Agradecimentos: The authors would like to thank the Comissão Nacional de Desenvolvimento Científico e Tecnológico (CNPq), FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DA BAHIA - FAPESB (FAPESB), FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP (FAPESP, 2008/53197-4), Banco do Nordeste Brasileiro (BNB), Comissão Executiva do Plano da Lavoura Cacaueira (CEPLAC), Universidade Estadual de Campinas (UNICAMP), Universidade Estadual de Santa Cruz (UESC), and COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPES (PROCAD-UESC, Computacional Biology Program) for the grants provided for this research, FAPESP for the PhD fellowship to CBCS (2010/0354-2, 2012/11109-0), and CNPq for the PhD fellowships to MAB, JRBFR and ESLS and for the research fellowships awarded to AAFG and APS. The authors would also like to thank the researchers from UNICAMP, UESC, MCCS and CEPLAC for supplying the physical structure required to perform this study. Additionally, the authors would like to thank Fernanda Bispo and Ademilde Cerqueira for assistance with black pod phenotyping, and Dr. Karina Gramacho for her invaluable help during the correction of the manuscript Ver menos

The cacao tree (Theobroma cacao L.) is a species of great importance because cacao beans are the raw material used in the production of chocolate. However, the economic success of cacao is largely limited by important diseases such as black pod, which is responsible for losses of up to 30–40% of the global cacao harvest. The discovery of resistance genes could extensively reduce these losses. Therefore, the aims of this study were to construct an integrated multipoint genetic map, align polymorphisms against the available cacao genome, and identify quantitative trait loci (QTLs) associated with resistance to black pod disease in cacao. The genetic map had a total length of 956.41 cM and included 186 simple sequence repeat (SSR) markers distributed among 10 linkage groups. The physical “in silico” map covered more than 200 Mb of the cacao genome. Based on the mixed model predicted means of Phytophthora evaluation, a total of 6 QTLs were detected for Phytophthora palmivora (1 QTL), Phytophthora citrophthora (1 QTL), and Phytophthora capsici (4 QTLs). Approximately 1.77–3.29% of the phenotypic variation could be explained by the mapped QTLs. Several SSR marker-flanking regions containing mapped QTLs were located in proximity to disease regions. The greatest number of resistance genes was detected in linkage group 6, which provides strong evidence for a QTL. This joint analysis involving multipoint and mixed-model approaches may provide a potentially promising technique for detecting genes resistant to black pod and could be very useful for future studies in cacao breeding Ver menos