Population Structure of Moniliophthora perniciosa in the Main Cacao Producing Departments of Colombia.

The witches' broom (Moniliophthora perniciosa) is considered as one of the main threats for cacao production and, consequently, for chocolate production worldwide. In this work, the genetic diversity and population structure of M. perniciosa were analyzed for 59 isolates collected in five departments of Colombia and using 10 microsatellite markers. Analyses revealed 35 multilocus genotypes and clonal populations structure according to linkage disequilibrium analysis. One of the objectives of this study was to determine whether populations were differentiated by geographic origin or Theobroma cacao host genotype. Analysis of molecular variance, discriminant analysis of principal components, and Bruvo genetic distance suggested that the genetic structure was driven by geographic origin and not by T. cacao genotype. The results of this study were consistent with previous findings obtained in other cocoa-producing countries. Important insights were discussed regarding the dispersal patterns of the pathogen in Colombia and the genetic change of its populations because of different environmental conditions.

Spatial and Temporal Analysis of Phytophthora megakarya Epidemic in Newly Established Cacao Plantations.

Studying spatial and temporal plant disease dynamics helps us to understand pathogen dispersal processes and improve disease control recommendations. In this study, three cacao plots devoid of primary inoculum of Phytophthora megakarya (causal agent of cacao black pod rot disease) upon establishment in 2006 were monitored for presence of disease on a weekly basis from 2009 to 2016. Ripley's K(r) function, join count statistics, and Fisher's Exact test were used to analyze spatial and temporal disease dynamics. Disease distribution maps showed aggregated disease patterns in all plots; however, for the years of disease onset, exogenous primary infections were mostly randomly distributed. The K(r) function confirmed these results indicating that inoculum generally disperses only over short distances. Moreover, significant positive spatial autocorrelations showed that diseased trees were often clustered up to a distance of 3 to 9 m. Temporal disease progression was low, meaning that endogenous inoculum failed to establish itself, which is partly explained by rigorous phytosanitation and partly by unfavorable microclimatic conditions for disease development. Because P. megakarya had difficulty establishing itself in the plots, proximity to already infected cacao plantations drove infection dynamics. Thus, isolation of newly established cacao plantations from infected ones and rigorous phytosanitation as a preventive strategy appears to be an effective approach to control cacao black pod rot disease for newly established cacao plantations.

Genetic and environmental links between traits of cocoa beans and pods clarify the phenotyping processes to be implemented.

The average weight of cocoa beans is not generally taken into account during breeding processes, although it is a trait of interest. Several studies indicate that the weight of the beans has a high heritability in Theobroma cacao. However, the values obtained from different countries for the same clone often vary. In this study, we analyzed the effect of different factors on the weight of the beans. Apart from the clone effect, three main factors had an impact: i) the number of beans per pod: a good filling of the pod with beans tended to limit the weight of the beans, ii) the position of the beans in the pod: beans in the apical part of the pod were significantly lighter than the others and iii) the longer the duration of the fructification cycle the heavier the beans were (positive genetics correlation). These results lead us to propose protocols aimed at normalizing the phenotypic values of the genetic material. To obtain a reliable estimate of the bean weight, the following is proposed: either to use beans obtained from manual pollination to saturate the pods with beans, or to systematically use the number beans in the pods as a covariable.

Unraveling the Complexity of Coffee Leaf Rust Behavior and Development in Different Coffea arabica Agroecosystems.

Crop health management systems can be designed according to practices that help to reduce crop losses by restricting pathogen development and promoting host plant growth. A good understanding of pathogen and host dynamics, which are interdependent, is therefore needed. In this article, we used a holistic approach to explain the behavior of coffee leaf rust (CLR), a major coffee disease. We monitored coffee plant and CLR dynamics simultaneously in plots under different disease management and agroforestry systems. Diseased leaves were also collected to characterize inoculum stock and rust life stages (latent rust area, area with uredospores, necrosis due to rust) through picture analysis. We used structural equation modeling to obtain an overview of CLR pathosystem functioning on a plant scale. This overview integrates processes such as disease dilution by host leaf renewal, direct and indirect effects of fruit load on CLR development, antagonistic effects of shading depending on rust life stages, the tonic effect of copper-based fungicides on leaf retention, and effects on rust life stages depending on fungicide types. From our results, we also deduced that the inoculum stock could be calculated in unsprayed plots from the rust area with uredospores, with uredospores at 58 × 103 cm-2, on average.

Factors Affecting the Dynamics of Frosty Pod Rot in the Main Cocoa Areas of Santander State, Colombia.

