title: A comprehensive study of the genomic differentiation between temperate Dent and Flint maize.
abstract: Dent and Flint represent two major germplasm pools exploited in maize breeding. Several traits differentiate the two pools, like cold tolerance, early vigor, and flowering time. A comparative investigation of their genomic architecture relevant for quantitative trait expression has not been reported so far. Understanding the genomic differences between germplasm pools may contribute to a better understanding of the complementarity in heterotic patterns exploited in hybrid breeding and of mechanisms involved in adaptation to different environments.
  
  
  
  We perform whole-genome screens for signatures of selection specific to temperate Dent and Flint maize by comparing high-density genotyping data of 70 American and European Dent and 66 European Flint inbred lines. We find 2.2 % and 1.4 % of the genes are under selective pressure, respectively, and identify candidate genes associated with agronomic traits known to differ between the two pools. Taking flowering time as an example for the differentiation between Dent and Flint, we investigate candidate genes involved in the flowering network by phenotypic analyses in a Dent-Flint introgression library and find that the Flint haplotypes of the candidates promote earlier flowering. Within the flowering network, the majority of Flint candidates are associated with endogenous pathways in contrast to Dent candidate genes, which are mainly involved in response to environmental factors like light and photoperiod. The diversity patterns of the candidates in a unique panel of more than 900 individuals from 38 European landraces indicate a major contribution of landraces from France, Germany, and Spain to the candidate gene diversity of the Flint elite lines.
  
  
  
  In this study, we report the investigation of pool-specific differences between temperate Dent and Flint on a genome-wide scale. The identified candidate genes represent a promising source for the functional investigation of pool-specific haplotypes in different genetic backgrounds and for the evaluation of their potential for future crop improvement like the adaptation to specific environments.
authors.affiliation: Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany.
authors.forename: Sandra
authors.initials: S
authors.lastname: Unterseer
authors.affiliation: Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany.
authors.forename: Saurabh D
authors.initials: SD
authors.lastname: Pophaly
authors.affiliation: Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany.
authors.forename: Regina
authors.initials: R
authors.lastname: Peis
authors.affiliation: Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany.|Present Address: Institute for Crop Science and Plant Breeding, Bavarian State Research Center, 85354, Freising, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Westermeier
authors.affiliation: Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany.
authors.forename: Manfred
authors.initials: M
authors.lastname: Mayer
authors.affiliation: Plant Genome and System Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Seidel
authors.affiliation: Plant Genome and System Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany.
authors.forename: Georg
authors.initials: G
authors.lastname: Haberer
authors.affiliation: Plant Genome and System Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany.
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.affiliation: Misión Biológica de Galicia, Spanish National Research Council (CSIC), 36080, Pontevedra, Spain.
authors.forename: Bernardo
authors.initials: B
authors.lastname: Ordas
authors.affiliation: Animal Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany.
authors.forename: Hubert
authors.initials: H
authors.lastname: Pausch
authors.affiliation: Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany.
authors.forename: Aurélien
authors.initials: A
authors.lastname: Tellier
authors.affiliation: Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany.
authors.forename: Eva
authors.initials: E
authors.lastname: Bauer
authors.affiliation: Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany. chris.schoen@tum.de.
authors.forename: Chris-Carolin
authors.initials: CC
authors.lastname: Schön
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D001947:Breeding; D035264:Flowers / Q000235:genetics* / Q000254:growth & development; D056726:Genetic Association Studies; D018745:Genome, Plant; D005838:Genotype; D015810:Linkage Disequilibrium; D010641:Phenotype; D040641:Quantitative Trait Loci / Q000235:genetics*; D012641:Selection, Genetic; D003313:Zea mays / Q000235:genetics* / Q000254:growth & development
keywords: Dent; Flint; Genome-wide screen; Genomics; Landraces; Maize; Population genetics; Selection