Marker-assisted farmer participatory selection of cacao (Theobroma cacao L.) – progress and challenges

Cacao (Theobroma cacao L.) is an important tropical crop that provides raw materials for chocolate industries. Farmer participatory selection is highly suitable for small-scale and resources-poor farmers and is complementary to centralized breeding programs in cacao producing countries. Recent progress in the development of cacao genomic resources has allowed the use of high-throughput SNP genotyping technology to backstop participatory selection. The applications included accurate genotype identification and elimination of redundancy among farmer selections, understanding on-farm genetic diversity, assessment of general combinability of parental clones through inference of parentage and sib-ship and rational deployment of new selections in rehabilitation programs. Our recent case studies showed that single nucleotide polymorphism (SNP) is a highly promising tool for marker-assisted participatory selection due to its efficiency and cost. However linking key agronomic traits in farmer selections with a small core set of SNP markers remains the main challenge.  Moreover, the large genotype x environment interaction and low heritability traits which are difficult for farmer to observe, such as tolerance to abiotic stress and flavor, call for the development of resources in cacao phenomics.