Andrew J. Daymond

Cacao leafroll virus (CaLRV; species Polerovirus CALRV, family Solemoviridae), previously referred to as cacao polerovirus, infects cacao (Theobroma cacao) germplasm in the Americas. Screening of 287 cacao accessions with three published multiplex RT-PCR assays detected CaLRV in nine accessions but produced reproducibly discordant results for the accession LCT EEN 412. Metatranscriptomic sequencing generated three near-complete CaLRV genome sequences, CaLRV-TSAN792, CaLRV-POUND15A, and CaLRV-LCTEEN412 (5985–5989 nt), from accessions originating from Brazil, Trinidad and Tobago, and Ecuador, respectively. The divergent CaLRV-LCTEEN412 assembly was verified by RT-PCR, cloning, and nanopore sequencing. In addition, analysis of five public cacao RNA-seq datasets yielded one near-complete CaLRV-PA16 assembly included in whole-genome analysis and four fragmented assemblies that informed primer design. Comparison of the four sequences characterised here with six previously reported genomes showed that nine shared 98.8–99.7% pairwise nucleotide identity, whereas CaLRV-LCTEEN412 shared 85.0–85.2%. Primer-binding-site mismatches in CaLRV-LCTEEN412 were consistent with its discordant detection by published assays. Two new multiplex RT-PCR assays were therefore designed from the expanded alignment and evaluated using four CaLRV-positive cacao accessions, including LCT EEN 412. These results expand known CaLRV genomic diversity and provide dual-target tools that reduce dependence on a single locus and enable recognition of target discordance.

Agriculture intensification is driving biodiversity decline in agroecosystems. Agroforestry systems can serve as a biodiversity refugia due to their structural complexity within agricultural landscapes. On-farm vegetation management is recognised as a key driver of biodiversity and ecosystem services, yet its effects on arthropod communities in agroforestry systems at the farm scale have received little attention. We investigated how understorey vegetation management and farm characteristics such as size and tree species richness influence arthropod abundance and community composition in smallholder cocoa agroforestry systems in South-East Sulawesi, Indonesia, a globally important region for production and biodiversity. Arthropods were sampled across 12 farms using sweep netting, pitfall trapping, and tap sampling at different distances from the farm edge. We found that farms with greater vegetation cover supported higher abundances across most arthropod orders, although responses varied among taxa and sampling methods. Vegetation characteristics, including flowering resources, cover of forbs and richness of tree species positively influenced key groups such as Araneae, Hymenoptera, and Diptera. Evidence of spillover from farm edges was limited, with Araneae, Hymenoptera, Diptera and Hemiptera showing higher abundance within farm centres. Community composition differed significantly between vegetation-rich and low-vegetation farms for cocoa canopy and vegetation associated arthropods, but not for ground-dwelling taxa. Our findings demonstrate that on-farm habitat management, particularly maintaining understorey vegetation and advocating for structural complexity, can increase arthropod biodiversity in cocoa agroforestry systems.

Despite multiple studies of the impact of climate change on temperate tree species, experiments on tropical and economically important tree crops, such as cacao (Theobroma cacao L.), are still limited. Here, we investigated the combined effects of increased temperature and atmospheric carbon dioxide concentration ([CO₂]) on the growth, photosynthesis and development of juvenile plants of two contrasting cacao genotypes: SCA 6 and PA 107. The factorial growth chamber experiment combined two [CO₂] treatments (410 and 700 p.p.m.) and three day/night temperature regimes (control: 31/22 °C, control + 2.5 °C: 33.5/24.5 °C and control + 5.0 °C: 36/27 °C) at a constant vapour pressure deficit (VPD) of 0.9 kPa. At elevated [CO₂], the final dry weight and the total and individual leaf areas increased in both genotypes, while the duration for individual leaf expansion declined in PA 107. For both genotypes, elevated [CO₂] also improved light-saturated net photosynthesis (P_n) and intrinsic water-use efficiency (iWUE), whereas leaf transpiration (E) and stomatal conductance (g_s) decreased. Under a constant low VPD, increasing temperatures above 31/22 °C enhanced the rates of P_n, E and g_s in both genotypes, suggesting that photosynthesis responds positively to higher temperatures than previously reported for cacao. However, dry weight and the total and individual leaf areas declined with increases in temperature, which was more evident in SCA 6 than PA 107, suggesting the latter genotype was more tolerant to elevated temperature. Our results suggest that the combined effect of elevated [CO₂] and temperature is likely to improve the early growth of high temperature-tolerant genotypes, while elevated [CO₂] appeared to ameliorate the negative effects of increased temperatures on growth parameters of more sensitive material. The evident genotypic variation observed in this study demonstrates the scope to select and breed cacao varieties capable of adapting to future climate change scenarios.

Cacao is an important tropical crop and requires high-fertility soils for better growth and productivity; nevertheless, soils where this crop is grown are, in general, acidic and low in fertility. Therefore, germplasm with tolerance to soil acidity is desirable for cacao genetic improvement. The objective of this study was to evaluate cacao germplasm for early growth, nutrient concentration, and potential tolerance to soil acidity. A greenhouse experiment was conducted to evaluate 60 cacao genotypes with diverse geographic origins. Cacao seedlings were grown for six months in acid soil with and without lime. Growth parameters and the total concentration of N, P, K, Ca, Mg, Fe, Cu, Mn, and Zn were measured in shoots after harvest. Our results indicate that the best early growth predictors of acid soil tolerance are the number of leaves and root area. N, Ca, Mg, and K uptake may have a potential role in tolerance to soil acidity. Finally, the results revealed a large difference among cacao genotypes in terms of their responses to acid soil stress, which led to the selection of ten genotypes: CCN-51, PH-21, CCN-10, PAS-91, ICT-1087, ICS-95, UF-667, TSH-565, PH-144, ICT-1189 that are potentially tolerant to soil acidity and could be used for breeding acid soil-tolerant cacao varieties.

