Identification and mapping of conserved ortholog set (COS) II sequences of cacao and their conversion to SNP markers for marker-assisted selection in Theobroma cacao and comparative genomics studies

Abstract

Theobroma cacao (cacao) is a tree cultivated in the tropics around the world for its seeds that are the source of both chocolate and cocoa butter. Genetic marker development for marker-assisted selection (MAS) is critical for the success of cacao breeding for disease resistance and yield. To develop conserved ortholog set II (COSII) single-nucleotide polymorphism (SNP) markers for MAS in cacao, we have used three strategies and three types of cacao genetic and sequence data to identify and map 98 cacao COSII genes. The resources available at the time these studies were first undertaken dictated the strategy utilized. For the first strategy, SNPs were identified using cacao expressed sequence tags homologous to COSII sequences. Strategy II utilized a leaf transcriptome of cacao genotype "Matina 1-6" and Strategy III the genomic sequence of a 3-Mb region of "Matina 1-6" linkage group 5 associated with an important quantitative trait locus (QTL) for resistance to black pod. We have identified SNP markers for 83 of the 98 mapped COSII genes, and 19 of these SNP markers co-locate with QTLs. These COSII SNP markers, the first identified for cacao, will be used for genotyping and off-typing in cacao breeding programs and employed for genetic mapping and syntenic studies to trace co-location of genes regulating traits of importance between cacao and other species. © 2011 Springer-Verlag (outside the USA).