Phytophthora megakarya (Pmeg) and Phytophthora palmivora (Ppal) are closely related species causing cacao black pod rot. Although Ppal is a cosmopolitan pathogen, cacao is the only known host of economic importance for Pmeg. Pmeg is more virulent on cacao than Ppal. We sequenced and compared the Pmeg and Ppal genomes and identified virulence-related putative gene models (PGeneM) that may be responsible for their differences in host specificities and virulence. Pmeg and Ppal have estimated genome sizes of 126.88 and 151.23 Mb and PGeneM numbers of 42,036 and 44,327, respectively. The evolutionary histories of Pmeg and Ppal appear quite different. Postspeciation, Ppal underwent whole-genome duplication whereas Pmeg has undergone selective increases in PGeneM numbers, likely through accelerated transposable element-driven duplications. Many PGeneMs in both species failed to match transcripts and may represent pseudogenes or cryptic genetic reservoirs. Pmeg appears to have amplified specific gene families, some of which are virulence-related. Analysis of mycelium, zoospore, and in planta transcriptome expression profiles using neural network self-organizing map analysis generated 24 multivariate and nonlinear self-organizing map classes. Many members of the RxLR, necrosis-inducing phytophthora protein, and pectinase genes families were specifically induced in planta. Pmeg displays a diverse virulence-related gene complement similar in size to and potentially of greater diversity than Ppal but it remains likely that the specific functions of the genes determine each species’ unique characteristics as pathogens.

Kouakou, K., Kébé, B.

A genetic analysis of resistance of cacao to Phytophthora palmivora was carried out in a 5 × 5 diallel and in a 4 × 2 NC II factorial design, involving cross-progenies and parental clones planted in the nursery and field, respectively. Resistance was scored in the laboratory by inoculation of leaf discs with P. palmivora spores with four replicates and, for the factorial design, results were compared with the percentage of rotten pods in the field assessed over a seven-year period. Significant differences between genotypes were observed for both laboratory and field evaluation methods. For the laboratory test, no reciprocal effect was observed and plant effects within seedling progenies were more significant than plant effects within clones. General combining ability was the main source of variation but specific combining ability was also significant for the leaf disc test applied to the diallel. Heritabilities increased with the number of replicates, reaching values of 0.34 and 0.67 for narrow sense heritability, and 0.60 and 0.67 for broad sense heritability, for the diallel and the factorial design, respectively. These values were higher than observed for the percentage of rotten pods in the field in the factorial design (0.42 and 0.47, respectively). For the leaf test, the expected genetic gains were around 30% with a selection intensity of 5%. The existence of significant genetic (0.71) and phenotypic (0.39) coefficients of correlation between resistance on leaves and percentage of rotten pods in the field in the factorial design confirms the feasibility of using the leaf disc test for early selection of resistance to Phytophthora pod rot of cacao.

The effects were studied of four leaf development stages (LDS) and three durations of incubation (DI) on the accuracy of leaf-disc tests on eight cacao (cocoa) clones (C) for predicting field resistance to phytophthora pod rot caused by Phytophthora palmivora . The clones were known to possess different general combining abilities (GCA) for pod resistance in the field, evaluated monthly at harvest over a 9-year period. Disease severity (DS) was affected strongly by C, DI and LDS, with increasing levels of significance. Two-and three-way interaction effects were smaller than the clone effect, but still significant. Clone effects were most significant for LDS3 (i.e. leaves 50 -60 days old) and for DI5 and DI7 (observations made 5 and 7 days after inoculation, respectively). Coefficients of rank correlation between DS and field results were significant for seven of the 12 treatments, with highest values obtained again for treatments LDS3/DI5 ( r = 0·87) and LSD3/DI7 ( r = 0·93). Pooling of data for different LDS and DI treatments did not further improve the correlation with field results. However, these correlations were improved (from an average of 0·74 to 0·88) when the GCA values for field resistance were based on weekly observations, carried out in one year, including losses of pods and cherelles. It was concluded that, when carried out in a standardized manner and under optimal conditions, the leaf-disc test may explain 75 -90% of the genetic variation for field resistance of cacao genotypes to P. palmivora .

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