Use of the Matina 1-6 Cacao Genome Sequence to Identify Marker-Trait Associations for Witches' Broom Resistance in Theobroma cacao L

Increasing yield, quality and disease resistance are important objectives for cacao breeding programs. In the main production areas, yields are reduced by diseases and pests that differ in each of the production areas. Black pod rot (Phytophtora spp) causes significant losses in all production areas. In the Americas, more specifically, frosty pod (Moniliophthora roreri) and witches’ broom (M. perniciosa) produce significant losses. We recently identified associations between simple sequence repeat (SSR) markers and witches’ broom (WB) resistance (cushion brooms, more specifically) using a segregating mapping population at the Mars Center for Cocoa Science (Brazil) between ‘TSH-1188’ (WB resistant) and ‘CCN-51’ (WB susceptible). A subset of 282 trees was genotyped using several hundred SSR markers, and phenotypic data was collected during 2008 and 2009. The resulting genetic linkage map was composed of 185 SSRs. Significant associations for cushion brooms were identified on linkage groups 4 and 9.  Use of 3,251 SNP markers, obtained via the cacao genome sequencing program, led to the creation of a more densely populated genetic map based on 461 trees. Further strategies, such as phasing of the parents and the offspring in order to reduce the size of the associated regions will be presented. The goal is to identify markers for Marker-Assisted-Breeding, and ultimately identify candidate genes involved in witches’ broom resistance.