title: Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and association panels.
abstract: Quantitative trait loci (QTL) have been identified using traditional linkage mapping and positional cloning identified several QTLs. However linkage mapping is limited to the analysis of traits differing between two lines and the impact of the genetic background on QTL effect has been underlined. Genome-wide association studies (GWAs) were proposed to circumvent these limitations. In tomato, we have shown that GWAs is possible, using the admixed nature of cherry tomato genomes that reduces the impact of population structure. Nevertheless, GWAs success might be limited due to the low decay of linkage disequilibrium, which varies along the genome in this species. Multi-parent advanced generation intercross (MAGIC) populations offer an alternative to traditional linkage and GWAs by increasing the precision of QTL mapping. We have developed a MAGIC population by crossing eight tomato lines whose genomes were resequenced. We showed the potential of the MAGIC population when coupled with whole genome sequencing to detect candidate single nucleotide polymorphisms (SNPs) underlying the QTLs. QTLs for fruit quality traits were mapped and related to the variations detected at the genome sequence and expression levels. The advantages and limitations of the three types of population, in the context of the available genome sequence and resequencing facilities, are discussed.
authors.affiliation: INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France.
authors.forename: Laura
authors.initials: L
authors.lastname: Pascual
authors.affiliation: INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France.
authors.forename: Elise
authors.initials: E
authors.lastname: Albert
authors.affiliation: INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France.
authors.forename: Christopher
authors.initials: C
authors.lastname: Sauvage
authors.affiliation: INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France.
authors.forename: Janejira
authors.initials: J
authors.lastname: Duangjit
authors.affiliation: INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France.
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Bouchet
authors.affiliation: INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France.
authors.forename: Frédérique
authors.initials: F
authors.lastname: Bitton
authors.affiliation: INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France.
authors.forename: Nelly
authors.initials: N
authors.lastname: Desplat
authors.affiliation: INRA, US1279, Etude du Polymorphisme des Génomes végétaux (EPGV), CEA-IG/CNG, 2 rue Gaston Crémieux, 91057 Evry, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Brunel
authors.affiliation: INRA, US1279, Etude du Polymorphisme des Génomes végétaux (EPGV), CEA-IG/CNG, 2 rue Gaston Crémieux, 91057 Evry, France.
authors.forename: Marie-Christine
authors.initials: MC
authors.lastname: Le Paslier
authors.affiliation: INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Ranc
authors.affiliation: Vilmorin S.A. - Groupe Limagrain, Centre de Recherche de La Costière, Route de Meynes, 30210 Ledenon, France.
authors.forename: Laure
authors.initials: L
authors.lastname: Bruguier
authors.affiliation: Vilmorin S.A. - Groupe Limagrain, Centre de Recherche de La Costière, Route de Meynes, 30210 Ledenon, France.
authors.forename: Betty
authors.initials: B
authors.lastname: Chauchard
authors.affiliation: Vilmorin S.A. - Groupe Limagrain, Centre de Recherche de La Costière, Route de Meynes, 30210 Ledenon, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Verschave
authors.affiliation: INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France. Electronic address: mathilde.causse@avignon.inra.fr.
authors.forename: Mathilde
authors.initials: M
authors.lastname: Causse
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D032461:Chromosomes, Plant / Q000235:genetics; D003433:Crosses, Genetic; D018703:Founder Effect; D005638:Fruit / Q000235:genetics; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D007178:Inbreeding; D018551:Solanum lycopersicum / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: Fruit quality; Genome-wide association; QTL mapping; Resequencing; Tomato