Consumer concerns about food safety have been translated into policy in consuming countries, including pesticide residues in cocoa. Such policy changes have an impact on cocoa producers and other supply chain stakeholders, as they have to comply with legislation or risk losing lucrative markets. Consequently, development and implementation of best practice for pesticide use is critical, but major challenges exist in-country. The chapter provides an overview of pesticide use in cocoa-producing countries and the challenge of improving pesticide regulation, before moving on to consider the development of best practice for pesticide use. The chapter provides detailed case studies on establishing baselines, promoting awareness and developing a holistic approach. Finally, the chapter looks ahead to future research trends and provides guidance for further reading in this area.

Frosty pod rot (FPR), caused by the basidiomycete Moniliophthora roreri, is a devastating disease of cacao. First discovered in Ecuador in 1917, FPR is present in the main cacao producing countries of Southern and Central America, except Brazil (López & Enríquez, 5; Evans, 3) but it has not been previously reported in the Caribbean. In August 2016, unusual symptoms were observed on cacao pods on farms in Crooked River located in the parish of Clarendon in Jamaica. Examination of affected pods and fungal spores by officers of the Research and Development Division (Ministry of Industry, Commerce, Agriculture and Fisheries) led to a tentative diagnosis of FPR. Following this discovery, infected pods were dispatched to the CABI Diagnostic and Advisory Service, Egham, United Kingdom for examination and analysis. Symptoms typical of FPR (Evans, 2) were observed, namely necrotic lesions, white fungal mycelium and cream/beige sporulation on the pod surface (Fig. 1) along with extensive brown necrosis of the internal pod tissues (Fig. 2). Spore samples were removed from the surface of pods with a sterile needle and tissue samples aseptically excised from both the surface tissues and internal pod tissues. Samples were plated on tap water agar, potato dextrose agar (PDA) and 2% malt extract agar (MEA) and incubated at 25°C. Emergent fungal colonies were purified by sub-culturing. Morphological characteristics of sporulating fungal colonies on MEA and PDA after 5 to 7 days growth were indicative of those of M. roreri as described previously (Evans, 2). DNA was extracted from selected colonies using MicrolysisPlus (Microzone Ltd, UK), amplified by PCR, purified and sequenced on the AB3130 Genetic Analyzer (Applied Biosystems, USA). For cultures derived from spore samples, the internal transcribed spacer and large subunit regions of the rDNA were amplified with primer pairs TW81/AB28 (Curran et al., 1) and NL1/NL4 (Kurtzman & Robnett, 4), respectively. For cultures derived from pod tissues, the translation elongation factor region was amplified using primer pair EF1T/EF2T (O'Donnell & Cigelnik, 6). Comparison of resulting sequences with representative sequences available in the ‘Fungi’ database of the European Molecular Biology Laboratory European Bioinformatics Institute using the FASTA algorithm confirmed the presence of M. roreri in cultures derived from all spore and tissue (99-100% homology). Two isolates were deposited in the CABI Genetic Resources Collection as IMI506582 and IMI506584. Reference sequences were deposited in Genbank as Accession Nos. MF139030 (IMI506582), MF139031 (IMI506584), MF139032, MF139033 and MF139034. Fine flavour cocoa is one of Jamaica's traditional export crops with an estimated 11,000 smallholders producing cacao commercially on holdings of less than 2 hectares. It is an important cash crop for farming communities in rural Jamaica as more than a quarter of the population in the cacao-producing parishes are living below the national poverty line. In 2016, Jamaica exported over USD 1.4 million in cacao and derivatives, which represents a significant source of income for cacao farmers. More than half of the cacao produced in Jamaica comes from Clarendon Parish and as such FPR will have a devastating impact. Efforts are underway to determine extent of the spread of the disease in Clarendon and surrounding parishes in an effort to isolate and manage it with a view to eradication. This is the first confirmed report of FPR on cacao in the Caribbean.

Variation of 45 Gibberella xylarioides cultures isolated from coffee trees in Africa was assessed by sequencing the partial translation elongation factor gene, by A + T rich DNA restriction fragment length polymorphism (RFLP) analysis and by inter-simple sequence repeat polymerase chain fingerprinting. Results were analysed in relation to host plant species and mating compatibilities to determined biological species (BS). Additionally, five “historical” strains isolated prior to the 1990s, and considered to belong to G. xylarioides , were obtained from internationally-recognised culture collections and a further 10 strains of various Gibberella / Fusarium spp., isolated from Coffea spp., were included to provide contextual comparisons. Ribosomal intergenic spacer (IGS) sequencing was undertaken for representatives of the suggested BS. Results confirmed all strains as G. xylarioides and that strains of sterile group 4 (SG4) may represent one or more additional “cryptic” species. ISSR fingerprints showed a single host correlated difference, suggesting stable clonal spread and this was supported by consistent A + T rich DNA band patterns for all strains. In contrast the IGS sequences identified potential phylogenetic events correlated to BS.

ABSTRACT Coffee is vital to the economy of East and Central Africa, providing a major source of foreign exchange earnings and, as a cash crop, supporting the livelihoods of millions involved in cultivation, processing, marketing, and export. Coffee wilt disease (CWD), attributed to Gibberella xylarioides (Fusarium xylarioides), has caused losses to coffee production in Africa since 1927 but has been largely contained through the use of host resistance and in some instances wide-scale sanitation practices. A reemergence of CWD on Coffea canephora (Robusta coffee) in Uganda, Democratic Republic of Congo, and Tanzania has already led to heavy losses and threatens future production in these countries and elsewhere in the region. The relevance of CWD is all the more pertinent given the impact of a considerable fall in world coffee prices over the last decade. Recent research has clarified the extent of the problem in the region and revealed a low level of diversity within the pathogen, suggesting that two genetically and biologically distinct forms are responsible for current problems. These findings and related research and development initiatives undertaken under the auspices of the Regional Coffee Wilt Programme are of fundamental importance in providing an urgently needed solution to this devastating disease.