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A linkage map of cacao based on codominant markers has been constructed by integrating 201 new simple sequence repeats (SSR) developed in this study with a number of isoenzymes, restriction fragment length polymorphisms (RFLP), microsatellite markers and resistance and defence gene analogs (Rgenes-RFLP) previously mapped in cacao. A genomic library enriched for (GA)(n) and (CA)(n) was constructed, and 201 new microsatellite loci were mapped on 135 individuals from the same mapping population used to establish the first reference maps. This progeny resulted from a cross between two heterozygous cacao clones: an Upper-Amazon Forastero (UPA 402) and a Trinitario (UF 676). The new map contains 465 markers (268 SSRs, 176 RFLPs, five isoenzymes and 16 Rgenes-RFLP) arranged in ten linkage groups corresponding to the haploid chromosome number of cacao. Its length is 782.8 cM, with an average interval distance between markers of 1.7 cM. The new microsatellite markers were distributed throughout all linkage groups of the map, but their distribution was not random. The length of the map established with only SSRs was 769.6 cM, representing 94.8% of the total map. The current level of genome coverage is approximately one microsatellite every 3 cM. This new reference map provides a set of useful markers that is transferable across different mapping populations and will allow the identification and comparison of the most important regions involved in the variation of the traits of interest and the development of marker-assisted selection strategies.

Quantitative trait loci (QTL) mapping for bean traits and the number of ovules per ovary was carried out in cocoa (Theobroma cacao L.) using three test-cross progenies derived from crosses between a lower Amazon Forastero male parent (Catongo) and three female parents: one upper Amazon Forastero (IMC78) and two Trinitario (DR1 and S52). RFLP (restriction fragment length polymorphism), microsatellite, and AFLP (amplified fragment lengthpolymorphism) markers were used for mapping. Between one and six QTL for bean traits (length, weight, and shape index) and one and four QTL for the number of ovules per ovary were detected using composite interval mapping (CIM). Individual QTL explained between 5 and 24% of the phenotypic variation. QTL clusters were identified on several chromosomes, but particularly on chromosome 4. QTL related to bean traits were detected in the same region in both Trinitario parents and in a close region in the upper Amazon Forastero parent. In reference to a previous diversity study where alleles specific to Criollo and Forastero genotypes were identified, it was possible to speculate on the putative origin (Criollo or Forastero) of favorable QTL alleles segregating in both Trinitario studied.

This study aimed to compare the genetic control of cacao resistance to three species of Phytophthora: Phytophthora palmivora, Phytophthora megakarya and Phytophthora capsici. The study was conducted on 151 hybrid progenies created in Côte d'Ivoire and grown in a green-house in Montpellier. Phytophthora resistance was screened by leaf-test inoculation with two different strains per species. Selection of the best individuals for resistance to P. palmivora at a 10% selection rate, would lead to a genetic progress of 47% in the disease evaluation for this species and a genetic progress of 42% and 21% for the two other species. A genetic map with a total length of 682 cM was built with 213 markers, 190 AFLPs and 23 microsatellites. QTLs were identified using composite interval mapping. QTLs were found located in six genomic regions. One of these was detected with five strains belonging to the three Phytophthora species. Two other regions were detected with two or three strains of two different species. Three additional QTLs were detected for only one species of Phytophthora. Each QTL explained between 8 to 12% of the phenotypic variation. For each strain, between 11.5% to 27.5% of the total phenotypic variation could be explained by the QTLs identified. The identification of multiple QTLs involved in resistance to Phytophthora offers the possibility to improve durability of resistance in cocoa by a possible cumulation of many different resistance genes located in different chromosome regions using marker-aided selection.

Quantitative trait loci (QTL) mapping for agronomic traits was carried out in cocoa (Theobroma cacao L.). Regions of the genome involved in yield, vigor, and resistance to Phytophthora palmivora were identified. Three heterozygous clones, one upper Amazon Forastero (IMC78) and two Trinitario (DR1 and S52), were crossed with the same male parent, a lower Amazon Forastero (Catongo), known to be highly homozygous. Observations were made on progeny over nine consecutive years. One to three QTL related to yield were detected in each of the three populations, located on chromosomes 1, 2, 4, 5, 9, and 10. They explained between 8.1 and 19.3% of the phenotypic variation and showed various levels of repeatability. In IMC78, the QTL detected on chromosome 5 was the most repeatable over years. The QTL for the average individual pod weight on chromosome 4 was the most significant with an LOD of 17.3 and an R2 of 43.7. QTL related to these traits were identified in the same region of the genome in clones of different genetic groups. This suggests that molecular markers can be used to improve cocoa varieties.

The genetic diversity of 106 genotypes of Theobroma cacao L. was assessed using RFLP and RAPD methods. Thirty-one cDNA probes and 19 primers generated, respectively, 87 and 49poly-morphic bands that were submitted to factorial and cluster analyses. Both RFLP and RAPD bands separated the individuals into three distinctive groups. Some genotypes did not correspond to the currently accepted classification and are considered to have been originally misclassified. The nature of RAPD bands was investigated by Southern analysis. There were as many highly repeated sequences as single copy sequences but the two types of sequences did not structure the variability in the same way. Similar results were obtained with RFLPs and RAPDs with regard to the genetic structure of Theobroma cacao L. Therefore, RAPDs appear to be as efficient as RFLPs for classifying cocoa genotypes.

No abstract

Phytophthora palmivora causes pod rot, a serious disease on cocoa widespread throughout the producing regions. In order to ascertain the genetic determination of cocoa resistance to P. palmivora, a study was carried out on two progenies derived from crosses between a heterozygous, moderately resistant Forastero clone, T60/887, and two closely related and highly susceptible Forastero clones, one completely homozygous, IFC2, and one partially heterozygous, IFC5. The cumulative size of both progenies was 112 individuals. Plants were subjected to natural and artificial inoculation of P. palmivora in C te d'Ivoire. The genetic maps of T60/887 and of IFC5 were constructed using amplified fragment length polymorphism (AFLP) markers and microsatellites. The map of T60/887 comprised 198 markers assembled in 11 linkage groups and representing a total length of 793 cM. The map of IFC5 comprised 55 AFLP markers that were assembled into six linkage groups for a total length of 244 cM. Ratio of rotten over total number of fruit under natural infection was measured for each tree over two harvests. Artificial inoculations were performed on leaves and pods. These tests were weakly correlated with the pod rot rate in the field. Five quantitative trait loci (QTLs) of resistance were detected for T60/887 but none were common between the three traits measured. Stability and reliability of the experimental procedures are discussed and revealed the difficult use of these artificial tests on adult trees for a good prediction of field resistance.