Identification of marker-trait associations for self-compatibility in a segregating mapping population of Theobroma cacao L.

Increasing yield, quality, and disease resistance are important objectives for cacao breeding programs. Yield reduction in material improved for other traits is one of the main constraints caused by self-incompatibility (SI). Genes regulating SI in cacao have not been identified; therefore, knowledge of the location of genetic markers for and the effects of alleles determining SI will be useful for selecting uniformly self-compatible cultivars with higher yields. In a mapping population originating from a cross between a self-incompatible clone, Pound-7, and a self-compatible clone, UF-273, we observed important differences in flower retention at 15, 21, and 28 days after pollination. Our results suggest that the best time to measure flower retention is 15 days after pollination or later and that selecting self-compatibility (SC) thresholds is genotype specific. Using marker-trait association analysis we identified one marker, mTcCIR222, strongly associated with SC, as well as three surrounding markers (mTcCIR168, mTcCIR115 and mTcCIR158), all located near the proximal end of linkage group 4. These markers are currently being tested in our marker-assisted selection program.