Building genomic resources for Theobroma cacao

Theobroma cacao L (cacao: Malvaceae) is a small tree endemic to the Amazonian rain forest, where it most likely evolved.  Cacao persists in populations of naturally outcrossing and inbreeding plants, as it is a species with a complex system of self-incompatibility, where only a fraction of the population is able to self-fertilize. Through a collaboration involving Stanford University, MARS and the USDA, we are generating full genome sequence data of 150 accessions to investigate the evolutionary history of cacao and identify the genetic basis of phenotypic traits of interest. Only a small group of cacao plants have been used for breeding programs worldwide, thus identifying genomic resources among natural accessions of cacao that could be of use in breeding programs is of uttermost importance. We present the advances and challenges of this project, emphasizing the importance of the identification of plants with reliable phenotyping and appropriate genotyping with microsatellite or single nucleotide polymorphism (SNP) data prior to sequencing. Preliminary results from the relative measures of heterozygosity among the accessions sequenced to date suggest that cacao is a highly diverse population, with around five SNPs per kilobase per individual. Our estimates of inbreeding, from microsatellite data, suggest that different populations undergo different degrees of selfing with rates that vary from 0.25 to 0.9, consistent with the range of inbreeding coefficients (F) estimated from individually sequenced genomes. This project highlights the utility of generating genomic resources for arboreal crops.