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Background and Aims The production of triploid banana and plantain (Musa spp.) cultivars with improved characteristics (e.g. greater disease resistance or higher yield), while still preserving the main features of current popular cultivars (e.g. taste and cooking quality), remains a major challenge for Musa breeders. In this regard, breeders require a sound knowledge of the lineage of the current sterile triploid cultivars, to select diploid parents that are able to transmit desirable traits, together with a breeding strategy ensuring final triploidization and sterility. Highly polymorphic single sequence repeats (SSRs) are valuable markers for investigating phylogenetic relationships. Methods Here, the allelic distribution of each of 22 SSR loci across 561 Musa accessions is analysed. Key Results and ConclusionsWe determine the closest diploid progenitors of the triploid 'Cavendish' and 'Gros Michel' subgroups, valuable information for breeding programmes. Nevertheless, in establishing the likely monoclonal origin of the main edible triploid banana subgroups (i.e. 'Cavendish', 'Plantain' and 'Mutika- Lujugira'), we postulated that the huge phenotypic diversity observed within these subgroups did not result from gamete recombination, but rather from epigenetic regulations. This emphasizes the need to investigate the regulatory mechanisms of genome expression on a unique model in the plant kingdom. We also propose experimental standards to compare additional and independent genotyping data for reference. (Resume d'auteur)

Knowledge of genebank and on-farm genetic diversity, particularly in an introduced crop species, is crucial to the management and utilization of the genetic resources available. Microsatellite markers were used to determine genetic diversity in 574 accessions of cacao, Theobroma cacao L., representing eight groups covering parental populations in West Africa, genebank, and farmers’ populations in Nigeria. From the 12 microsatellite markers used, a total of 144 alleles were detected with a mean allelic richness of 4.39 alleles/locus. The largest genetic diversity was found in the Upper Amazon parent population (Hnb = 0.730), followed by the 1944 Posnette’s Introduction (Hnb = 0.704), and was lowest in the Local parent population (Hnb = 0.471). Gene diversity was appreciably high in the farmers’ populations (Hnb = 0.563–0.624); however, the effective number of alleles was lower than that found in the genebank’s Posnette’s population. Fixation index estimates indicated deficiency of heterozygotes in the Upper Amazon and the Local parent populations (Fis = 0.209 and 0.160, respectively), and excess of heterozygotes in the Trinitario parent population (Fis = −0.341). The presence of inbreeding in the Local parent populations and substructure (Wahlund effect) in the Upper Amazon were suggested for the deficiency of heterozygotes observed. Non-significant genetic differentiation observed between the genebank’s and farmers’ populations indicated significant impact of national breeding programs on varieties grown in farmers’ plantations. From this study, we showed that appreciable genetic diversity was present in on-farm and field genebank collections of cacao that can be exploited for crop improvement in West Africa. Suggestions for future conservation of on-farm genetic diversity and local landraces are further discussed.

Theobroma cacao L. with its center of diversity in Central and South America was first introduced to West Africa in the mid-19th century and today the region produces 70% of the world's cocoa. Several distinct cocoa types have been introduced, cultivated, and intercrossed across the region. Also, bi-parental crosses involving selections from various introductions have been planted on a large scale. Consequently, a wide range of genetic diversity that could be exploited for crop improvement is expected. The present study has been, therefore, undertaken to assess the degree and distribution of genetic diversity present in cocoa germplasm collections from the Cocoa Research Institute (CRIG), seed gardens and materials from farmers' plantations in Ghana, using molecular markers. Two hundred and thirty-five trees representing all the cocoa-growing regions of Ghana were sampled in situ from farmers' fields and grouped as farmers' collection. Another set of 104 trees was collected from breeders' seed ga...

As part of a participatory selection programme, promising individual trees were selected in 2004 in cocoa farms of southern and western Cameroon regions for yield and for low incidence of Phytophthora pod rot (Ppr) caused by Phytophthora megakarya. The aim of this study was to compare the levels of resistance to Ppr between farm accessions (FA), introduced and local genebank accessions (GA). In total, 234 FA were grafted in the nursery together with 22 introduced GA and 73 local GA, and tested for resistance to P. megakarya by leaf disc inoculations. The introduced GA, that were reported as resistant to Ppr in other countries, proved to be more resistant than the selected FA and unselected FA and also more resistant than the 3 control clones for Ppr resistance used in the study. However, approximately 10% of the FA were as resistant as the average of the introduced GA, showing the potential of selection for resistance to Ppr in farmers’ fields. The average level of resistance of the FA was relatively higher than that of the local GA. The FA selected for yield and low Ppr incidence in the field were more resistant in the leaf disc test than the unselected FA. The use of FA and of farmers’ knowledge in the participatory selection process is valuable in obtaining Ppr-resistant cultivars.

