Lobell DB, Tebaldi C. Getting caught with our plants down: the risks of a global crop yield slowdown from climate trends in the next two decades. Environ Res Lett. 2014;9:074003.
Article
Google Scholar
Smith CW, Betrán J, Runge ECA. Corn: origin, history, technology, and production. 1st ed. Hoboken, NJ: John Wiley & Sons Inc.; 2004.
Google Scholar
Brown WL, Anderson E. The northern flint corn. Ann Mo Bot Gard. 1947;34:1–28.
Article
Google Scholar
Rebourg C, Chastanet M, Gouesnard B, Welcker C, Dubreuil P, Charcosset A. Maize introduction into Europe: the history reviewed in the light of molecular data. Theor Appl Genet. 2003;106:895–903.
CAS
PubMed
Google Scholar
Dubreuil P, Dufour P, Krejci E, Causse M, deVienne D, Gallais A, et al. Organization of RFLP diversity among inbred lines of maize representing the most significant heterotic groups. Crop Sci. 1996;36:790–9.
Article
Google Scholar
Bauer E, Falque M, Walter H, Bauland C, Camisan C, Campo L, et al. Intraspecific variation of recombination rate in maize. Genome Biol. 2013;14:R103.
Article
PubMed
PubMed Central
Google Scholar
Giraud H, Lehermeier C, Bauer E, Falque M, Segura V, Bauland C, et al. Linkage disequilibrium with linkage analysis of multiline crosses reveals different multiallelic QTL for hybrid performance in the flint and dent heterotic groups of maize. Genetics. 2014;198:1717–34.
Article
PubMed
PubMed Central
Google Scholar
Nielsen R. Molecular signatures of natural selection. Annu Rev Genet. 2005;39:197–218.
Article
CAS
PubMed
Google Scholar
Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics. 1983;105:437–60.
CAS
PubMed
PubMed Central
Google Scholar
Tajima F. Statistical-method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123:585–95.
CAS
PubMed
PubMed Central
Google Scholar
Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C. Genomic scans for selective sweeps using SNP data. Genome Res. 2005;15:1566–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, Schaffner SF, et al. Detecting recent positive selection in the human genome from haplotype structure. Nature. 2002;419:832–7.
Article
CAS
PubMed
Google Scholar
Voight BF, Kudaravalli S, Wen XQ, Pritchard JK. A map of recent positive selection in the human genome. PLoS Biol. 2006;4:446–58.
Article
CAS
Google Scholar
Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, et al. Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet. 2013;45:884–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ, Absher D, et al. Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 2009;19:826–37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Qanbari S, Gianola D, Hayes B, Schenkel F, Miller S, Moore S, et al. Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. BMC Genomics. 2011;12:318.
Article
PubMed
PubMed Central
Google Scholar
Hufford MB, Xu X, van Heerwaarden J, Pyhäjärvi T, Chia JM, Cartwright RA, et al. Comparative population genomics of maize domestication and improvement. Nat Genet. 2012;44:808–U118.
Article
CAS
PubMed
Google Scholar
Jiao YP, Zhao HN, Ren LH, Song WB, Zeng B, Guo JJ, et al. Genome-wide genetic changes during modern breeding of maize. Nat Genet. 2012;44:812–U124.
Article
CAS
PubMed
Google Scholar
Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, et al. Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc Natl Acad Sci U S A. 2002;99:9650–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yamasaki M, Tenaillon MI, Bi IV, Schroeder SG, Sanchez-Villeda H, Doebley JF, et al. A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell. 2005;17:2859–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Unterseer S, Bauer E, Haberer G, Seidel M, Knaak C, Ouzunova M, et al. A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array. BMC Genomics. 2014;15:823.
Article
PubMed
PubMed Central
Google Scholar
Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, et al. Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet. 2012;44:803–7.
Article
CAS
PubMed
Google Scholar
Camus-Kulandaivelu L, Veyrieras JB, Madur D, Combes V, Fourmann M, Barraud S, et al. Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene. Genetics. 2006;172:2449–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Revilla P, Rodríguez VM, Ordás A, Rincent R, Charcosset A, Giauffret C, et al. Cold tolerance in two large maize inbred panels adapted to European climates. Crop Sci. 2014;54:1981–91.
