Identification of Candidate Genes Involved in Witches’ Broom Disease Resistance in a Segregating Mapping Population of Theobroma cacao L. in Brazil

Witches’ broom disease (WBD) caused by the fungus Moniliophthora perniciosa is responsible for considerable economic losses for cacao producers in the Americas. Protective fungicides are ineffective, and disease management involving repeated phytosanitary removals increases labor costs.  The best alternative would be the use of resistant cultivars. Resistance may be governed by one or a few genetic factors, mainly found in wild germplasm. We discuss the development of a dense genetic linkage map, which contains 3,526 SNP and has a length of 852.8 cM, based on 459 trees of a cross between a resistant genotype ‘TSH 1188’ and a tolerant genotype ‘CCN 51’ at the Mars Center for Cocoa Science (MCCS) in Barro Preto, Bahia, Brazil. Furthermore, we describe the identification of seven QTL on five different chromosomes associated with WBD using a multi-trait QTL analysis for outbreeders, and problems encountered during the QTL mapping process. We identified various potential candidate genes, which may be involved in different steps in disease resistance, such as pathogen recognition, activation of reactive oxygen species (ROS), the mitogen-activated protein kinase (MAPK) pathway, and the ubiquitin/26S proteasome-mediated pathway. Some of the candidate genes may also be involved in salicylic acid (SA)-dependent signaling versus jasmonic acid (JA) and ethylene (ET) signaling, given the hemibiotrophic nature of the fungus.