Identification of a major QTL in cocoa (Theobroma cacao L.) associated with resistance to witches' broom disease

The witches’ broom disease caused by the fungus Crinipellis perniciosa is the main limiting factor for cocoa production in South America and the Caribbean. In Brazil, this disease affects almost all cocoa‐growing regions, causing serious economic, social and ecological damage. The aim of this study was to map genomic regions associated with resistance to C. perniciosa using an F₂ population derived from a cross between ‘Scavina‐6’(resistant) and ‘ICS‐1’(susceptible). The phenotypic index was determined as the average number of vegetative witches’ brooms per canopy area of each plant, the witches’ brooms were counted and eliminated during six field evaluations between May 1998 and August 1999. A total of 124 random amplified polymorphic DNA (RAPD) and 69 amplified fragment length polymorphism (AFLP) markers were mapped along 25 linkage groups covering 1713 cM of cocoa genome. After employing single factor and composite interval mapping analyses, a major quantitative trait loci (QTL) flanked by the marker AV14.940 was identified in the linkage group 11, explaining almost 35% of the resistance to witches’ broom. The present result suggests that this QTL acts as a major dominant component of resistance to this pathogen, with great potential for use in marker‐assisted selection procedures in cocoa breeding programmes.