title: Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites.
abstract: OBJECTIVE
  The coffee genus (Coffea) comprises 124 species, and is indigenous to the Old World Tropics. Due to its immense economic importance, Coffea has been the focus of numerous genetic diversity studies, but despite this effort it remains insufficiently studied. In this study the genetic diversity and genetic structure of Coffea across Africa and the Indian Ocean islands is investigated.
  
  
  METHODS
  Genetic data were produced using 13 polymorphic nuclear microsatellite markers (simple sequence repeats, SSRs), including seven expressed sequence tag-SSRs, and the data were analysed using model- and non-model-based methods. The study includes a total of 728 individuals from 60 species.
  
  
  RESULTS
  Across Africa and the Indian Ocean islands Coffea comprises a closely related group of species with an overall pattern of genotypes running from west to east. Genetic structure was identified in accordance with pre-determined geographical regions and phylogenetic groups. There is a good relationship between morpho-taxonomic species delimitations and genetic units. Genetic diversity in African and Indian Ocean Coffea is high in terms of number of alleles detected, and Madagascar appears to represent a place of significant diversification in terms of allelic richness and species diversity.
  
  
  CONCLUSIONS
  Cross-species SSR transferability in African and Indian Ocean islands Coffea was very efficient. On the basis of the number of private alleles, diversification in East Africa and the Indian Ocean islands appears to be more recent than in West and West-Central Africa, although this general trend is complicated in Africa by the position of species belonging to lineages connecting the main geographical regions. The general pattern of phylogeography is not in agreement with an overall east to west (Mascarene, Madagascar, East Africa, West Africa) increase in genome size, the high proportion of shared alleles between the four regions or the high numbers of exclusive shared alleles between pairs or triplets of regions.
authors.affiliation: UMR DIADE, IRD, BP, Montpellier cedex, France. nororaza@yahoo.fr
authors.forename: Norosoa J
authors.initials: NJ
authors.lastname: Razafinarivo
authors.forename: Romain
authors.initials: R
authors.lastname: Guyot
authors.forename: Aaron P
authors.initials: AP
authors.lastname: Davis
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Couturon
authors.forename: Serge
authors.initials: S
authors.lastname: Hamon
authors.forename: Dominique
authors.initials: D
authors.lastname: Crouzillat
authors.forename: Michel
authors.initials: M
authors.lastname: Rigoreau
authors.forename: Christine
authors.initials: C
authors.lastname: Dubreuil-Tranchant
authors.forename: Valerie
authors.initials: V
authors.lastname: Poncet
authors.forename: Alexandre
authors.initials: A
authors.lastname: De Kochko
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Rakotomalala
authors.forename: Perla
authors.initials: P
authors.lastname: Hamon
mesh_terms: D000349:Africa; D000483:Alleles; D040503:Coffea / Q000235:genetics*; D040342:Genetic Structures; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D005843:Geography; D007195:Indian Ocean Islands; D018895:Microsatellite Repeats / Q000235:genetics*; D010802:Phylogeny