Cacao is an understory plant cultivated under full-sun monocultures to multi-strata agroforestry systems, where cocoa trees are planted together with fruit, timber, firewood, and leguminous trees, or grown within thinned native forests. Under agroforestry systems of cultivation, cacao is subjected to excess shade due to high density of shade trees, and overgrown or unmanaged pruning of shade trees. Cacao is tolerant to shade, and the maximum photosynthetic rate occurs around irradiance of 400 μmol m⁻² s⁻¹ but excess shade reduces the irradiance further which is detrimental to photosynthesis and growth functions. Intra-specific variation is known to exist in cacao for the required saturation irradiance. A greenhouse study was implemented with 58 cacao genotypes selected from four geographically diverse groups: (i) wild cacao from river basins of the Peruvian Amazon, (PWC), (ii) Peruvian farmers’ collection (PFC), (iii) Brazilian cacao collection (BCC) and (iv) national and international cacao collections (NIC). All the cacao genotypes were subjected to 50% and 80% shade where photosynthetic photon flux density (PPFD) was 1000 and 400 μmol m^-2 ּs^-1 respectively. Intra-specific variations were observed for growth, physiological and nutritional traits, and tolerance to shade. Cacao genotypes tolerant to shade were: UNG-77 and UGU-130 from PWC; ICT-2173, ICT-2142, ICT-2172, ICT-1506, ICT-1087, and ICT-2171 from the PFC; PH-21, CA-14, PH-990 and PH-144 from BCC; and ICS-1, ICS-39, UF-613 and POUND-12 from NIC. Genotypes that tolerate excess shade might be useful plant types to maintain productivity and sustainability in agroforestry systems of cacao management.

Background Tropical and subtropical crops such as coffee, cacao, and papaya are valuable commodities and its consumption is a seemingly indispensable part of the daily lives of billions of people across the world. Conventional breeding in these crops is lengthy and yields are threatened by runaway global warming. In this review we propose the application of chromosome engineering and synthetic biology principles in order to enhance synthesis of key metabolites, and transmission of wild traits for resistance to stress and disease. Conclusions It is hoped that the adoption of such technological approaches may enhance the resilience of agricultural communities, lead to economic growth and secure the availability of key resources for generations to come.

Inorganic pollutants in Colombian cocoa (Theobroma cacao L.) agrosystems cause problems in the production, quality, and exportation of this raw material. There has been an increased interest in bioprospecting studies of different fungal species focused on the biosorption of heavy metals. Furthermore, fungi constitute a valuable, profitable, ecological, and efficient natural soil resource that could be considered in the integrated management of cadmium mitigation. In this study, we report a new species of Talaromyces, isolated from cocoa soil from San Vicente de Chucurí-Colombia. The characterization of the culture was performed on six different standardized media and was distinguished by characteristic colony morphology: biverticillate and monoverticillate penicilli, acerose phialides, and slightly globose smooth-walled conidia. Culture was featured by bright yellow mycelium in young culture on CYA and CYAS medium. Colonies grew faster on Malt and Oat agar, attaining 36 and 32 mm diameter after seven days at 20 ºC. High acid production on CREA medium at 20-30 ºC was observed. Phylogenetic analysis was based on the ITS region and the RPB2, Calmodulin (CaM) and β-Tubulin genes that indicate that it is new to science and is named Talaromyces santanderensis sp. nov. This new species belongs to the Talaromyces section and is closely related to T. lentulus and related to T. soli, T. tumuli and T. pratensis (inside the T. pinophilus species complex) in the inferred phylogeny. Mycelia growth of the fungal strains was subjected to a range of 0-400 ppm Cd and incorporated into malt extract agar (MEA) in triplicates. Fungal radial growth was recorded every three days over a 13-days incubation period and In vitro cadmium tolerance tests showed a high tolerance index = 0,81 when the mycelium was exposed to 300 ppm of Cd. Results suggest T. santanderensis showed tolerance to Cd concentrations that exceed the permissible limits for contaminated soils, and it is promising for its use in bioremediation strategies to eliminate Cd from highly contaminated agricultural soils.

Frosty pod rot, caused by Moniliophthora roreri, is the most damaging disease of cacao in Latin America. However, to better comprehend its epidemiology, we must understand its dissemination and proliferation. Still, we ignore how loads of M. roreri spores fluctuate across growing seasons since we lack a reliable technique to quantify M. roreri spores in the fields. Therefore, we developed a method that uses a spore trap to capture M. roreri spores and qPCR to quantify them. This study demonstrated that this technique could quantify 3.9 x104 M. roreri spores with a 95 % confidence level. However, it could not differentiate between M. roreri and its close relative, M. perniciosa. Despite this limitation, we could detect and quantify Moniliophthora spores from environmental samples taken from a cacao field. This technique can help the phytopathologist address studies more accurately in disseminating cacao pathogens.

Cocoa bean quality depends mainly on genetic material, edaphoclimatic factors and post-harvest processes such as fermentation. The impact of the fermentation process on the chemical and func-tional composition of different cocoa clones grown in southern Colombia was analyzed. A facto-rial design with repeated measures over time was used to analyze the effect of clone and fermen-tation time on chemical characteristics (bromatology, phenolic compounds and antioxidant ac-tivity). The bromatological characteristics showed significant differences between clones and fermentation time. Clones EET-8 and CCN-51 showed higher contents of acidity (0.51%), fat (63.61%), protein (12.85%) and carbohydrates (1.63 mg g-1). Moisture, acidity and sucrose in-creased their values between day 4 and day 6 of fermentation (P<0.05). Phenolic compounds and antioxidant activity had significant differences between clones, where clones CCN-51 and ICS-95 had high contents of phenols (64.56 mg g-1), flavonoids (3.30 mg g-1) and DPPH reducing capacity (325.55 µmol g-1). In this sense, we consider the FSV-41 clone as the major grain quality index based on the results of chemical composition at bromatological level, antioxidant activity and phenolic compounds.