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Population Genomics of microorganisms and their hosts in health and disease Current Research

Cacao Tree (Theobroma cacao) evolutionary genomics

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).

Previous work of our collaborator Juan Carlos Motamayor has shown that there are at least 10 main groups of genetically differentiated populations of cacao. This work has been based on the analysis of microsatellite markers. We are leveraging these results to inform strategies to characterize genomic variation in cacao.

We are developing cacao as a model system for how to understand the process of domestication and map complex traits in long-lived tropical trees where generating multi generational mapping populations is not feasible.

We are developing analyses on 200 accessions of Theobroma cacao sequenced at Stanford University to understand the evolutionary history of cacao and develop cacao into a system to investigate the evolution of genomic architecture. Any student interested in plant population genomics should not doubt in contacting me as there are several aspects of this project that will perfectly fit a PhD thesis. We are working in collaboration with the University of West Indies and the Cocoa Research Center, as well as the USDA to gather phenotypic information for all accessions sequenced and we plan on performing genome wide association studies aimed at identifying the genes responsible for differences in phenotypes of interest that range from disease susceptibility to cotyledon size and productivity in broad sense.

We are developing analyses on 200 accessions of Theobroma cacao sequenced at Stanford University to understand the evolutionary history of cacao and develop cacao into a system to investigate the evolution of genomic architecture. Any student interested in plant population genomics should not doubt in contacting me as there are several aspects of this project that will perfectly fit a PhD thesis. We are working in collaboration with the University of West Indies and the Cocoa Research Center, as well as the USDA to gather phenotypic information for all accessions sequenced and we plan on performing genome wide association studies aimed at identifying the genes responsible for differences in phenotypes of interest that range from disease susceptibility to cotyledon size and productivity in broad sense.

We are interested in leveraging this incredible dataset to explore basic population genetic questions:

  1. What is the evolutionary history of the domesticated cacao and the natural populations of T. cacao?
  2. Are there regional process and local process of selection working similarly in multiple populations of cacao in the Amazon Basin?
  3. What is the effect of inbreeding and selfing on the mutational load of cacao?
  4. What are the differences in the rate of evolution of methylation target sites CpG, CpH, CpHpH sites in plant genomes?
  5. How does recombination, mutation and selection in the context of populations with variable number of selfing individuals contribute to shape genomic variation, defining the genome architecture of the species?

Anthurium andraeanum functional genomics

In collaboration with Dr. Pathmanathan Umaharan at the University of West Indies in Trinidad and Tobago we are initiating a project aimed at understanding the genetic bases that determine spathe color in the flowers of Anthurium andraeanum a plant of the Araceae family. These plants are economically important in tropical countries because of the great interest that the breeders have in developing new colors or selecting colors that result valuable in the flower market. In addition, and perhaps of broader interest, these plants have been suggested to be efficient at removing pollutants like formaldehyde, xylene, toluene, and ammonia.

Development of genomic resources for crops of interest

Our lab has established a partnership with Corpoica (Colombia, South America), the institution equivalent to the ARCs (Agricultural Research Centers) in order to develop genomic resources aimed at improving crops of interest like cacao (Theobroma cacao), oil palm (Elaeis guineensis, Elaeis oleifera and hybrids), “uchuva” fruit (Physalis peruviana). Additionally we maintain a collaboration to generate genomic resources for important pathogens of crops in the region, specially Moniliophthora roreri.

Relevant publications