Article
Google Scholar
Chardon F, Virlon B, Moreau L, Falque M, Joets J, Decousset L, et al. Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genetics. 2004;168:2169–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, et al. The genetic architecture of maize flowering time. Science. 2009;325:714–8.
Article
CAS
PubMed
Google Scholar
Colasanti J, Yuan Z, Sundaresan V. The indeterminate gene encodes a zinc finger protein and regulates a leaf-generated signal required for the transition to flowering in maize. Cell. 1998;93:593–603.
Article
CAS
PubMed
Google Scholar
Muszynski MG, Dam T, Li B, Shirbroun DM, Hou Z, Bruggemann E, et al. Delayed flowering1 encodes a basic leucine zipper protein that mediates floral inductive signals at the shoot apex in maize. Plant Physiol. 2006;142:1523–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Salvi S, Tuberosa R, Chiapparino E, Maccaferri M, Veillet S, van Beuningen L, et al. Toward positional cloning of Vgt1, a QTL controlling the transition from the vegetative to the reproductive phase in maize. Plant Mol Biol. 2002;48:601–13.
Article
CAS
PubMed
Google Scholar
Vladutu C, McLaughlin J, Phillips RL. Fine mapping and characterization of linked quantitative trait loci involved in the transition of the maize apical meristem from vegetative to generative structures. Genetics. 1999;153:993–1007.
CAS
PubMed
PubMed Central
Google Scholar
Chen C, DeClerck G, Tian F, Spooner W, McCouch S, Buckler E. PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants. PLoS One. 2012;7:e46596.
Article
CAS
PubMed
PubMed Central
Google Scholar
Danilevskaya ON, Meng X, Hou Z, Ananiev EV, Simmons CR. A genomic and expression compendium of the expanded PEBP gene family from maize. Plant Physiol. 2008;146:250–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dong Z, Danilevskaya O, Abadie T, Messina C, Coles N, Cooper M. A gene regulatory network model for floral transition of the shoot apex in maize and its dynamic modeling. PLoS One. 2012;7:e43450.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ducrocq S, Madur D, Veyrieras JB, Camus-Kulandaivelu L, Kloiber-Maitz M, Presterl T, et al. Key impact of Vgt1 on flowering time adaptation in maize: evidence from association mapping and ecogeographical information. Genetics. 2008;178:2433–7.
Article
PubMed
PubMed Central
Google Scholar
Xu J, Liu Y, Liu J, Cao M, Wang J, Lan H, et al. The genetic architecture of flowering time and photoperiod sensitivity in maize as revealed by QTL review and meta analysis. J Integr Plant Biol. 2012;54:358–373.
Article
CAS
PubMed
Google Scholar
Romay MC, Millard MJ, Glaubitz JC, Peiffer JA, Swarts KL, Casstevens TM, et al. Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol. 2013;14:R55.
Article
PubMed
PubMed Central
Google Scholar
Castelletti S, Tuberosa R, Pindo M, Salvi S. A MITE transposon insertion is associated with differential methylation at the maize flowering time QTL Vgt1. G3 (Bethesda). 2014;4:805–12.
Article
CAS
Google Scholar
McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, et al. Genetic properties of the maize nested association mapping population. Science. 2009;325:737–40.
Article
CAS
PubMed
Google Scholar
Lehermeier C, Krämer N, Bauer E, Bauland C, Camisan C, Campo L, et al. Usefulness of multiparental populations of maize (Zea mays L.) for genome-based prediction. Genetics. 2014;198:3–16.
Article
PubMed
PubMed Central
Google Scholar
Mikel MA. Availability and analysis of proprietary dent corn inbred lines with expired US plant variety protection. Crop Sci. 2006;46:2555–60.
Article
Google Scholar
Mikel MA, Dudley JW. Evolution of North American dent corn from public to proprietary germplasm. Crop Sci. 2006;46:1193–205.
Article
Google Scholar
Flint-Garcia SA, Thuillet AC, Yu J, Pressoir G, Romero SM, Mitchell SE, et al. Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J. 2005;44:1054–64.
Article
CAS
PubMed
Google Scholar
Nelson PT, Coles ND, Holland JB, Bubeck DM, Smith S, Goodman MM. Molecular characterization of maize inbreds with expired US plant variety protection. Crop Sci. 2008;48:1673–85.
