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.

Among the Phytophthora species that cause black pod of cacao, P. megakarya is the most virulent, posing a serious threat to cacao production in Africa. Correct identification of the species causing the black pod and understanding the virulence factors involved are important for developing sustainable disease management strategies. A simple PCR-based species identification method was developed using the species-specific sequences in the ITS regions of the rRNA gene. A phylogenetic tree generated for 119 Phytophthora isolates, based on the 60S ribosomal protein L10 gene and rDNA sequence, verified the PCR-based identification assay and showed high interspecific variation among the species causing black pod. Phytophthora megakarya isolates were uniformly virulent in an assay using susceptible cacao pod husks inoculated with zoospores, while the P. palmivora isolates showed greater divergence in virulence. The virulence of P. megakarya was associated with earlier production of sporangia and an accelerated induction of necrosis. While zoospore germ tubes of both species penetrated pods through stomata, only P. megakarya produced significant numbers of appressoria. A hypersensitive-like response was observed when attached SCA-6 pods were inoculated with P. palmivora. SCA-6 pods became vulnerable to P. palmivora when wounded prior to zoospore inoculation. Phytophthora megakarya was more aggressive than P. palmivora on attached SCA-6 pods, causing expanding necrotic lesions with or without wounding. Phytophthora megakarya is predominant in the Volta region of Ghana and it remains to be seen whether it can displace P. palmivora from cacao plantations of Ghana as it has in Nigeria and Cameroon.

Theobroma cacao (chocolate tree) is currently under serious threat from thread blight disease (TBD), which has been attributed to the causal agent Marasmiellus scandens in other regions of the world. TBD in Ghana has similar symptomology but variable signs. This study sought to determine whether TBD in Ghana was caused by a single agent and whether Marasmiellus scandens was a significant agent of TBD. Forty-eight isolates were collected from eight geographical locations in Ghana for morphological and molecular characterization. Disease signs occurred as vegetative rhizomorphs or hyphal aggregates, which were classified into five morphotypes: A, abundant thin, black, “horse hair”-type rhizomorphs; B, scattered brown rhizomorphs; C, whitish to brownish-white; D, faint cream or dull white; and E, aggregates of shiny or silky white hyphae. Sequencing and analyses of three loci—the internal transcribed spacer region of the nuclear ribosomal repeat, nuclear large subunit, and mitochondrial small subunit—detected four species, all members of the Marasmiaceae, causing TBD-like disease. These were identified as Marasmius crinis-equi (morphotype A), Marasmius tenuissimus (morphotypes B and C), Marasmiellus palmivorus (morphotype E), and Marasmiellus scandens (morphotype D). Marasmius tenuissimus, the most frequently isolated TBD fungus in this study, is primarily an Asian fungus and not previously associated with diseases of cacao. Marasmiellus palmivorus, the second most frequently isolated fungus, is a pan-tropical pathogen with a broad host range; this is the first report of the fungus causing TBD on cacao. Marasmius crinis-equi also has a broad pan-tropical distribution and host range and causes thread blight on several tropical tree crops. Surprisingly, Marasmiellus scandens, the most frequently cited agent of TBD in cacao, made up only 8% of the isolates.

White thread blight disease (WTBD) is currently emerging as an important foliar disease on cocoa in Ghana. The disease has been known in the country for many years. Yet, the incidence and severity levels on cocoa in the growing regions are not known. Surveys and sampling were conducted between 2011 and 2013 to estimate incidence and severity of WTBD in the six cocoa growing regions (Ashanti, Brong-Ahafo, Central, Eastern, Western and Volta) of Ghana. Diseased samples were assayed for the infecting fungus and its identification. Chi square tests were used to find relationships between age, sanitation practice and the disease severity. Effectiveness of chemical and cultural control methods against the disease were tested. The disease was found in all the cocoa growing regions of Ghana and out of 24,000 trees inspected, 1,281 (5.3%) were infected. The majority of infected trees (74.2%) were moderately affected but 3.2% of the trees were very severely affected and almost dead. A positive correlation (r = 0.889) was found between WTBD incidence and the severity. The most severely affected regions were Ashanti (13.8%), Brong-Ahafo (10.2%) and Western (7.6%) regions. Poor maintenance significantly (p=0.0001) increased the levels of disease occurrence and severity. Older cocoa trees also appeared more susceptible than younger ones. Pruning of affected branches controlled the disease better than fungicides spray. However, Nordox (75% copper (I) oxide) at 5 g/l and Metalm (12% metalaxyl and (60% copper (I) oxide) at 3.3 g/l fungicides were effective in reducing mycelial growth of the Marasmiellus fungus. Therefore, fungicide should be used in situations of severe infection to supplement pruning.

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Phytophthora spp. is a major disease of cacao (Theobroma cacao L.), and there is a need to develop cultivars that are resistant to this disease. Among the various genetic groups of cacao, the Guiana (GU) has received little attention in developing varieties even though they are known to be tolerant to black pod disease. The objective of this study was to estimate combining abilities and heritability of selected GU clones for bean yield and black pod resistance. Twenty‐four F1 progenies were derived by crossing three seed garden parental clones with eight GU clones as males in a three‐by‐eight North Carolina II (NC II) complete factorial mating design. These were evaluated together with four standard varieties over a 4‐yr period in a randomized complete block design with four replications at two contrasting locations in Ghana. Progeny, year, and location effects were significant (p < .01) for all traits, whereas progeny × location was significant for only number of beans per pod. The general combining ability (GCA) effects of females and males and specific combining ability (SCA) of female × male were significant (p < .01) for all traits, indicating that both additive and dominant effects are important in the inheritance of the traits. Heritability ranged from 0.14–0.51 for broad sense and 0.10−0.37 for narrow sense. The best general combiners identified—GU 125/C, GU 144/C, and GU 290/H—were involved in crosses that combines high bean yield with high black pod resistance. They could be added to parental clones currently used in producing cacao varieties in areas with high black pod incidence.