Frosty pod rot (FPR) caused by Moniliophthora roreri is the primary disease affecting cacao production in the major producing countries of the Americas and is one of the major threats to cacao worldwide. The incidence of FPR on clones with different levels of resistance was investigated in four localities of Santander State, Colombia, between July 2013 and May 2015. Dynamics of diseased pods were modeled using boosted regression trees, a machine learning technique that allows regressions to be performed without prior statistical assumptions. The results suggested that FPR epidemics varied according to plot location, clone, weeks of observation, and total pods produced. Dynamics in the phenology of pods had an effect on the epidemics, and this dynamic could partially explain the difference in resistance among clones. Although not total, partial resistance of ICS 95 was confirmed. An important wilt effect was observed, particularly in the resistant clones; consequently, differences in harvested pods were not significant among clones. Pod stripping remains a good practice for the management of the disease and this practice could also have an effect on the pod dynamics and wilt phenomenon.

Geographic Differentiation and Population Genetic Structure of Moniliophthora roreri in the Principal Cocoa Production Areas in Colombia.

Frosty pod rot (FPR) disease on cocoa, caused by Moniliophthora roreri, is one of the most devastating cocoa disease in the Western Hemisphere. In Colombia, the disease is particularly severe in the Magdalena Valley, which is considered the possible center of origin for the pathogen species. We analyzed the genetic diversity of isolates from the departments of Santander, Antioquia, Tolima, and Huila in Colombia using 23 simple-sequence repeats (SSR) markers. In total, 117 different multilocus genotypes were found among 120 isolates, each one representing a unique haplotype. High mutation rates in the SSR and gene flow can explain the high levels of diversity. Also, the observed and standardized indexes of association (IA and rd) indicate that the populations of M. roreri are clonal. Furthermore, given the high haplotype diversity and the significant linkage disequilibrium observed, we hypothesize that M. roreri could be a primarily asexual species undergoing sporadic recombination or partial recombination through parasexuality. A Bayesian clustering analysis implemented by STRUCTURE showed that the most probable number of genetic groups in the data was three, confirming the geographical differentiation among isolates. Similar results were obtained by a discriminant analysis of principal components, a principal coordinate analysis, and a neighbor-joining tree from microsatellite loci base on Nei distance. Cacao genotypes and environmental variables did contribute to the genetic differentiation of the groups. We discuss how this information could be used to improve the management of FPR at the regional level.

Pantoea coffeiphila sp. nov., cause of the 'potato taste' of Arabica coffee from the African Great Lakes region.

Six isolates recovered from coffee seeds giving off a potato-like flavour were studied. Gene sequencing (rrs and rpoB) showed they belong to the genus Pantoea. By DNA-DNA hybridization, the isolates constituted a genomic species with less than 17% relatedness to 96 strains representing enterobacterial species. Multilocus sequence analysis (gyrB, rpoB, atpD and infB genes) showed the isolates to represent a discrete species of the genus Pantoea. Nutritional versatility of the novel species was poor. The novel species is proposed as Pantoea coffeiphila sp.nov. and its type strain is Ca04(T) ( =CIP 110718(T) =DSM 28482(T)).

Tree spatial structure, host composition and resource availability influence mirid density or black pod prevalence in cacao agroforests in Cameroon.

Combining crop plants with other plant species in agro-ecosystems is one way to enhance ecological pest and disease regulation mechanisms. Resource availability and microclimatic variation mechanisms affect processes related to pest and pathogen life cycles. These mechanisms are supported both by empirical research and by epidemiological models, yet their relative importance in a real complex agro-ecosystem is still not known. Our aim was thus to assess the independent effects and the relative importance of different variables related to resource availability and microclimatic variation that explain pest and disease occurrence at the plot scale in real complex agro-ecosystems. The study was conducted in cacao (Theobroma cacao) agroforests in Cameroon, where cocoa production is mainly impacted by the mirid bug, Sahlbergella singularis, and black pod disease, caused by Phytophthora megakarya. Vegetation composition and spatial structure, resource availability and pest and disease occurrence were characterized in 20 real agroforest plots. Hierarchical partitioning was used to identify the causal variables that explain mirid density and black pod prevalence. The results of this study show that cacao agroforests can be differentiated on the basis of vegetation composition and spatial structure. This original approach revealed that mirid density decreased when a minimum number of randomly distributed forest trees were present compared with the aggregated distribution of forest trees, or when forest tree density was low. Moreover, a decrease in mirid density was also related to decreased availability of sensitive tissue, independently of the effect of forest tree structure. Contrary to expectations, black pod prevalence decreased with increasing cacao tree abundance. By revealing the effects of vegetation composition and spatial structure on mirids and black pod, this study opens new perspectives for the joint agro-ecological management of cacao pests and diseases at the plot scale, through the optimization of the spatial structure and composition of the vegetation.

Shade tree spatial structure and pod production explain frosty pod rot intensity in cacao agroforests, Costa Rica.

