Coffea rizetiana Stoff. & M.Noirot, sp. nov., a diploid species only known from a single wild population in South-West Cameroon, is formally described here. It is probably extinct in the wild, but is present in the germplasm collection in Bassin Martin (Reunion, France) and Meise Botanic Garden (Belgium). Phylogenetic analyses reveal a close relationship with C. montekupensis Stoff., a species endemic to the same region but occurring at higher elevations, and with C. liberica Bull. ex Hiern, a species with a wide Central and West African distribution. The new species can be distinguished from other Coffea species from Central Africa by its large black fleshy fruits with thick mesocarp. It can be differentiated from its close relative C. montekupensis by its larger less obovate leaves, longer corolla tube and larger fruits; and from C. liberica by its shorter petiole, acuminate leaf tip, cuneate leaf base, thinner leaf blade, shorter corolla tube, longer corolla lobes and black fruits with a thick fleshy pericarp. The evolutionary importance of the fruit colour is discussed, as well as the role of Mount Kupe, the Bakossi Mountains and the broader South-West Cameroon region as the principal Coffea diversity hotspot on the African continent.

Introduction The concept of a 'core collection' was proposed to enable efficient and cost-effective management and utilization of crop genetic resources (FrankeI1984; Frankel and Brown 1984) and has been interpreted in various ways (van Hintum et al. 2000). Frankel (1984) defined a core collection as a limited set of accessions representing, with a minimum of repetitiveness, the genetic diversity of crop species and its wild relatives. For practical uses, the core collections allow setting up a large representation of the genetic diversity within a reduced set of genotypes, which can be intensively evaluated and widely distributed. However an IPGRl survey of 1346 genebanks and institutions worldwide pointed out considerable confusion and lack of knowledge on what a core collection is (Brown and Spillane 1999). For all intent and purposes, core collections were never intended for conservation purposes, but rather to facilitate use of conserved material. If core collections are to have a meaningful impact On management of germplasm collections, there is a need for greater consensus and knowledge among the curators and users on what is and is not a core collection. The experience reported here is based on the construction and management of C. arabica core collections in CATIE, firstly for evaluation (Anthony et al. 2001), then for long-term conservation (Vasquez et al. 2005).

One hundred and forty six cuttings representing duplicates of 73 wild accessions from 16 coffee species were evaluated for resistance to Meloidogyne incognita race 1. Five species were subdivided on the basis of geographical origin because morphological differences were previously observed. Two well-characterized susceptible and resistant cultivars were used as comparative controls. The experiments were conducted in a greenhouse using a clonal population of M. incognita from Brazil. The reproduction factor (RF) was used to evaluate the resistance (RF<1) or susceptibility (RF>1) to the nematode infection. Plants of both controls were discriminated on the basis of RF values. Both duplicate cuttings of the wild accessions were identically classified as resistant or susceptible. Eight species displayed a resistant reaction, one species was considered to be susceptible, and seven species presented both susceptible and resistant accessions. Resistance to M. incognita appeared to be a more frequent character than susceptibility within the gene pool of wild coffee. These results provide coffee breeders with material whose resistance can be transferred into commercial cultivars.

The former Coffea subgenus is a species complex showing qualitative gene flow and reproductive barriers between species. Such qualitative gene flow allowed its evolution over time, particularly during the successive forest expansion-regression cycles in relation with glaciation periods.

Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora , which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N -methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.

The diversity of root knot nematodes parasitizing coffee orchards in Central America was newly assessed through a broad regional survey. Populations of Meloidogyne spp. were identified by their esterase phenotype. Eleven esterase phenotypes were observed and nine species identified. Meloidogyne exigua was the most widely distributed while M. arabicida, M. arenaria, M. hapla, M. izalcoensis and M. paranaensis appeared to be much more localized. Concerning M. paranaensis, only observed in Guatemala, the two-band esterase phenotypes prevailed. About M. arenaria, the one-band esterase phenotype (A1) was observed for the first time on coffee in one population in Guatemala. A three-band esterase phenotype (A3) was observed in two populations in El Salvador and could belong to M. morocciensis. The presence of M. enterolobii on coffee in Central America was confirmed with one population from Guatemala and another one from Costa Rica as a new report. Based on esterase diagnosis identifications of M. incognita were made for the first time on coffee in the region: in Costa Rica, El Salvador and Guatemala. Taken together, the results of the survey revealed a high number of root knot nematode species present on coffee throughout Central America.

Coffee is one of the world’s most important agricultural commodities. Coffee belongs to the Rubiaceae family in the euasterid I clade of dicotyledonous plants, to which the Solanaceae family also belongs. Two bacterial artificial chromosome (BAC) libraries of a homozygous doubled haploid plant of Coffea canephora were constructed using two enzymes, HindIII and BstYI. A total of 134,827 high quality BAC-end sequences (BESs) were generated from the 73,728 clones of the two libraries, and 131,412 BESs were conserved for further analysis after elimination of chloroplast and mitochondrial sequences. This corresponded to almost 13 % of the estimated size of the C. canephora genome. 6.7 % of BESs contained simple sequence repeats, the most abundant (47.8 %) being mononucleotide motifs. These sequences allow the development of numerous useful marker sites. Potential transposable elements (TEs) represented 11.9 % of the full length BESs. A difference was observed between the BstYI and HindIII libraries (14.9 vs. 8.8 %). Analysis of BESs against known coding sequences of TEs indicated that 11.9 % of the genome corresponded to known repeat sequences, like for other flowering plants. The number of genes in the coffee genome was estimated at 41,973 which is probably overestimated. Comparative genome mapping revealed that microsynteny was higher between coffee and grapevine than between coffee and tomato or Arabidopsis. BESs constitute valuable resources for the first genome wide survey of coffee and provide new insights into the composition and evolution of the coffee genome.

Self-incompatibility (SI) is widespread in the angiosperms, but identifying the biochemical components of SI mechanisms has proven to be difficult in most lineages. Coffea (coffee; Rubiaceae) is a genus of old-world tropical understory trees in which the vast majority of diploid species utilize a mechanism of gametophytic self-incompatibility (GSI). The S-RNase GSI system was one of the first SI mechanisms to be biochemically characterized, and likely represents the ancestral Eudicot condition as evidenced by its functional characterization in both asterid (Solanaceae, Plantaginaceae) and rosid (Rosaceae) lineages. The S-RNase GSI mechanism employs the activity of class III RNase T2 proteins to terminate the growth of "self" pollen tubes. Here, we investigate the mechanism of Coffea GSI and specifically examine the potential for homology to S-RNase GSI by sequencing class III RNase T2 genes in populations of 14 African and Madagascan Coffea species and the closely related self-compatible species Psilanthus ebracteolatus. Phylogenetic analyses of these sequences aligned to a diverse sample of plant RNase T2 genes show that the Coffea genome contains at least three class III RNase T2 genes. Patterns of tissue-specific gene expression identify one of these RNase T2 genes as the putative Coffea S-RNase gene. We show that populations of SI Coffea are remarkably polymorphic for putative S-RNase alleles, and exhibit a persistent pattern of trans-specific polymorphism characteristic of all S-RNase genes previously isolated from GSI Eudicot lineages. We thus conclude that Coffea GSI is most likely homologous to the classic Eudicot S-RNase system, which was retained since the divergence of the Rubiaceae lineage from an ancient SI Eudicot ancestor, nearly 90 million years ago.