Technological advances in maize breeding: past, present and future

  • Carson Andorf
  • William D. Beavis
  • Matthew Hufford
  • Stephen Smith
  • Walter P. Suza
  • Kan Wang
  • Margaret Woodhouse
  • Jianming Yu
  • Thomas LübberstedtEmail author
Review Article


Maize has for many decades been both one of the most important crops worldwide and one of the primary genetic model organisms. More recently, maize breeding has been impacted by rapid technological advances in sequencing and genotyping technology, transformation including genome editing, doubled haploid technology, parallelled by progress in data sciences and the development of novel breeding approaches utilizing genomic information. Herein, we report on past, current and future developments relevant for maize breeding with regard to (1) genome analysis, (2) germplasm diversity characterization and utilization, (3) manipulation of genetic diversity by transformation and genome editing, (4) inbred line development and hybrid seed production, (5) understanding and prediction of hybrid performance, (6) breeding methodology and (7) synthesis of opportunities and challenges for future maize breeding.



The authors would like to thank USDA’s National Institute of Food and Agriculture (Project numbers: IOW04314, IOW05520), as well as the RF Baker Center for Plant Breeding at Iowa State University for supporting this work.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


  1. Akdemir D, Sanchez JI (2016) Efficient breeding by genomic mating. Front Genet 7:1–12Google Scholar
  2. Akdemir D, Beavis W, Fritsche-Neto R, Singh AK, Isidro-Sánchez J (2018) Multi-objective optimized genomic breeding strategies for sustainable food improvement. Heredity. PubMedGoogle Scholar
  3. Amano E, Smith HH (1965) Mutations induced by ethyl methanesulfonate in maize. Mutat Res 2:344–354PubMedGoogle Scholar
  4. Anderson E, Cutler HC (1942) Races of Zea mays. I. Their recognition and classification. Ann Mo Bot Gard 29:69–89Google Scholar
  5. Andorf CM, Cannon EK, Portwood JL 2nd, Gardiner JM, Harper LC, Schaeffer ML, Braun BL, Campbell DA, Vinnakota AG, Sribalusu VV, Huerta M, Cho KT, Wimalanathan K, Richter JD, Mauch ED, Rao BS, Birkett SM, Sen TZ, Lawrence-Dill CJ (2016) MaizeGDB update: new tools, data and interface for the maize model organism database. Nucleic Acids Res 44:D1195–D1201PubMedGoogle Scholar
  6. Baldauf JA, Marcon C, Lithio A, Vedder L, Altrogge L, Piepho H-P, Schoof H, Nettleton D, Hochholdinger F (2018) Single-parent expression is a general mechanism driving extensive complementation of non-syntenic genes in maize hybrids. Curr Biol 28:431–437PubMedGoogle Scholar
  7. Barnabás B, Obert B, Kovács G (1999) Colchicine, an efficient genome-doubling agent for maize (Zea mays L.) microspores cultured in anthero. Plant Cell Rep 18:858–862Google Scholar
  8. Bauer E, Falque M, Walter H, Bauland C, Camisan C, Campo L, Meyer N, Ranc N, Rincent R, Schipprack W, Altmann T, Flament P, Melchinger AE, Menz M, Moreno-Gonzalez J, Ouzunova M, Revilla P, Charcosset A, Martin OC, Schön CC (2013) Intraspecific variation of recombination rate in maize. Genome Biol 14(9):R103PubMedPubMedCentralGoogle Scholar
  9. Beavis WD, Grant D (1991) A linkage map based on information from four F2 populations of maize. Theor Appl Genet 82:636–644PubMedGoogle Scholar
  10. Beckett TJ, Morales AJ, Koehler KL, Rocheford TR (2017) Genetic relatedness of previously Plant-variety-protected commercial maize inbreds. PLoS ONE 12(12):e0189277PubMedPubMedCentralGoogle Scholar
