A Core Set of SNPs for Cacao Genotyping

Theobroma cacao L. (cacao) is an understory tropical tree whose fermented seeds are the source of cocoa butter and cocoa for chocolate production.  Breeding programs to improve disease resistance and productivity in cacao depend on the correct genotyping of breeding material and accessions in germplasm collections, which has been done with microsatellite markers.  Due to the platform dependence of such markers, it has not been possible to produce widely agreed upon reference genotypes, which has significantly hindered breeding progress.

We produced a 6k Illumina Infinium SNP chip from SNPs called from transcriptome sequence data (exons) of genetically diverse individuals.  We genotyped 19 individuals that represented the breadth of genetic diversity in cacao and filtered this data to identify SNPs that occurred in single copy genes, had high minor allele frequencies, were evenly distributed across the 10 linkage groups of cacao based on mapping to the Matina1-6 genome sequence, and, when possible, caused an amino acid change in the coding sequence.

From this filtering process, we are proposing a core set of 100 SNPs, 10 per linkage group, to be used in genotyping the germplasm collections and the material used in breeding programs around the world so that a single, verifiable reference genotype will be available for the majority of identified cultivars.  Because SNPs are platform independent, both low and high throughput methods can be used to assay the complete core set or informative subsets based on the needs of the germplasm curator or breeder.