Article
Google Scholar
Barrière Y, Alber D, Dolstra O, Lapierre C, Motto M, Ordas A, et al. Past and prospects of forage maize breeding in Europe: II. History, germplasm evolution and correlative agronomic changes. Maydica. 2006;51:435–49.
Google Scholar
Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution. 1984;38:1358–70.
Article
Google Scholar
Parat F, Schwertfirm G, Rudolph U, Miedaner T, Korzun V, Bauer E, et al. Geography and end use drive the diversification of worldwide winter rye populations. Mol Ecol. 2016;25:500–14.
Article
PubMed
Google Scholar
Qanbari S, Pausch H, Jansen S, Somel M, Strom TM, Fries R, et al. Classic selective sweeps revealed by massive sequencing in cattle. PLoS Genet. 2014;10:e1004148.
Article
PubMed
PubMed Central
Google Scholar
Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, et al. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat Genet. 2012;44:212–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stephan W. Genetic hitchhiking versus background selection: the controversy and its implications. Philos Trans R Soc Lond B Biol Sci. 2010;365:1245–53.
Article
PubMed
PubMed Central
Google Scholar
Charlesworth B, Morgan MT, Charlesworth D. The effect of deleterious mutations on neutral molecular variation. Genetics. 1993;134:1289–303.
CAS
PubMed
PubMed Central
Google Scholar
Hudson RR, Kaplan NL. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics. 1985;111:147–64.
CAS
PubMed
PubMed Central
Google Scholar
Zeng K, Fu YX, Shi SH, Wu CI. Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics. 2006;174:1431–9.
Article
PubMed
PubMed Central
Google Scholar
Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, et al. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 2004;37:914–39.
Article
CAS
PubMed
Google Scholar
Zhou M, Zhang Q, Wang C, Chen L, Sun Z, Zhu X, et al. Characterization of genes involved in isoprenoid diphosphate biosynthesis in maize. J Plant Growth Regul. 2015;34:294–308.
Article
CAS
Google Scholar
van Schie CC, Ament K, Schmidt A, Lange T, Haring MA, Schuurink RC. Geranyl diphosphate synthase is required for biosynthesis of gibberellins. Plant J. 2007;52:752–62.
Article
PubMed
Google Scholar
Degen T, Dillmann C, Marion-Poll F, Turlings TC. High genetic variability of herbivore-induced volatile emission within a broad range of maize inbred lines. Plant Physiol. 2004;135:1928–38.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kollner TG, Held M, Lenk C, Hiltpold I, Turlings TC, Gershenzon J, et al. A maize (E)-beta-caryophyllene synthase implicated in indirect defense responses against herbivores is not expressed in most American maize varieties. Plant Cell. 2008;20:482–94.
Article
PubMed
PubMed Central
Google Scholar
Trzcinska-Danielewicz J, Bilska A, Fronk J, Zielenkiewicz P, Jarochowska E, Roszczyk M, et al. Global analysis of gene expression in maize leaves treated with low temperature I. Moderate chilling (14 °C). Plant Sci. 2009;177:648–58.
Article
CAS
Google Scholar
Sobkowiak A, Jonczyk M, Jarochowska E, Biecek P, Trzcinska-Danielewicz J, Leipner J, et al. Genome-wide transcriptomic analysis of response to low temperature reveals candidate genes determining divergent cold-sensitivity of maize inbred lines. Plant Mol Biol. 2014;85:317–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yan SP, Zhang QY, Tang ZC, Su WA, Sun WN. Comparative proteomic analysis provides new insights into chilling stress responses in rice. Mol Cell Proteomics. 2006;5:484–96.
Article
CAS
PubMed
Google Scholar
Hung HY, Shannon LM, Tian F, Bradbury PJ, Chen C, Flint-Garcia SA, et al. ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. Proc Natl Acad Sci U S A. 2012;109:E1913–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Salvi S, Sponza G, Morgante M, Tomes D, Niu X, Fengler KA, et al. Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc Natl Acad Sci U S A. 2007;104:11376–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Danilevskaya ON, Meng X, Ananiev EV. Concerted modification of flowering time and inflorescence architecture by ectopic expression of TFL1-like genes in maize. Plant Physiol. 2010;153:238–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kobayashi Y, Kaya H, Goto K, Iwabuchi M, Araki T. A pair of related genes with antagonistic roles in mediating flowering signals. Science. 1999;286:1960–2.
