Ancient genomes shed light on common bean (Phaseoulus vulgaris) spatio-temporal patterns of domestication in South America.

LARI M.; NANNI L.; XU C.; BABOT M.P; NEME, G; CARAMELLI D.; BOESSENKOOL S.; TRUCCHI E.; VAI S.; BELLUCCI E.; BENAZZO A.; LEMA V.; IOB A.; BITOCCHI E; GIL A.; DE LORENZI M.; JACKSON S. A.; DE BOER H.; OLISZEWSKI, O; BERTORELLE G.; MICHIELI T.; STAR B.; PAPA R.

Montpellier

Congreso; II Joint Congress on Evolutionary Biology; 2018

Investigating the domestication history of cultivated plants in different geographic areas is relevant to understanding human history, human-induced changes in plant genomes, and local adaptations to new environments, and it can help protecting crop genetic and phenotypic diversity. Genomic analyses on modern common bean (P. vulgaris) accessions indicate that two major genetic pools can be associated to Mesoamerica and the Andes, supporting the hypothesis of two independent domestication events occurred approximately 8,000 years ago. To investigate the process of domestication in the Andes, we extracted high quality DNA in 19 seeds from Northern Argentinian archeological sites, we radiocarbon dated them between 600 and 6,000 years ago, and we sequenced their genomes with coverage between 1 and 18X. All the seeds showed a domestication-associated phenotype. Using a panel of modern genomes, which included wild and domesticated samples from Central and South America, we find that ancient seeds have not their closest relatives among the modern varieties cultivated in the same region today. On the contrary, they show higher genetic similarity to modern accessions commonly found in Chile, possibly as a consequence of ancient trades or ancestral traits sharing. Ancient seeds cluster in one genetic group indicating that these varieties i) were likely the product of a single domestication event, which could be dated before 6,000 years ago, and ii) were cultivated in that area without major transitions at least until the Spanish colonization of South America. Whole genomes allowed us to investigate the different levels of similarity and dissimilarity between modern (wild and domestic) and ancient seeds at different genes, with the final goal to study the dynamic and the genetic basis of the phenotypic changes occurred during domestication.