Plant Population Genomics

 

Evolutionary genomics of Theobroma cacao, the chocolate tree

Theobroma cacao L (cacao: Malvaceae) is a small tree endemic to the amazonian rain forest, where it most likely evolved, and it persists in natural populations of naturally interbreeding plants (and inbreeding plants, as it is a species with a complex system of self-incompatibility, where a fraction of the population is able to self-fertilize).

We have developed cacao as a genomics model system suitable to understand the process of domestication of trees and understand how arboreal species adapt to changing environments. We have developed genomic resources for over 200 accessions of Theobroma cacao. Our work shows 10 major genetic groups that contribute to most of the genetic variability in cacao, consistent with previous observations.

Domestication of the Chocolate Tree

We identified for the fist time the most closely related population (Curaray) to domesticated cacao (cacao Criollo), using genomic data. We used this information to estimate the time of domestication and founding population size of domesticated cacao. Our analyses are congruent with archaeological data suggesting that domestication of cacao occurred around 3600 years ago from a few hundred individuals.

Genetic cost of domestication in arboreal crops

The “cost of domestication” hypothesis states that the process of domestication of wild species results in an increase in the number and frequency of deleterious mutations that are fixed or segregating in the genomes of domesticated species. We showed that Theobroma cacao has an increased proportion of deleterious and tolerated mutations in the domesticated Criollo population, but more importantly, we show that the increase in genetic ancestry of the domesticated Criollo in cultivated hybrids is associated to decrease fitness (productivity of beans). Our current efforts are focused on trying to understand if Hill-Robertson effects can explain the general phenomenon.

Relevant publications