  11. Bedoya CA, Dreisigacker S, Hearne S, Franco J, Mir C, Prasanna BM et al (2017) Genetic diversity and population structure of native maize populations in Latin America and the Caribbean. PLoS ONE 12(4):e0173488PubMedPubMedCentralGoogle Scholar
  12. Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J (2012) Hi-C: a comprehensive technique to capture the conformation of genomes. Methods 58:268–276PubMedGoogle Scholar
  13. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2013) GenBank. Nucleic Acids Res 41:D36–D42PubMedGoogle Scholar
  14. Bernardo R (1994) Prediction of maize single-cross performance using RFLPs and information from related hybrids. Crop Sci 34:20–25Google Scholar
  15. Bernardo R (1996a) Best linear unbiased prediction of maize single-cross performance. Crop Sci 36:50–56Google Scholar
  16. Bernardo R (1996b) Best linear unbiased prediction of the performance of crosses between untested maize inbreds. Crop Sci 36:872–876Google Scholar
  17. Bernardo R (2009) Genomewide selection for rapid introgression of exotic germplasm in maize. Crop Sci 49:419–425Google Scholar
  18. Bernardo R, Yu J (2007) Prospects for genomewide selection for quantitative traits in maize. Crop Sci 47:1082–1090Google Scholar
  19. Betran FJ, Ribaut JM, Beck D, Gonzalez de Leon D (2003) Genetic diversity, specific combining ability, and heterosis in tropical maize under stress and nonstress environments. Crop Sci 43:797–806Google Scholar
  20. Birchler JA (1980) The cytogenetic localization of the alcohol dehydrogenase-1 locus in maize. Genetics 94:687–700PubMedPubMedCentralGoogle Scholar
  21. Bird RM, Neuffer MG (1987) Induced mutations in maize. In: Janick J (ed) Plant breeding reviews. Van Nostrand Reinhold, New York, pp 139–180Google Scholar
  22. Birge JR, Louveaux V (2011) Introduction to stochastic programming. Springer, New YorkGoogle Scholar
  23. Boles JN (1955) Linear programming and farm management analysis. J Farm Econ 37:1–37Google Scholar
  24. Bolser DM, Staines DM, Perry E, Kersey PJ (2017) Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomic data. Methods Mol Biol 1533:1–31PubMedGoogle Scholar
  25. Bommert P, Nagasawa NS, Jackson D (2013) Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus. Nat Genet 45:334–337PubMedGoogle Scholar
  26. Bouchet S, Servin B, Bertin P, Madur D, Combes V, Dumas F, Brunel D, Laborde J, Charcosset A, Nicolas S (2013) Adaptation of maize to temperate climates: mid-density genome-wide association genetics and diversity patterns reveal key genomic regions, with a major contribution of the Vgt2 (ZCN8) locus. PLoS ONE 8(8):e71377PubMedPubMedCentralGoogle Scholar
  27. Brandenburg J-T, Mary-Huard T, Rigaill G, Hearne SJ, Corti H, Joets J, Vitte C, Charcosset A, Nicolas S, Tenaillon M (2017) Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts. PLoS Genet 13(3):e1006666PubMedPubMedCentralGoogle Scholar
  28. Brown WL, Goodman MM (1977) Races of corn. In: Sprague GF (ed) Corn and corn improvement. Amer Soc Agron, Madison, pp 49–88Google Scholar
  29. Brown AHD, Hodgkin T (2015) Indicators of genetic diversity, genetic erosion, and genetic vulnerability for plant genetic resources. In: Ahuja MR Jain SM (eds) Genetic diversity and erosion in plants, sustainable development and biodiversity vol 7, pp 25–53Google Scholar
  30. Bruce AB (1910) The Mendelian theory of heredity and the augmentation of vigor. Science 32:627–628PubMedGoogle Scholar
