Evolutionary aspects of wild potatoes (section Petota, Solanum L., Solanaceae) from the Southern Cone of South America

Abstract

Solanum section Petota comprises all tuber-bearing potato species, including the cultivated potato (S. tuberosum) and more than one hundred wild relatives that represent valuable genetic resources for crop improvement. Despite the ecological and agronomic importance of wild triploids, their evolutionary origin and genome organization remain poorly understood. In particular, the processes underlying the origin of natural triploids and the effects of triploidization on genome evolution have not been comprehensively investigated. This thesis aimed to investigate the origin and evolutionary history of natural triploids of Solanum chacoense, S. commersonii and S. malmeanum, as well as to characterize the dynamics of their repetitive DNA fraction following triploidization. To achieve these objectives, phylogenetic analyses based on complete plastid genomes, 35S and 5S ribosomal DNA, low-copy nuclear genes, and genotyping-by-sequencing (GBS) data were integrated with molecular cytogenetics and comparative repeatome analyses using the RepeatExplorer pipeline. Comparative phylogenetic analyses revealed that triploids originated through multiple independent evolutionary events involving distinct maternal and paternal lineages. Different categories of triploids were identified, including interspecific allotriploids involving S. chacoense, S. commersonii and S. malmeanum, as well as intraspecific autotriploids of S. commersonii and S. malmeanum. These lineages exhibited distinct geographic distributions, indicating that triploidization has occurred repeatedly during the recent evolutionary history of southern South American wild potatoes. Comparative repeatome analyses demonstrated that triploid genomes consistently contain a larger repetitive fraction than their diploid counterparts. This increase was primarily associated with the expansion of LTR retrotransposons, particularly the Tekay lineage of the Ty3/Gypsy superfamily, together with changes in the abundance of tandem repeats and a proportional reduction in DNA transposons. These findings indicate that triploidization is accompanied by extensive remodeling of the repetitive genome fraction, contributing to genome diversification among closely related species. Overall, this thesis demonstrates that natural triploids in Solanum section Petota have multiple independent origins and that triploidization is associated with repeatome remodeling, providing new insights into the evolutionary dynamics of polyploid genomes. By integrating phylogenomics, cytogenetics, population genomics, and repeatome analyses, this work establishes a comprehensive framework for investigating genome evolution in wild polyploid plants while generating knowledge directly applicable to potato breeding and the conservation of wild genetic resources.