Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone : cumulative impact of ancient climatic changes and recent human activities

Background: Among Coffea species, C. canephora has the widest natural distribution area in tropical African forests. It represents a good model for analyzing the geographical distribution of diversity in relation to locations proposed as part of the "refuge theory". In this study, we used both microsatellite (simple sequence repeat, SSR) and restriction fragment length polymorphism (RFLP) markers to investigate the genetic variation pattern of C. canephora in the Guineo-Congolean distribution zone. Results: Both markers were first compared in terms of their informativeness and efficiency in a study of genetic diversity and relationships among wild C. canephora genotypes. As expected, SSR markers were found to have a higher genetic distance detection capacity than RFLP. Nevertheless, similarity matrices showed significant correlations when Mantel's test was carried out (r = 0.66, p < 0.0001). Finally, both markers were equally effective for group discrimination and phylogenetic studies, but SSR markers tended to outperform RFLP markers in discriminating the source of an individual among diversity groups and in putative hybrid detection. Five well defined genetic groups, one in the Upper Guinean forests, the four others in the Lower Guinean forests, were identified, corresponding to geographical patterning in the individuals. Conclusion: Our data suggested that the Dahomey Gap, a biogeographical barrier, played a role in wild C. canephora differentiation. Climatic variations during the Pleistocene and/or Holocene probably caused the subgroup differentiation in the Congolese zone through the presence of a mosaic of putative refugia. Recent hybridization between C. canephora diversity groups, both for spontaneous individuals and cultivars, was further characterised according to their geographic dissemination or breeding history as a consequence of human activities

Les ignames sauvages d'Afrique de l'Ouest. Caractéristiques morphologiques

En Afrique, le rôle des plantes dites mineures (non importantes dans l'économie mondiale) est fondamental car, en permettant une diversification des cultures, elles contribuent à assurer l'autosuffisance alimentaire. L'igname est une de ces plantes, traditionnellement exploitée en Afrique de l'Ouest pour ses multiples vertus. Le genre Dioscorea comporte, de par le monde, plusieurs centaines d'espèces d'ignames sauvages dont l'identification n'est pas toujours aisée en raison de descriptions incomplètes et des nombreuses synonymies. Or, à des degrés divers, les espèces sauvages ont joué et jouent un rôle fondamental dans l'évolution des formes cultivées. Leur identification est donc une nécessité en vue de leur préservation et de leur utilisation judicieuse. Ce manuel propose une reconnaissance des espèces in situ et, compte tenu de la grande diversité des ignames, amorce une réflexion sur la conservation et l'évaluation de leurs ressources génétiques

Large distribution and high sequence identity of a Copia&#8209;type retrotransposon in angiosperm families

International audienceRetrotransposons are the main component of plant genomes. Recent studies have revealed the complexity of their evolutionary dynamics. Here, we have identified Copia25 in Coffea canephora, a new plant retrotransposon belonging to the Ty1-Copia superfamily. In the Coffea genomes analyzed, Copia25 is present in relatively low copy numbers and transcribed. Similarity sequence searches and PCR analyses show that this retrotransposon with LTRs (Long Terminal Repeats) is widely distributed among the Rubiaceae family and that it is also present in other distantly related species belonging to Asterids, Rosids and monocots. A particular situation is the high sequence identity found between the Copia25 sequences of Musa, a monocot, and Ixora, a dicot species (Rubiaceae). Our results reveal the complexity of the evolutionary dynamics of the ancient element Copia25 in angiosperm, involving several processes including sequence conservation, rapid turnover, stochastic losses and horizontal transfer

Ancestral synteny shared between distantly-related plant species from the asterid (Coffea canephora and Solanum Sp.) and rosid (Vitis vinifera) clades

Background: Coffee trees (Rubiaceae) and tomato (Solanaceae) belong to the Asterid clade, while grapevine (Vitaceae) belongs to the Rosid clade. Coffee and tomato separated from grapevine 125 million years ago, while coffee and tomato diverged 83-89 million years ago. These long periods of divergent evolution should have permitted the genomes to reorganize significantly. So far, very few comparative mappings have been performed between very distantly related species belonging to different clades. We report the first multiple comparison between species from Asterid and Rosid clades, to examine both macro-and microsynteny relationships. Results: Thanks to a set of 867 COSII markers, macrosynteny was detected between coffee, tomato and grapevine. While coffee and tomato genomes share 318 orthologous markers and 27 conserved syntenic segments (CSSs), coffee and grapevine also share a similar number of syntenic markers and CSSs: 299 and 29 respectively. Despite large genome macrostructure reorganization, several large chromosome segments showed outstanding macrosynteny shedding new insights into chromosome evolution between Asterids and Rosids. We also analyzed a sequence of 174 kb containing the ovate gene, conserved in a syntenic block between coffee, tomato and grapevine that showed a high-level of microstructure conservation. A higher level of conservation was observed between coffee and grapevine, both woody and long life-cycle plants, than between coffee and tomato. Out of 16 coffee genes of this syntenic segment, 7 and 14 showed complete synteny between coffee and tomato or grapevine, respectively. Conclusions: These results show that significant conservation is found between distantly related species from the Asterid (Coffea canephora and Solanum sp.) and Rosid (Vitis vinifera) clades, at the genome macrostructure and microstructure levels. At the ovate locus, conservation did not decline in relation to increasing phylogenetic distance, suggesting that the time factor alone does not explain divergences. Our results are considerably useful for syntenic studies between supposedly remote species for the isolation of important genes for agronomy

Flowering phenology and yield-related traits in an interspecific cross between Coffea pseudozanguebariae Bridson and C. canephora Pierre

Higher caffeine content and cup beverage bitterness considerably depreciated the commercial value of Coffea canephora Pierre (CAN) compared with C. arabica L (ARA). Wild caffeine-free species like C. pseudozanguebariae Bridson (PSE) offer the opportunity to produce new CAN varieties containing little or no caffeine. F1 plants resulting from a PSE × CAN cross, and BC1 individuals, derived from the first backcross generation (PSE × CAN) × CAN) were produced. In order to assess flowering phenology and yield traits in F1 and BC1 hybrids, six morphological characters including flowering time, pollen viability (PV), fructification rate (FR), seed set (SSET), flower number per node (NFN) and 100-bean weight (W100) were studied under environmental conditions in Côte d&#8217;Ivoire. The results showed that F1 plants flowered only in February while, for BC1, 20% and 80% of the plants flowered in January and February, respectively

Site-Specific Insertion Polymorphism of the MITE Alex-1 in the Genus Coffea Suggests Interspecific Gene Flow

Miniature Inverted-repeat Transposable Elements (MITEs) are small nonautonomous class-II transposable elements distributed throughout eukaryotic genomes. We identified a novel family of MITEs (named Alex) in the Coffea canephora genome often associated with expressed sequences. The Alex-1 element is inserted in an intron of a gene at the CcEIN4 locus. Its mobility was demonstrated by sequencing the insertion site in C. canephora accessions and Coffea species. Analysis of the insertion polymorphism of Alex-1 at this locus in Coffea species and in C. canephora showed that there was no relationship between the geographical distribution of the species, their phylogenetic relationships, and insertion polymorphism. The intraspecific distribution of C. canephora revealed an original situation within the E diversity group. These results suggest possibly greater gene flow between species than previously thought. This MITE family will enable the study of the C. canephora genome evolution, phylogenetic relationships, and possible gene flows within the Coffea genus