Vegetation composition and plant spatial structure affect disease intensity through resource and microclimatic variation effects. The aim of this study was to evaluate the independent effect and relative importance of host composition and plant spatial structure variables in explaining disease intensity at the plot scale. For that purpose, frosty pod rot intensity, a disease caused by Moniliophthora roreri on cacao pods, was monitored in 36 cacao agroforests in Costa Rica in order to assess the vegetation composition and spatial structure variables conducive to the disease. Hierarchical partitioning was used to identify the most causal factors. Firstly, pod production, cacao tree density and shade tree spatial structure had significant independent effects on disease intensity. In our case study, the amount of susceptible tissue was the most relevant host composition variable for explaining disease intensity by resource dilution. Indeed, cacao tree density probably affected disease intensity more by the creation of self-shading rather than by host dilution. Lastly, only regularly distributed forest trees, and not aggregated or randomly distributed forest trees, reduced disease intensity in comparison to plots with a low forest tree density. A regular spatial structure is probably crucial to the creation of moderate and uniform shade as recommended for frosty pod rot management. As pod production is an important service expected from these agroforests, shade tree spatial structure may be a lever for integrated management of frosty pod rot in cacao agroforests.

Geographical differentiation of the molecular diversity of cacao swollen shoot virus in Togo.

The variability of cacao swollen shoot virus (CSSV) was studied in two areas of Togo with distinct epidemiological backgrounds, Kloto and Litimé. This molecular study was based on 120 sequence comparisons of the first part of ORF3 of the viral genome. The phylogenetic study distinguished three groups of CSSV isolates, A, B, and C, with clear geographical differentiation between the Kloto and Litimé areas. The only group detected in Kloto was group C, whereas the Litimé area only contained isolates from groups A and B, which most probably originated from Ghana. The divergence between the three groups strongly suggests a different origin for each of the groups.

Effect of genotype of cocoa (Theobroma cacao) on attractiveness to the mirid Sahlbergella singularis (Hemiptera: Miridae) in the laboratory.

BACKGROUND: Mirids are a major constraint to cocoa growing in Africa. Cocoa breeding for tolerance/resistance could be effective in an integrated pest management system. Attractiveness is one aspect of tolerance/resistance, and decreasing the attractiveness of cocoa trees should be a good way of reducing damage. RESULTS: Small-scale laboratory tests were carried out in Cameroon to assess differences in the attractiveness to mirids of eleven cocoa genotypes. The genotypes were ranked according to their attractiveness score and a distance from a mean value. An analysis of variance was performed and revealed significant differences between cocoa genotypes (F=3.15, P<0.001). The cocoa genotype groupings revealed three major categories, with BE10 and SNK413 proving to be the most attractive. In contrast, five genotypes, IMC60, the Catongo Trinitario genotypes, Playa Alta2 (from Venezuela), SIC5 and SNK614, proved to be less attractive than the mean. Four genotypes (PA107, SNK619, UPA134 and T60/887) displayed similar attractiveness to the mean. CONCLUSION: The circular microtest offered the advantage of not needing a reference cocoa genotype. The least attractive clones, such as IMC60, were also the most tolerant in the field. Comparisons with the results of other studies are proposed.

Dissecting apple tree architecture into genetic, ontogenetic and environmental effects: mixed linear modelling of repeated spatial and temporal measures.

The present study aimed to dissect tree architectural plasticity into genetic, ontogenetic and environmental effects over the first 4 yr of growth of an apple (Malus x domestica) F1 progeny by means of mixed linear modelling of repeated data. Traits related to both growth and branching processes were annually assessed on different axes of the trees planted in a staggered-start design. Both spatial repetitions, (i.e. different axis types) and temporal repetitions (i.e. successive ages of trees) were considered in a mixed linear model of repeated data. A significant genotype effect was found for most studied traits and interactions between genotype and year and/or age were also detected. The analysis of repeated temporal measures highlighted that the magnitude of the decrease in primary growth is mainly determined by the first year of growth, and the decrease in bottom diameter increment is concomitant with the first fruiting occurrence. This approach allowed us to distinguish among the traits that were under genetic control, those for which this control is exerted differentially throughout tree life or depending on climatic conditions or an axis type. Mapping quantitative trait loci (QTL) that are specific to these different effects will constitute the next step in the research.

Topography and crop management are key factors for the development of american leaf spot epidemics on coffee in costa rica.

