• Characterization of the Genomic Changes producing during the Plant Domestication using XVIII Century Floral Crops as Model Organisms.

We want to use floral crops as a model for plant domestication, specifically plants that were domesticated during the XVIII century after the botanical expeditions to South America. There are several reasons to use them as a model: Flowers are easy to phenotype; The source of these species is well documented in the archives of several botanical gardens; Most of the breeding history is well know; They contains accessions representing common events during the breeding of these plants such as hybrids and polyploids and introgressions with other wild species; The selection process is comparable along different species from different clades (they have been selected for the same traits); Finally they have relatively small genome sizes (between 300 Mb and 1.2 Gb) that makes applicable most of the genomic tools such as whole genome re-sequencing. Our primary objective is to characterize the genetic and genomic changes produced during the domestication and breeding of three popular ornamental plants: Petunias (Petunia hybrida), gloxinias (Sinningia speciosa) and begonias (several species and hybrids such as Begonia x semperflorens).

Specific objectives are:

1. Evaluate the genetic diversity in the wild and in the domesticated accessions to find the genetic bottlenecks during the domestication.
2. Characterize the genetic history of specific popular accessions in terms of polyploidization, hybridization and introgression of other species using Whole Genome Resequencing (WGR).
3. Identify regions selected during the domestication by Quantitative Trait Loci (QTL) analysis of a segregant population of wild/domesticated crosses.
4. Identify positive selected genes during the domestication using RNASeq expression analysis.
5. Evaluate the genomic instability based in the transposon movements during the process of intensive breeding and hybridization with other species.
6. Characterize the role of the epigenetic regulation during the process of intensive breeding and hybridization.
7. Integrate the previous results to create a model about the contribution of gene selection, gene lost, gene conversions, transposon movements and epigenetic regulations to the phenotypic diversity during domestication.

Our studies about the domestication of the species Sinningia speciosa have revealed that the possible founder of the cultivated accessions are populations from the Rio de Janerio area (Avenida Niemeyer) 150 years ago.

 Figure 1: A- Co-ancestry map representing the genetic relationships between Sinningia accessions. Wild and domesticated clusters are highlighted with a purple and blue squares respectively. The closest wild accession to the domesticated lines is marked with a purple arrow (“Avenida Niemeyer”). B- Pictures of the wild accessions “Buzios” (top-left) and “Avenida Niemeyer” (top-right) and the domesticated single corolla “Empress” (bottom-left) and “Blue Knight” (bottom-right) representing the phenotypic diversity in the species.