Identification, analysis and mapping of SNP markers in Theobroma cacao

The identification and analysis of genetic markers serves as the foundation for Marker Assisted Selection.  To this end a Theobroma cacao single nucleotide polymorphism (SNP) discovery project was undertaken to create saturated genetic maps to guide genome assembly and to benefit cacao breeders worldwide.  Over 48,000 high quality SNPs were identified from RNA of 15 individual cacao lines, representing the 10 genetically diverse groups of cacao.  These SNPs have been filtered for various purposes including the creation of a 6k Illumina Infinium genotyping SNP chip.  With this Infinium chip 1,152 individual cacao plants representing different mapping populations were genotyped.  Genetic recombination maps were generated and compared to previously published microsatellite based genetic maps as well as the position of QTLs identified for both types of maps.  Allele calls and Minor Allele Frequencies estimated from the short read sequencing used to identify SNPs are evaluated with regards to the observed SNP chip genotypic data.  Furthermore, genotype data has been characterized to isolate different subsets of SNP markers (e.g. unique to a diversity group).    SNP markers identified in this, and similar, SNP discovery projects can be directly converted into easily assayable markers for cacao breeders using a variety of assay platforms of low to high throughput.  The ability to assay SNPs in cacao growing regions will positively impact cacao breeders throughout the world.