Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites [plus supplementary data]

2013

Article référencé dans le Web of Science WOS:000314057400007

Razafinarivo Norosoa, Guyot Romain, Davis A.P., Couturon Emmanuel, Hamon Serge, Crouzillat D., Rigoreau M., Dubreuil Tranchant Christine, Poncet Valérie, Kochko Alexandre de, Rakotomalala J. J., Hamon Perla

Annals of Botany, 2013, 111 (2), p. 229-248 [+ supplementary data : 5 p.] ISSN 0305-7364

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. 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. 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. 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.

Sciences fondamentales / Techniques d'analyse et de recherche [020] ; Sciences du monde végétal [076] ; Etudes, transformation, conservation du milieu naturel [082]

AFRIQUE ; OCEAN INDIEN ; MADAGASCAR ; MASCAREIGNES

Fonds IRD [F B010058979]

fdi:010058979