Christian Cilas

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.

Genetic diversity and structure of farm and GenBank accessions of cacao (Theobroma cacao L.) in Cameroon revealed by microsatellite markers

The genetic diversity of 400 accessions collected in cacao farms, 95 GenBank, and 31 reference accessions was analyzed using the 12 microsatellite markers. The GenBank and reference accessions were subdivided into 12 accession groups (AG) that belong to the traditional cacao genetic groups (GG) Lower Amazon Forastero (LA), Upper Amazon Forastero (UA), Trinitario, and Criollo (Cr). The 12-microsatellite loci revealed a total of 125 alleles, 113 of which were present in the farm accession group (FA). The within and between group variation for all AGs accounted respectively for 81% and 19% of the total molecular variation. The average Fis for the FA was 0.15 suggesting a moderate level of inbreeding. Significant differences for the level of gene diversity were found between the farm (0.50), GenBank (0.42 to 0.62), and reference (0.10 to 0.60) AGs. Genetic differentiation among AGs was variable with Fst values varying between 0.14 and 0.57 for the different AGs. Analysis using a Bayesian model-based method showed the existence of a high level of admixture for the farm accessions group. The LA genes were most represented in the FA (54%), followed by UA (33%) and Cr (7%). The genes of LA were also the most represented in the GenBank (48%), followed by UA (24%) and Cr (14%). Only 14% and 6% of the genes of the GenBank and farm accessions, respectively, could not be attributed to any of the reference GGs. The results suggest the predominating presence of LA genes in the Cameroon farm accessions and a high level of admixture, with apparent presence of genes of more than three GGs in most accessions. The traditional Trinitario types appear to have almost disappeared from farmers fields. The admixture must be the result of hybridization and recombination of these genes from the different GGs in seed gardens and in farmers’ fields. The use of selected farm accessions will depend on the GG that it belongs to and also on their level of heterozygosity. Further implications of the results for breeding and for introduction of new germplasm into the Cameroon GenBank are discussed.

Impact of shade on the spatial distribution of Sahlbergella singularis in traditional cocoa agroforests

1 Shade management is commonly considered to be an effective pest management strategy for cocoa mirids, yet shade management recommendations are not based on extensive knowledge of the mirid ecology in traditional cocoa agroforests. 2 The main objectives of the present study were an assessment of the impact of shade on the spatial distribution of mirid populations and thus the evaluation of shade management strategies. 3 Mirid densities were measured and shade was characterized for three plots located in three different agroecological zones in the Centre region of Cameroon. Mirid densities generally followed a negative binomial law. Geostatistical procedures were used to characterize spatial distribution of mirid density. Light conditions were assessed using hemispherical photography. 4 Populations of Sahlbergella singularis were highly aggregated in the plots. Semivariance analysis and kriging visualized the spatial dependence of mirid densities. Clearly distinguishable mirid pockets of 20–30 adjacent infested cocoa trees were identified in two of the three plots. 5 The high diversity of shade tree species and the large variability in density and size of shade trees resulted in a considerable heterogeneity of plot light conditions. Percentage transmitted light varied in the range 9.4–80.1% in the most heterogeneous plot. 6 For two of the three plots, mirid pockets were aggregated in those areas where light transmission was highest. In the third plot, relatively high mirid densities and the presence of an alternative host resulted in a more homogeneous distribution. The importance of these findings for improved mirid control is discussed.

Spatio-Temporal Dynamics of Arabica Coffee Berry Disease Caused by Colletotrichum kahawae on a Plot Scale

Coffee berry disease (CBD) is caused by Colletotrichum kahawae. This pathogen only attacks green berries; it causes cherry rot and premature fruit fall. The disease leads to major harvest losses in the western highland region of Cameroon. The origin of the primary inoculum and the beginning of epidemics are unknown. The interactions between the pathogen and its host were studied at locations where CBD was known to cause severe disease. The disease was monitored weekly in uniform plots of adjacent coffee trees at Santa (1,750 m) in 2003 and 2004 and Bafou (1,820 m) in 2004 and 2005. The logistic model provided good fit of the epidemics temporal dynamics. The spatial distribution of CBD over time indicated that plants in a plot were contaminated stepwise from the first infected coffee tree. An analysis of semi-variograms and the disease dispersal maps obtained by kriging revealed primary infection foci at both sites. They were observed from the 8th to the 10th week after flowering at Bafou and from the 11th to the 13th week at Santa. CBD affected the entire plots 3 weeks after the foci first appeared. These results suggest that inoculum from previous epidemics survives at points in the initial foci in a coffee plantation.

Yield stability in clones of Coffea canephora in the short and medium term: longitudinal data analyses and measures of stability over time

In perennial crops like coffee, genetic improvement efficiency is limited by several factors. These include determining the acceptable minimum observation period for yield traits, and also variation of the traits over time, in order to develop breeding objectives that incorporate stability and persistence of the desired traits. Yield data from a trial comparing 20 Coffea canephora clones in Ivory Coast, monitored over nine production years, were analyzed by two different methods. (1) After studying genetic correlations between yields in successive years, longitudinal data analyses were applied to understand relationships between years. Several models were tested and the Compound Symmetry model, with heterogeneous variances (CSH model), best described the data structure. For instance, at tree level, correlations between yields of the different years were moderately stable, which revealed a major tree effect within clones. (2) Subsequently, derived index traits were considered, characterizing yield distribution over the different years. The traits involved were earliness, alternation, and the intensity of variations between years. Despite a marked tendency towards biennial cropping, especially in the early years, the estimated genetic correlations between years, and between individual years and cumulative yield were generally high. The intensity of the relative differences between yields in successive years was heritable only in the second production cycle. Despite some clonal differences in yield-stability variables, clonal yields in single years or groups of years evidently reflected both cumulative yields and comparative yield stability.

