Genome-wide association in tomato Reveals 44 candidate loci for fruit metabolic traits
2014
Sauvage, Christopher | Segura, Vincent | Bauchet, Guillaume | Stevens, Rebecca | Do, Phuc Thi | Nikoloski, Zoran | Fernie, Alisdair R | Causse, Mathilde | Génétique et Amélioration des Fruits et Légumes (GAFL) ; Institut National de la Recherche Agronomique (INRA) | Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF) ; Institut National de la Recherche Agronomique (INRA) | Faculty of Biology ; Vietnam National University | Max Planck Institute of Molecular Plant Physiology (MPI-MP) ; Max-Planck-Gesellschaft | Syngeta Seeds | European Union [PL016214-2]
Genome-wide association studies have been successful in identifying genes involved in polygenic traits and are valuable for crop improvement. Tomato ([i]Solanum lycopersicum[/i]) is a major crop and is highly appreciated worldwide for its health value. We used a core collection of 163 tomato accessions composed of [i]S. lycopersicum,[/i] [i]S. lycopersicum var cerasiforme[/i], and [i]Solanum pimpinellifolium[/i] to map loci controlling variation in fruit metabolites. Fruits were phenotyped for a broad range of metabolites, including amino acids, sugars, and ascorbate. In parallel, the accessions were genotyped with 5,995 single-nucleotide polymorphism markers spread over the whole genome. Genome-wide association analysis was conducted on a large set of metabolic traits that were stable over 2 years using a multilocus mixed model as a general method for mapping complex traits in structured populations and applied to tomato. We detected a total of 44 loci that were significantly associated with a total of 19 traits, including sucrose, ascorbate, malate, and citrate levels. These results not only provide a list of candidate loci to be functionally validated but also a powerful analytical approach for finding genetic variants that can be directly used for crop improvement and deciphering the genetic architecture of complex traits
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