction in a vegetatively propagated crop. The case of yam in Benin.

The impact of traditional farmers' management on genetic diversity of vegetatively propagated crops is poorly documented. In this study, we analysed the impact of ennoblement of spontaneous yams, an original traditional farmers' practice, on the genetic diversity of yam (Dioscorea sp.) in Benin. We used 11 microsatellite markers on yam tubers from a small village in northern Benin and demonstrated that wild x cultivated hybrids are spontaneously formed. Many of the spontaneous yams collected by farmers from surrounding savannah areas for ennoblement were shown to be of wild and hybrid genotypes. Moreover, we demonstrated that some yam varieties have a wild or hybrid signature. Lastly, we performed a broader ranging genetic analysis on yam material from throughout Benin and showed that this practice is used in different ecological and ethno-linguistic regions. Through this practice, farmers create new varieties with new genetic combinations via sexual reproduction of wild and cultivated yams. This system, whereby a sexual cycle and asexual propagation are mixed, ensures potential large-scale cultivation of the best genotypes while preserving the potential for future adaptation.

Use of cpSSRs for the characterisation of yam phylogeny in Benin.

The Dioscorea cayenensis - Dioscorea rotundata species complex is the most widely cultivated yam in West Africa. This species complex has been described as deriving from wild yams belonging to the Enanthiophyllum section through domestication by African farmers. To study patterns of yam evolution and to establish phylogenetic relationships existing between wild and cultivated species sampled in Benin, we investigated changes in chloroplast DNA simple sequence repeats (cpSSR) in 148 yam accessions selected to cover the wider possible genetic diversity existing in the country. Dioscorea cayenensis and D. rotundata share the same haplotype. The morphotype "abyssinica" appeared to be subdivided into 2 haplotypes. One of these haplotypes shares the same haplotype with the Dioscorea cayenensis - Dioscorea rotundata species complex and with morphotypes praehensilis, suggesting that they might belong to the same species. Relationships among sections Lasiophyton, Macrocapaea, Opsophyton, and Enanthiophyllum were clarified, and some taxonomic changes within the Enanthiophyllum section were suggested. Dioscorea minutiflora, D. smilacifolia, and D. burkilliana might be considered as 1 single genetic group, and they are suspected of belonging to the same species.

Amylase gene duplication: an ancestral trait in the Drosophila melanogaster species subgroup.

Electrophoretic polymorphism of amylases was studied in 45 geographic populations of the two cosmopolitan sibling species, D. melanogaster and D. simulans, and in one to three populations or strains of six other species in the D. melanogaster subgroup. Two species, D. erecta and D. orena, for which only a few strains were available were monomorphic. In the other species 2 or 3 amylase variants were identified while in D. melanogaster, 12 electrophoretic variants were characterized. Altogether 17 different amylase isozymes have been observed. The contrast in the level of polymorphism between D. melanogaster and the other species cannot be explained simply by the occurrence of a duplication in the former species. Genetic analysis demonstrated the existence of a duplication in at least 4 other species, namely D. simulans, D. mauritiana, D. yakuba, and D. teissieri. It is therefore suggested that the duplication occurred in a common ancestor and the phylogenetic implications of these observations are discussed.