Inadequate knowledge of the population structure and diversity present often hamper the efficient use of germplasm collections. Using a high through-put system, twelve microsatellite loci were used to analyze genetic diversity and population structure in a national field genebank repository of 243 cacao accessions grouped into 11 populations based on their known sources. Based on multi-locus profiles, the Bayesian method was used for individual assignment to verify membership in each population, determine mislabeling and ancestry of some important accessions used in breeding program. A total of 218 alleles was revealed with a mean number of 18.2 alleles per locus. Gene diversity (He= 0.70) and allelic richness (4.34 alleles per locus) were highest in the F1 hybrid population. Differential mating system was suggested as responsible for the observed deficit and excess of heterozygotes observed among the populations. Analysis of molecular variance showed that within-population variance accounted for 63.0% of the total variance while the rest 37% was accounted for by the among-population variance. Cluster dendrogram based on UPGMA revealed two main subsets. The first group was made up of the Amelonado/Trinitario ancestry and the other of Nanay/Parinari ancestry. We found that Nanay and Parinari populations were the major source of Upper Amazon genes utilized while a large proportion of genetic diversity in the field genebank remained under-utilized in development of improved cultivars released to farmers in Nigeria. This study showed that the presence of alleles of the Upper Amazon Forasteros (Nanay, Parinari and Iquitos Mixed Calabacillo) genetic materials in the locally available accessions predated the formal large scale introduction of Upper Amazon materials in 1944. This is the first report of population structure of field genebank collections of cacao in Nigeria since more than seven decades of formal cacao breeding research.

In Cote dIvoire, the cocoa breeding programme has been based on the creation of hybrids between different genetic groups. From 1990 onward, a reciprocal recurrent selection programme has been set up with the purpose of improving simultaneously the characteristics of the two main genetic groups: Upper Amazon Forastero (UA) and a mixture of Lower Amazon Forastero (LA) and Trinitario (T). Based on data obtained from 12 microsatellite primers, the genetic diversity and genetic distances of the parental populations used in the first and second selection cycles are presented. The results revealed that the diversity of populations UA0 and UA1 on the one hand and (LA+T)0 and (LA+T)1 on the other is similar. The genetic distances were small between the parental populations used for the first and second cycles. Genetic diversity was greater in the UA group than in the LA+T group. The number of rare and of private alleles was reduced for both genetic groups, as well as the number of the frequent alleles in the LA+T group.

International audience; The genetic diversity of 400 accessions collected in cacao farms, 95 GenBank, and 31 reference accessions was analyzed using the 12 microsatellite markers. The GenBank and reference accessions were subdivided into 12 accession groups (AG) that belong to the traditional cacao genetic groups (GG) Lower Amazon Forastero (LA), Upper Amazon Forastero (UA), Trinitario, and Criollo (Cr). The 12-microsatellite loci revealed a total of 125 alleles, 113 of which were present in the farm accession group (FA). The within and between group variation for all AGs accounted respectively for 81% and 19% of the total molecular variation. The average Fis for the FAwas 0.15 suggesting a moderate level of inbreeding. Significant differences for the level of gene diversity were found between the farm (0.50), GenBank (0.42 to 0.62), and reference (0.10 to 0.60) AGs. Genetic differentiation among AGs was variable with Fst values varying between 0.14 and 0.57 for the different AGs. Analysis using a Bayesian model-based method showed the existence of a high level of admixture for the farm accessions group. The LA genes were most represented in the FA (54%), followed by UA (33%) and Cr (7%). The genes of LAwere also the most represented in the GenBank (48%), followed by UA (24%) and Cr (14%). Only 14% and 6% of the genes of the GenBank and farm accessions, respectively, could not be attributed to any of the reference GGs. The results suggest the predominating presence of LA genes in the Cameroon farm accessions and a high level of admixture, with apparent presence of genes of more than three GGs in most accessions. The traditional Trinitario types appear to have almost disappeared from farmers fields. The admixture must be the result of hybridization and recombination of these genes from the different GGs in seed gardens and in farmers’ fields. The use of selected farm accessions will depend on the GG that it belongs to and also on their level of heterozygosity. Further implications of the results for breeding and for introduction of new germplasm into the Cameroon GenBank are discussed.

DNA extraction is a time-consuming and expensive component of molecular marker analysis, constituting about 30–60% of the total time required for sample processing. Furthermore, the procedure for extracting high-quality DNA from tree species such as cocoa differs from extraction protocols suitable for other crop plants. This is accompanied by problems in collecting leaf tissues from field-grown cocoa trees, where storage facilities are not available and where transporting samples to laboratory for immediate refrigeration is usually impossible. We preserved cocoa leaf tissues in the field in an NaCl-CTAB-azide solution (as described in Rogstad, 1992), which did not require immediate refrigeration. This method also allowed preservation of leaf tissues for a few days during transportation and protected leaf tissues from bacterial and fungal attacks. Once transported to the laboratory, the samples were stored at 4°C for almost 1 y. To isolate good-quality DNA from stored leaf tissues, a rapid semiautomated and relatively high-throughput protocol was established. The procedure followed a modified CTAB/β-mercaptoethanol method of DNA extraction in a 96-well plate, and an automated system (i.e., GenoGrinder 2000) was used to grind the leaf tissues. The quality of DNA was not affected by long storage, and the quantity obtained per sample was adequate for about 1000 PCR reactions. Thus, this method allowed isolation of about 200 samples per day at a cost of $0.60 per sample and is a relatively high-throughput, low-cost extraction compared with conventional methods that use manual grinding and/or expensive kits.