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Deciphering the genetic footprints of domestication in Solanaceae: Understanding the past to
foresee the future.
Arnoux S., Duboscq R., Causse M., Sauvage C.
INRA, UR 1052 Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, 67 Allée des Chênes
CS60094, 84143 Montfavet Cedex, France.
Key words: Domestication, Solanaceae, Evolutionary history, Genomic.
The process of domestication started with the shift from hunter/gatherer to agrarian societies.
Plants were selected for crop farming based on specific phenotypes. This stringent selection often results
in a genetic bottleneck that marked the genome. Much remains unknown about the demographic history
that occurred during crop domestication. My project focuses on detecting these footprints and
reconstructing statistically the evolutionary history of 3 major species of Solanaceae (pepper, eggplant
and tomato) of economically and scientific interest.
To unravel the domestication process of the Solanaceae family, I will compare the genome wide
patterns of nucleotide diversity between wild species with their domesticated homologs to pinpoint the
intra-specific differences. Then, I will use the population genetic estimators of diversity to infer their
evolutionary history via coalescence theory. I am planning to infer the most probable models with the
ðaði software (diffusion approximation for demographic inference) to estimate parameters such as
migration rate or strength of the domestication bottleneck. Finally, I will compare the evolutionary
history inter-specifically to determine if the most probable scenarios are converging in Solanaceae or if
it is species-specific.
Our genetic data are samples coming from domesticated and cultivated populations as well as
outgroup species. I focus on the genetic variations of the coding regions filtered from RNAseq data. My
preliminary results reveal yet a genetic likeness of the crop compared to their wild relatives, going along
with a genome wide nucleotide diversity decrease in these 3 crop species. With this comparative
analyses I expect to highlight genes part of pathways that are involved in phenotypic traits that were
selected through domestication.
My project aims to facilitate the future of Solanaceae breeding by gaining a better understanding
of the foregoing evolutionary process of domestication. It will improve the knowledge on crop wild
relatives’ diversity source for breeding companies.