A phylogenetic framework to study desirable traits in the wild relatives of Theobroma cacao (Malvaceae)

• Published in: Journal of systematics and evolution : JSE 2024-09, Vol.62 (5), p.963-978
• Main Authors: Bossa‐Castro, Ana M., Colli‐Silva, Matheus, Pirani, José R., Whitlock, Barbara A., Morales Mancera, Laura T., Contreras‐Ortiz, Natalia, Cepeda‐Hernández, Martha L., Di Palma, Federica, Vives, Martha, Richardson, James E.
• Format: Article
• Language: English
• Subjects: Agronomy; Bayesian analysis; cacao; Chocolate; Climate change; Cocoa; crop wild relatives; Evolution; Evolutionary genetics; Genera; Genetic diversity; Herrania; Malvaceae; morphological and molecular characters; Morphology; Nucleotide sequence; Phylogenetics; Phylogeny; Theobroma; Theobroma cacao; trait evolution; Wild type
• ISSN: 1674-4918; 1759-6831
• DOI: 10.1111/jse.13045

Crop wild relatives (CWRs) of cultivated species may provide a source of genetic variation that can contribute to improving product quantity and quality. To adequately use these potential resources, it is useful to understand how CWRs are related to the cultivated species and to each other to determine how key crop traits have evolved and discover potentially usable genetic information. The chocolate industry is expanding and yet is under threat from a variety of causes, including pathogens and climate change. Theobroma cacao L. (Malvaceae), the source of chocolate, is a representative of the tribe Theobromateae that consists of four genera and c. 40 species that began to diversify over 25 million years ago. The great diversity within the tribe suggests that its representatives could exhibit advantageous agronomic traits. In this study, we present the most taxonomically comprehensive phylogeny of Theobromateae to date. DNA sequence data from WRKY genes were assembled into a matrix that included 56 morphological characters and analyzed using a Bayesian approach. The inclusion of a morphological data set increased resolution and support for some branches of the phylogenetic tree. The evolutionary trajectory of selected morphological characters was reconstructed onto the phylogeny. This phylogeny provides a framework for the study of morphological and physiological trait evolution, which can facilitate the search for agronomically relevant traits. In this study, we aimed to reconstruct the phylogeny of the Theobromateae tribe with as many species as possible using WRKY DNA sequence and morphological data from herbarium specimens. We characterize the evolutionary trajectory of morphological characters and provide a framework that permits the study of crop wild relatives and the evolution of key agronomic traits in cacao and its wild relatives.