A method based on haplotype analysis offers insights into tomato history and domestication

Recently, scientists from Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana have provided further insights into tomato history and domestication using Procrustes analysis and automatic classification (Fig. 1).

In this study, scientists developed a novel method for performing genome-wide haplotype analysis by combining Procrustes-aligned PCoA output with automatic unsupervised classification. This new method enabled detailed, quantitative inspection of the haplotype composition of each accession and population. The haplotype PCoA results, in agreement with those of fastStructure, suggested the existence of three haplotype types (hPe, hEc, and hSL) related to the main tomato taxonomic groups.

The new analysis method based on Procrustes and automatic haplotype classification allowed the researchers to propose a new hypothesis for the complex evolution of wild and cultivated tomato plants. The wild populations were Peruvian and Ecuadorian Solanum pimpinellifolium and Mesoamerican Solanum lycopersicum var. cerasiforme (SLC). After migrating back to Ecuador and Peru, SLC was domesticated, and the Mexican Solanum lycopersicum var. lycopersicum was derived from these improved materials. This model is backed by traditional population genetic indexes, parametric statistical models, morphological and passport data, and the new haplotype analysis. The researchers identified genomic regions associated with the latitudinal migration experienced by tomato plants that will be useful for adapting currently cultivated varieties to new latitudes, particularly in a world affected by climate change. “Similar approaches can be used to study the complex domestication histories of other species,” Prof. Jose Blanca said.

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Reference

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

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

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

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

About Dr. Jose Blanca

Prof. Jose Blanca works at Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana and has published 160 papers to date.