title: Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits.
abstract: Genome-wide association studies have been successful in identifying genes involved in polygenic traits and are valuable for crop improvement. Tomato (Solanum lycopersicum) is a major crop and is highly appreciated worldwide for its health value. We used a core collection of 163 tomato accessions composed of S. lycopersicum, S. lycopersicum var cerasiforme, and Solanum pimpinellifolium 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.
authors.affiliation: Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.) christopher.sauvage@avignon.inra.fr.
authors.forename: Christopher
authors.initials: C
authors.lastname: Sauvage
authors.affiliation: Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.).
authors.forename: Vincent
authors.initials: V
authors.lastname: Segura
authors.affiliation: Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.).
authors.forename: Guillaume
authors.initials: G
authors.lastname: Bauchet
authors.affiliation: Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.).
authors.forename: Rebecca
authors.initials: R
authors.lastname: Stevens
authors.affiliation: Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.).
authors.forename: Phuc Thi
authors.initials: PT
authors.lastname: Do
authors.affiliation: Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.).
authors.forename: Zoran
authors.initials: Z
authors.lastname: Nikoloski
authors.affiliation: Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.).
authors.forename: Alisdair R
authors.initials: AR
authors.lastname: Fernie
authors.affiliation: Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.).
authors.forename: Mathilde
authors.initials: M
authors.lastname: Causse