Genotyping of cacao (Theobroma cacao L.) germplasm resources with SNP markers linked to agronomic traits reveals signs of selection

Abstract

The Amazonian cacao tree or the chocolate tree (Theobroma cacao L.) is cultivated to produce seeds, the valuable raw material for the chocolate industry. However, cacao yield is hampered by diseases and low productivity. Cacao single nucleotide polymorphism (SNP) markers associated with breeding and adaptive traits provide a genetic tool for improving selection and reducing breeding cycles. Here, we genotyped 40 published SNPs associated with disease resistance and 11 SNPs with yield traits in 346 accessions using the MassARRAY® system. These 51 SNPs were identified in different breeding experiments in Costa Rica, Brazil, and Trinidad and Tobago. Four genetic clusters were identified, and two of them were observed in high proportion in managed cacao, characterized by a high proportion of admixed individuals reflecting the man-made hybrids. One cluster overrepresented in managed cacao is associated with the preference to keep superior flavor in cultivated cacao from Criollo ancestry. Introgression of wild material collected in Peru associated with disease resistance to witches’ broom disease (WBD) was also observed. Underutilized genetic resources were observed in managed cacao such as the Guiana cacao, while previous agronomic evaluation has demonstrated its good yield potential. Yield and disease resistance traits (mainly resistance to WBD) show divergence between wild and managed cacao (FST > 0.05) probably reflecting selection during domestication, cultivation, and breeding efforts. Eleven SNPs showed a divergence between wild and managed cacao and can be used to build breeding populations. New collections of wild cacao followed by agronomic evaluations can broaden the genetic base of cultivated cacao, especially for such traits as disease resistance to frosty pod rot (FPR).