title: Efficiently tracking selection in a multiparental population: the case of earliness in wheat.
abstract: Multiparental populations are innovative tools for fine mapping large numbers of loci. Here we explored the application of a wheat Multiparent Advanced Generation Inter-Cross (MAGIC) population for QTL mapping. This population was created by 12 generations of free recombination among 60 founder lines, following modification of the mating system from strict selfing to strict outcrossing using the ms1b nuclear male sterility gene. Available parents and a subset of 380 SSD lines of the resulting MAGIC population were phenotyped for earliness and genotyped with the 9K i-Select SNP array and additional markers in candidate genes controlling heading date. We demonstrated that 12 generations of strict outcrossing rapidly and drastically reduced linkage disequilibrium to very low levels even at short map distances and also greatly reduced the population structure exhibited among the parents. We developed a Bayesian method, based on allelic frequency, to estimate the contribution of each parent in the evolved population. To detect loci under selection and estimate selective pressure, we also developed a new method comparing shifts in allelic frequency between the initial and the evolved populations due to both selection and genetic drift with expectations under drift only. This evolutionary approach allowed us to identify 26 genomic areas under selection. Using association tests between flowering time and polymorphisms, 6 of these genomic areas appeared to carry flowering time QTL, 1 of which corresponds to Ppd-D1, a major gene involved in the photoperiod sensitivity. Frequency shifts at 4 of 6 areas were consistent with earlier flowering of the evolved population relative to the initial population. The use of this new outcrossing wheat population, mixing numerous initial parental lines through multiple generations of panmixia, is discussed in terms of power to detect genes under selection and association mapping. Furthermore we provide new statistical methods for use in future analyses of multiparental populations.
authors.affiliation: Université Paris-Sud, Unité Mixte de Recherche 0320/Unité Mixte de Recherche 8120, Génétique Végétale, F-91190 Gif-sur-Yvette, France Institut National de la Recherche Agronomique, Unité Mixte de Recherche 0320/Unité Mixte de Recherche 8120, Génétique Végétale, F-91190 Gif-sur-Yvette, France stephanie.thepot@gmail.com.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Thépot
authors.affiliation: Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8079, Université Paris-Sud, Orsay, France.
authors.forename: Gwendal
authors.initials: G
authors.lastname: Restoux
authors.affiliation: Institut National de la Recherche Agronomique, Unité Mixte de Recherche 0320/Unité Mixte de Recherche 8120, Génétique Végétale, F-91190 Gif-sur-Yvette, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Goldringer
authors.affiliation: Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1313 Génétique Animale et Biologie Intégrative, F-78352 Jouy en Josas, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Hospital
authors.affiliation: Arvalis, Institut du Végétal, Station Expérimentale, F-91720 Boigneville, France.
authors.forename: David
authors.initials: D
authors.lastname: Gouache
authors.affiliation: National Institute of Agricultural Botany, Huntingdon Road, Cambridge CB3 0LE, United Kingdom.
authors.forename: Ian
authors.initials: I
authors.lastname: Mackay
authors.affiliation: Institut National de la Recherche Agronomique, Unité Mixte de Recherche 0320/Unité Mixte de Recherche 8120, Génétique Végétale, F-91190 Gif-sur-Yvette, France.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Enjalbert
mesh_terms: D000465:Algorithms; D000483:Alleles; D032461:Chromosomes, Plant; D003433:Crosses, Genetic; D019143:Evolution, Molecular; D005787:Gene Frequency; D005828:Genetics, Population; D055106:Genome-Wide Association Study; D005838:Genotype; D008957:Models, Genetic; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D014908:Triticum / Q000235:genetics*
keywords: MPP; Multiparent Advanced Generation Inter-Cross (MAGIC); QTL detection; experimental evolution; multiparental populations; parental contribution; recombinant population; selection detection