SNP markers associated with resistance to frosty pod and black pod rot diseases in an F1 population of Theobroma cacao L

Economically, cacao ( Theobroma cacao L.) is a major tropical commodity for the Americas; however, severe losses due to Moniliophthora roreri (Cif. and Par.), which causes frosty pod rot (FPR), and Phytophthora spp., which causes black pod rot (BPR), have reduced cacao production in the Americas. The objectives of this study are to (i) re-confirm the QTL using different marker set; (ii) discover new QTL associated with FPR and BPR resistance using SNP markers; and (iii) find genes in the candidate QTL regions. At CATIE in Turrialba, Costa Rica, an F 1 mapping population of cacao was obtained by crossing “POUND 7,” a clone moderately susceptible to FPR and resistant to BPR, with “UF 273,” resistant to FPR and highly susceptible to BPR. A total of 179 F 1 progeny were fingerprinted with 5149 SNP markers and a dense linkage map composed of 10 linkage groups was developed using 2910 polymorphic SNP markers. Also segregating F 1 trees were screened for resistance to FPR and BPR diseases. Seven QTL previously reported on chromosomes 2, 7, and 8 for FPR resistance and on chromosomes 4, 8, and 10 for BPR resistance were confirmed. Additionally, eight QTL were identified for FPR resistance (chromosomes 4, 9, and 10) and BPR resistance (chromosome 2). The expression of genes commonly associated with plant defense and disease resistance that are located within the identified QTL was confirmed.