Effect of cultural practices on the development of arabica coffee berry disease, caused by Colletotrichum kahawae

In the high altitude regions of Africa, coffee berry disease (CBD), caused by Colletotrichum kahawae, is the main constraint for arabica coffee (Coffea arabica) production. However, certain agricultural practices can reduce losses caused by the disease and thereby promote optimum production. On small family farms in Cameroon, mixed cropping with fruit trees, intercropping with food crops and maintenance pruning of coffee trees are very widespread agricultural practices that can affect CBD epidemics. Consequently, an epidemiological study was conducted to assess how cultural practices affected the disease in an arabica coffee smallholding in Cameroon. The disease was monitored on a weekly basis over four successive years (2002–2005) on coffee trees in diverse cultural situations. Cultural practices likely to reduce losses due to CBD were identified. The infection rate was significantly lower on coffee trees grown intensively than on coffee trees grown in the traditional manner. Coffee trees located under the shade of fruit trees were significantly less attacked than those located in full sunlight. In addition, berries on the leafless parts of branches, near the main trunk of the coffee tree, were less infected than those on leafy sections. These results show that maintenance pruning, removal of mummified berries, and mixed cropping with shade plants are cultural practices which create environmental conditions that limit CBD development.

Spatial and temporal analysis of coffee wilt disease caused by Fusarium xylarioides in Coffea canephora

Coffee wilt disease (CWD) caused by Fusarium xylarioides, considered to be a soil-inhabiting fungus, is endemic in several African countries, affecting commercially important coffee species and causing serious economic losses. Coffee wilt disease development in naturally infected Coffea canephora fields at the Coffee Research Institute in Uganda was assessed from April 2001 to March 2006 to generate information about temporal and spatial spread of the disease. Maps of diseased trees were also generated from the data. Semi-variance analysis was performed on the data to show the spatio-temporal structure of disease. Host influence on the spatio-temporal structure was deduced from the distribution pattern of diseased and healthy trees and analysis of variance. Results show that the temporal disease epidemic progress was slow. The disease was found to spread from initial infections to healthy neighbouring trees, resulting in an aggregated pattern. An infected tree could infect up to three healthy trees away, in any direction. Disease foci formed and expanded with time, coalescing but punctuated in spots planted with resistant hosts. There were varying levels of susceptibility among host genotypes, affecting the rates and levels of epidemic development. The implications of the findings to the control of CWD are discussed.

Influence of host resistance and phenology on South American leaf blight of the rubber tree with special consideration of temporal dynamics

South American leaf blight (SALB), the most dangerous disease of the rubber tree, is responsible for the lack of significant natural rubber production in South America and is a major threat to rubber tree plantations in Asia and Africa. Although the selection of resistant clones is the preferred disease control method, greater knowledge is required of the relationship between host and pathogen, in order to construct more durable resistance. Based on small-scale trials, this study set out to compare the dynamics of SALB on two highly susceptible and one moderately susceptible clone and to analyse the effect of host phenology on disease severity, at leaflet and flush scales. Clonal resistance was found to have a noticeable effect on disease severity, asexual sporulation and stromatal density at both leaflet and flush levels, and on disease dynamics at a leaflet level; time for symptom and sporulation appearance were longer on the moderately susceptible clone than on the susceptible clones. On the moderately susceptible clone, the stromatal density was largely dependent on disease severity. The phenology did not differ among the three clones and could not be considered as a factor in genetic resistance to SALB. However, for the three clones, the position of the leaflet in the flush affected the duration of the immature stages and the disease: the shorter the duration of leaflet development, the lower the disease severity, the sporulation intensity and the stromatal density.

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.

Relations between several traits linked to sexual plant reproduction in Theobroma cacao L.: number of ovules per ovary, number of seeds per pod, and seed weight

Tropical perennial plants cultivated outside their place of origin call for major germplasm characterization and prebreeding work. For cacao breeding, the selection process has to optimize the weight of cacao beans produced per tree by increasing the number of pods produced, the number of seeds per pod (NoSP), and the mean weight of seeds produced (SW). NoSP and SW were studied over nine consecutive years in a collection of more than 200 clones. The number of ovules per ovary (NoOV) was also examined in a subsample of this collection in order to evaluate the ability to predict NoSP. NoSP and SW showed a relatively normal distribution with heritabilities of 0.29 and 0.51, respectively. The composite trait “mean seed weight per pod” showed a generalized extreme value distribution of intermediate heritability (0.43). NoSP and SW were found to be genetically independent. NoOV was highly heritable (h2 = 0.810), but it did not provide good prediction of NoSP. The largest seeds were observed in genotypes derived from crosses between cultivated cacao trees, which had been formerly domesticated. Domestication therefore favored seed size, while for the other traits examined, similar variation was found between wild and domesticated populations.