Article
CAS
PubMed
Google Scholar
Koornneef M, Hanhart CJ, van der Veen JH. A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana. Mol Gen Genet. 1991;229:57–66.
Article
CAS
PubMed
Google Scholar
Hanano S, Goto K. Arabidopsis TERMINAL FLOWER1 is involved in the regulation of flowering time and inflorescence development through transcriptional repression. Plant Cell. 2011;23:3172–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hirsch CN, Foerster JM, Johnson JM, Sekhon RS, Muttoni G, Vaillancourt B, et al. Insights into the maize pan-genome and pan-transcriptome. Plant Cell. 2014;26:121–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Briggs WH, McMullen MD, Gaut BS, Doebley J. Linkage mapping of domestication loci in a large maize teosinte backcross resource. Genetics. 2007;177:1915–28.
Article
PubMed
PubMed Central
Google Scholar
Zhao Q, Weber AL, McMullen MD, Guill K, Doebley J. MADS-box genes of maize: frequent targets of selection during domestication. Genet Res (Camb). 2011;93:65–75.
Article
CAS
Google Scholar
Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, Swapan D, et al. Green revolution: A mutant gibberellin-synthesis gene in rice - New insight into the rice variant that helped to avert famine over thirty years ago. Nature. 2002;416:701–2.
Article
CAS
PubMed
Google Scholar
Bolduc N, Hake S. The maize transcription factor KNOTTED1 directly regulates the gibberellin catabolism gene ga2ox1. Plant Cell. 2009;21:1647–58.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miller TA, Muslin EH, Dorweiler JE. A maize CONSTANS-like gene, conz1, exhibits distinct diurnal expression patterns in varied photoperiods. Planta. 2008;227:1377–88.
Article
CAS
PubMed
Google Scholar
Wang RL, Stec A, Hey J, Lukens L, Doebley J. The limits of selection during maize domestication. Nature. 1999;398:236–9.
Article
CAS
PubMed
Google Scholar
Wang H, Nussbaum-Wagler T, Li B, Zhao Q, Vigouroux Y, Faller M, et al. The origin of the naked grains of maize. Nature. 2005;436:714–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lemmon ZH, Bukowski R, Sun Q, Doebley JF. The role of cis regulatory evolution in maize domestication. PLoS Genet. 2014;10:e1004745.
Article
PubMed
PubMed Central
Google Scholar
R Core Team. R: A language and environment for statistical computing. Vienna: R Foundation; 2013.
Google Scholar
Ganal MW, Durstewitz G, Polley A, Berard A, Buckler ES, Charcosset A, et al. A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One. 2011;6:e28334.
Article
CAS
PubMed
PubMed Central
Google Scholar
Browning BL, Browning SR. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet. 2009;84:210–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wimmer V, Albrecht T, Auinger HJ, Schön C-C. Synbreed: a framework for the analysis of genomic prediction data using R. Bioinformatics. 2012;28:2086–7.
Article
CAS
PubMed
Google Scholar
Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19:1655–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015;4:7.
Article
PubMed
PubMed Central
Google Scholar
Zeileis A, Grothendieck G. zoo: S3 infrastructure for regular and irregular time series. J Stat Softw. 2005;14:1–27.
Article
Google Scholar
Du Z, Zhou X, Ling Y, Zhang Z, Su Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010;38:W64–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann Statist. 2001;29:1165–88.
Article
Google Scholar
Hutter S, Vilella AJ, Rozas J. Genome-wide DNA polymorphism analyses using VariScan. BMC Bioinformatics. 2006;7:409.
Article
PubMed
PubMed Central
Google Scholar
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27:2156–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wilcoxon F. Individual comparisons by ranking methods. Biometrics Bull. 1945;1:80–3.
Article
Google Scholar
Gresset S, Westermeier P, Rademacher S, Ouzunova M, Presterl T, Westhoff P, et al. Stable carbon isotope discrimination is under genetic control in the C4 species maize with several genomic regions influencing trait expression. Plant Physiol. 2014;164:131–43.
Article
CAS
PubMed
Google Scholar
Utz HF. PLABSTAT - A computer program for statistical analysis of Plant Bred experiments. Version 3A. Stuttgart: Universität Hohenheim; 2011.
Google Scholar