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.