ABSTRACT We monitored the development of American leaf spot of coffee, a disease caused by the gemmiferous fungus Mycena citricolor, in 57 plots in Costa Rica for 1 or 2 years in order to gain a clearer understanding of conditions conducive to the disease and improve its control. During the investigation, characteristics of the coffee trees, crop management, and the environment were recorded. For the analyses, we used partial least-squares regression via the spline functions (PLSS), which is a nonlinear extension to partial least-squares regression (PLS). The fungus developed well in areas located between approximately 1,100 and 1,550 m above sea level. Slopes were conducive to its development, but eastern-facing slopes were less affected than the others, probably because they were more exposed to sunlight, especially in the rainy season. The distance between planting rows, the shade percentage, coffee tree height, the type of shade, and the pruning system explained disease intensity due to their effects on coffee tree shading and, possibly, on the humidity conditions in the plot. Forest trees and fruit trees intercropped with coffee provided particularly propitious conditions. Apparently, fertilization was unfavorable for the disease, probably due to dilution phenomena associated with faster coffee tree growth. Finally, series of wet spells interspersed with dry spells, which were frequent in the middle of the rainy season, were critical for the disease, probably because they affected the production and release of gemmae and their viability. These results could be used to draw up a map of epidemic risks taking topographical factors into account. To reduce those risks and improve chemical control, our results suggested that farmers should space planting rows further apart, maintain light shading in the plantation, and prune their coffee trees.

Definition of architectural ideotypes for good yield capacity in Coffea canephora.

BACKGROUND: Yield capacity is a target trait for selection of agronomically desirable lines; it is preferred to simple yields recorded over different harvests. Yield capacity is derived using certain architectural parameters used to measure the components of yield capacity. METHODS: Observation protocols for describing architecture and yield capacity were applied to six clones of coffee trees (Coffea canephora) in a comparative trial. The observations were used to establish architectural databases, which were explored using AMAPmod, a software dedicated to the analyses of plant architecture data. The traits extracted from the database were used to identify architectural parameters for predicting the yield of the plant material studied. CONCLUSIONS: Architectural traits are highly heritable and some display strong genetic correlations with cumulated yield. In particular, the proportion of fruiting nodes at plagiotropic level 15 counting from the top of the tree proved to be a good predictor of yield over two fruiting cycles.

Characterization of branching in two Hevea brasiliensis clones.

Rubber has been grown for several decades in Africa, notably in Ivory Coast. Although the yields obtained with selected clones are good, some problems with adaptation to edaphic and climatic conditions have yet to be solved. Of these problems, tree breakage due to violent winds during frequent storms is a major handicap. Some clones are more resistant to wind damage. However, this resistance trait remains difficult to measure, and detecting it at an early stage appeared important. As no differences have been found in the physical properties of the wood of different clones, the search for differences between clones displaying resistance and susceptibility to wind damage was switched to architectural structures. Architectural traits were thus studied on two rubber clones with very different resistances to wind. Observations were focused both on young trees and adult trees. Of all the architectural traits observed, a description of branching provided information likely to explain differences in the way the clones being studied developed over time. The clone GT1 which is resistant to wind, developed more lateral branches but they did not grow much in length. On the other hand, fewer axillary branches appeared on the susceptible clone PB235 but they grew longer. Moreover, as some of these traits proved to be similar in both young and adult trees, they could be detected at a sufficiently early stage for use as early prediction traits, if their involvement in susceptibility to wind damage is confirmed.

Estimation of production losses caused by the coffee berry borer (Coleoptera: Scolytidae) and calculation of an economic damage threshold in Togolese coffee plots.

The coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Scolytidae), which exists in all coffee producing zones, is a major pest. The seriousness of this scolytid was assessed in Togolese plots spread over five agroclimatic zones, by determining the attack rate from a sample of coffee trees. The work was carried out over 2 yr and revealed that weight losses were proportional to the attack rates. The average infestation rates were 5.64% in the first year and 6.36% in the second year, while total production losses amounted to 2.60% and 3.18%, respectively, for the same periods. Generally speaking, attack rates in the plots were low and varied considerably within a given zone. Plantations located on plateau were more severely attacked than those in the plains. A relationship was established between total losses and the cost of insecticide treatment; this relationship was used to calculate an economic damage threshold beyond which control proves to be cost effective.

Assessment of the value of doubled haploids as progenitors in cocoa (Theobroma cacao L.) breeding.

In order to evaluate twelve doubled haploids (DHs) of Theobroma cacao L. used as parents, a trial was set up in Côte d'Ivoire. Several traits were observed, such as yield, vigour, yield/vigour ratios, resistance to the black pod disease caused by Phytophthora, percentage of flat beans and mean weight of 100 cocoa beans. Out of the three progenies derived from crosses between two DHs, two showed severe drawbacks. A reduction of the heterogeneity within these progenies was occasionally observed for some of the traits, but failed to be consistent. When tested as female parents in combination with diploid testers, some of the DHs showea significantly higher combining value than their parents for traits such as the mean weight of 100 beans and the yield/canopy surface ratio. The results showed the potential of DHs to improve selected parents in only one cycle of selection but more crosses between two DHs need to be tested in order to evaluate potential of the resulting F(1) progenies.