title: Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts.
abstract: Through the local selection of landraces, humans have guided the adaptation of crops to a vast range of climatic and ecological conditions. This is particularly true of maize, which was domesticated in a restricted area of Mexico but now displays one of the broadest cultivated ranges worldwide. Here, we sequenced 67 genomes with an average sequencing depth of 18x to document routes of introduction, admixture and selective history of European maize and its American counterparts. To avoid the confounding effects of recent breeding, we targeted germplasm (lines) directly derived from landraces. Among our lines, we discovered 22,294,769 SNPs and between 0.9% to 4.1% residual heterozygosity. Using a segmentation method, we identified 6,978 segments of unexpectedly high rate of heterozygosity. These segments point to genes potentially involved in inbreeding depression, and to a lesser extent to the presence of structural variants. Genetic structuring and inferences of historical splits revealed 5 genetic groups and two independent European introductions, with modest bottleneck signatures. Our results further revealed admixtures between distinct sources that have contributed to the establishment of 3 groups at intermediate latitudes in North America and Europe. We combined differentiation- and diversity-based statistics to identify both genes and gene networks displaying strong signals of selection. These include genes/gene networks involved in flowering time, drought and cold tolerance, plant defense and starch properties. Overall, our results provide novel insights into the evolutionary history of European maize and highlight a major role of admixture in environmental adaptation, paralleling recent findings in humans.
authors.affiliation: Génétique Quantitative et Evolution - Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France.
authors.forename: Jean-Tristan
authors.initials: JT
authors.lastname: Brandenburg
authors.affiliation: Génétique Quantitative et Evolution - Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France.|UMR 518 AgroParisTech/INRA, France.
authors.forename: Tristan
authors.initials: T
authors.lastname: Mary-Huard
authors.affiliation: Institute of Plant Sciences Paris-Saclay, UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, France.
authors.forename: Guillem
authors.initials: G
authors.lastname: Rigaill
authors.affiliation: CIMMYT (International Maize and Wheat Improvement Centre), El Batan, Texcoco, Edo de Mexico, Mexico.
authors.forename: Sarah J
authors.identifier: 0000-0003-2015-2450
authors.initials: SJ
authors.lastname: Hearne
authors.affiliation: Génétique Quantitative et Evolution - Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Corti
authors.affiliation: Génétique Quantitative et Evolution - Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France.
authors.forename: Johann
authors.identifier: 0000-0002-5353-5100
authors.initials: J
authors.lastname: Joets
authors.affiliation: Génétique Quantitative et Evolution - Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France.
authors.forename: Clémentine
authors.initials: C
authors.lastname: Vitte
authors.affiliation: Génétique Quantitative et Evolution - Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Charcosset
authors.affiliation: Génétique Quantitative et Evolution - Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France.
authors.forename: Stéphane D
authors.identifier: 0000-0003-0758-9930
authors.initials: SD
authors.lastname: Nicolas
authors.affiliation: Génétique Quantitative et Evolution - Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France.
authors.forename: Maud I
authors.initials: MI
authors.lastname: Tenaillon
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D005060:Europe; D017343:Genes, Plant / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics; D005843:Geography; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008957:Models, Genetic; D010802:Phylogeny; D000069600:Plant Breeding / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D014481:United States; D003313:Zea mays / Q000145:classification / Q000235:genetics*