Tracing the roots of tomato domestication: Novel study unravels genetic journey from wild ancestors to global cultivation

Domestication has transformed wild plants to suit human needs, leading to crops with altered traits.  In tomatoes, studies focus on the wild Solanum pimpinellifolium (SP) and its relation to the domesticated Solanum lycopersicum (SL), including two botanical varieties, S.l. var. lycopersicum (SLL) and S.l. var. cerasiforme (SLC). Tomato has a complex history of domestication. Traditional genetic analysis methods, such as genetic diversity and linkage disequilibrium, offer limited insights due to their simplicity and potential misleading nature. Sophisticated statistical models present alternatives but has its own limitations. Moreover, the paucity of linguistic and historical evidence hinders full understanding of tomato domestication. Consequently, current research struggles to coherently integrate molecular, morphological, and passport data into a unified domestication model for tomatoes.

In February 2022, Horticulture Research published a research article entitled by “Haplotype analyses reveal novel insights into tomato history and domestication driven by long-distance migrations and latitudinal adaptations”.  

In this study, the researchers employed a unique approach involving haplotype principal coordinate analyses (PCoAs) and unsupervised automatic classification with Procrustes alignment to understand the domestication history of tomato. This method divided the euchromatic region of the entire tomato genome into multiple segments, resulting in numerous haplotypes. These haplotypes were subsequently classified into three types (hPe, hEc, hSL) corresponding to the main taxonomic groups of tomatoes. Genetic diversity within these haplotype types was assessed and showed that SP Pe as the most diverse population for hPe, SP Ec for hEc, and Mesoamerican SLC for hSL. This diversity corresponds with the ancestral populations suggested by other genetic analyses like fastStructure and TreeMix. The study also explored gene flow and introgression patterns, revealing that Ecuadorian and Peruvian SLC populations might have originated from SLC in Mesoamerica, with subsequent introgressions from local SP populations. Further, the research conducted detailed morphological analysis,  including ecological and morphological data from accession collection sites, and assessed the haplotype composition of each population. It showed significant genetic and morphological diversity among SP, SLC, and Solanum lycopersicum var. lycopersicum (SLL) populations. Also, genes associated with photosynthesis and flowering time were selected for during latitudinal migration. Analyses of genetic diversity, linkage disequilibrium (LD), and morphological traits indicated a two-step domestication process, with Peruvian domesticated SLCs migrating north to Mexico and evolving into SLL.

In summary, this study provides deep insights into the complex history of tomato domestication by using a novel method combining Procrustes-aligned PCoA output with automatic unsupervised classification. The model developed challenges previous assumptions and aligns with all available genetic, morphological, and geographical data. It underscores the intricate journey of tomato domestication from South American SP populations to the globally cultivated varieties of today, offering valuable insights for future research crop domestication and adaptation studies.

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References

Authors

Jose Blanca^1,*, David Sanchez-Matarredona¹, Peio Ziarsolo¹, Javier Montero-Pau¹, Esther van der Knaap^2,3, Ma José Díez¹ and Joaquín Cañizares¹

Affiliations

¹Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, COMAV, Universitat Politècnica de València, Valencia 46022, Spain

²Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA

³Department of Horticulture, University of Georgia, Athens, GA 30602, USA