Cocoa, Theobroma cacao, is an important tropical perennial crop grown widely in the humid tropics. The exchange of cocoa germplasm between germplasm collections and breeding centres is vital for varietal development. Intermediate quarantine facilities, such as the International Cocoa Quarantine Centre, Reading UK (ICQC-R) play a vital role in ensuring the transfer of germplasm whilst minimising the risk of spreading pests and diseases. Current screening procedures combine visual inspection and molecular techniques, which are effective in detecting Cocoa swollen shoot virus (CSSV), a badnavirus, which causes severe losses but are restricted to West Africa. However, the detection of latent or mild virus infections that produce no visual symptoms has been a challenge. Recently two badnavirus species of cocoa producing mild symptoms, cacao mild mosaic virus (CaMMV) and cacao yellow vein-banding virus (CYVBV), have been sequenced. Here, we report new assays for the detection of these two species, for the first time in non-symptomatic accessions. Evolutionary and bioinformatic analyses of the viruses suggest their most recent source was from Trinidad, though there is historic evidence that these viruses may have their origin in South America and then become widespread globally over the last century. We also report a novel colorimetric Loop-mediated isothermal amplification (LAMP) assay for the detection of CYVBV. This simple and accurate method could be employed in field virus testing.

Climate change poses a significant threat to agricultural production in the tropics, yet relatively little research has been carried out to understand its impact on mature tropical tree crops. This research aims to understand the genotypic variation in growth and photosynthesis in mature cacao trees in response to elevated CO₂ and water deficit. Six genotypes were grown under greenhouse conditions at ambient (ca. 437 ppm) and elevated CO₂ (ca. 724 ppm) and under well-watered and water deficit conditions for 23 months. Leaf- and canopy-level photosynthesis, water-use efficiency, and vegetative growth increased significantly in response to elevated CO₂. Water deficit had a significant negative effect on many photosynthetic parameters and significantly reduced biomass production. The negative effect of water deficit on quantum efficiency was alleviated by elevated CO₂. Genotypic variation was observed in several parameters including stomatal conductance, stomatal density and index, quantum efficiency, and biomass production, indicating the potential to develop more climate-change-resilient genotypes that can cope with predicted future climate change conditions. Elevated CO₂ reduced some of the negative effects of water deficit through changes in water-use efficiency and light utilisation and reduced the negative impact of water deficit on biomass accumulation, but this was genotype-specific.

The potential effect of climate change on regional suitability for cocoa cultivation is a serious economic concern for West Africa—especially for Ghana and Côte d’Ivoire, whose cocoa cultivation accounts for respectively ∼19% and ∼45% of world production. Here, we present a modelling and observational study of cocoa net primary productivity (NPP) in present day and future West African climates. Our analysis uses a data assimilation technique to parameterise a process-based land-surface model. The parameterisation is based on laboratory observations of cocoa, grown under both ambient and elevated CO₂. Present day and end of 21st century cocoa cultivation scenarios are produced by driving the parameterised land-surface model with output from a high-resolution climate model. This represents a significant advance on previous work, because unlike the CMIP5 models, the high-resolution model used in this study accurately captures the observed precipitation seasonality in the cocoa-growing regions of West Africa—a key sensitivity for perennials like cocoa. We find that temperature is projected to increase significantly and precipitation is projected to increase slightly, although not in all parts of the region of interest. We find, furthermore, that the physiological effect of higher atmospheric CO₂concentration ameliorates the impacts of high temperature and variation in precipitation thereby reducing some of the negative impacts of climate change and maintaining NPP in West Africa, for the whole 21st Century, even under a high emissions scenario. Although NPP is an indicator of general vegetation condition, it is not equivalent to yield or bean quality. The study presented here is, nevertheless, a strong basis for further field and modelling studies of cultivation under elevated CO₂conditions.

A survey was conducted of Indonesian cocoa farms to assess the extent of yield variation and factors associated with this variation. The survey of 120 farms during the course of 3 years encompassed four provinces in Sulawesi (South, South-East, West and Central), Western Sumatra, Lampung, East Java and West Papua. A high degree of yield variation was observed between farms, the average over 3 years ranged from 39 to 3586 kg ha⁻¹. Overall, yields were greater on farms that were classified as ‘highly managed’, compared to ‘moderately’ and ‘less managed’. Seasonal variability in yields was generally greater in districts with a more pronounced dry season such as South Sulawesi and Lampung. Multiple regression analyses revealed particular husbandry practices that were linked with higher cocoa yields. Specifically, the use of inorganic fertilisers, application of fungicides against blackpod and weeding were all practices that were associated with higher yields. A positive association between rainfall and yield was observed for the years 2014/15 and 2015/16 but not 2016/17, which was a La Niña year (when rainfall totals were higher). Some of the farms surveyed were planted with cocoa at very low densities implying an opportunity for yield improvement through gap filling or replanting at higher densities (although it was noted that some farmers maintained lower planting densities due to the cultivation of companion crops). Given the smallholder status of most cocoa farms in Indonesia (mean area in this study was 0.71 ha) it is important that farmers are able to maximise returns from their land in order to maintain a livelihood. This study illustrated the potential for yield improvement on Indonesian cocoa farms through adoption of best agronomic practice.