  31. Brunelle DC, Clark JK, Sheridan WF (2017) Genetics screening for EMS-induced maize embryo-specific mutants altered in embryo morphogenesis. G3 7:3559–3570PubMedGoogle Scholar
  32. Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman MM, Harjes C, Guill K, Kroon DE, Larsson S, Lepak NK, Li H, Mitchell SE, Pressoir G, Peiffer JA, Rosas MO, Rocheford TR, Romay MC, Romero S, Salvo S, Sanchez Villeda H, da Silva HS, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu J, Zhang Z, Kresovich S, McMullen MD (2009) The genetic architecture of maize flowering time. Science 325:714–718PubMedGoogle Scholar
  33. Bukowski R, Guo X, Lu Y, Zou C, He B, Rong Z, Wang B, Xu D, Yang B, Xie C, Fan L, Gao S, Xu X, Zhang G, Li Y, Jiao Y, Doebley JF, Ross-Ibarra J, Lorant A, Buffalo V, Romay MC, Buckler ES, Ware D, Lai J, Sun Q, Xu Y (2018) Construction of the third-generation Zea mays haplotype map. GigaScience 7:1–12PubMedGoogle Scholar
  34. Bulmer MG (1971) The effect of selection on genetic variability. Am Nat 105:201–211Google Scholar
  35. Burr B, Burr FA, Thompson KH, Albertson MC, Stuber CW (1988) Gene mapping with recombinant inbreds in maize. Genetics 118:519–526PubMedPubMedCentralGoogle Scholar
  36. Byrum J, Davis C, Doonan G, Doubler T, Foster D, Luzzi B, Mowers R, Zinselmeier C, Klober J, Culhane D, Mack S (2016) Advanced analytics for agricultural product development. Interfaces 46:5–17Google Scholar
  37. Byrum J, Davis C, Doonan G, Doubler T, Foster D et al (2017) Genetic gain performance metric accelerates agricultural productivity. Interfaces 47:442–453Google Scholar
  38. Cameron JN, Han Y, Wang L, Beavis WD (2017) Systematic design for trait introgression projects. Theor Appl Genet 130:1993–2004PubMedPubMedCentralGoogle Scholar
  39. Canzar S, El-Kebir M (2011) A mathematical programming approach to marker-assisted gene pyramiding. In: Proceedings of the 11th workshop on algorithms in bioinformatics. Springer, pp 26–38Google Scholar
  40. Castiglioni P, Ajmone-Marsan P, van Wijk R, Motto M (1999) AFLP markers in a molecular linkage map of maize: codominant scoring and linkage group ditsribution. Theor Appl Gen 99:425–431Google Scholar
  41. CGC (2018) Crop germplasm committees. Briefings 2010–2018 USDA-ARS GRIN.
  42. Chalyk ST (1994) Properties of maternal haploid maize plants and potential application to maize breeding. Euphytica 79:13–18Google Scholar
  43. Char SN, Unger-Wallace E, Frame B, Briggs SA, Main M, Spalding MH, Vollbrecht E, Wang K, Yang B (2015) Heritable site-specific mutagenesis using TALENs in maize. Plant Biotechnol J 13:1002–1010PubMedGoogle Scholar
  44. Char SN, Neelakandan AK, Nahampun H, Frame B, Main M, Spalding MH, Becraft PW, Meyers BC, Walbot V, Wang K, Yang B (2017) An Agrobacterium-delivered CRISPR/Cas9 system for high-frequency targeted mutagenesis in maize. Plant Biotechnol J 15:257–268PubMedGoogle Scholar
  45. Chase SS (1949) Monoploid frequencies in a commercial double cross hybrid maize, and in its component single cross hybrids and inbred lines. Genetics 34:328–332PubMedPubMedCentralGoogle Scholar
  46. Chase SS (1951) Efficient methods of developing and improving inbred lines. The monoploid method of developing inbred lines. Report of 6th hybrid corn industry research conference, pp 29–34Google Scholar
  47. Chase SS (1952) Production of homozygous diploids of maize from monoploids. Agron 44:263–267Google Scholar
  48. Chevalet C, Mulsant P (1992) Using markers in gene introgression breeding programs. Genetics 132:1199–1210PubMedPubMedCentralGoogle Scholar
  49. Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, Elshire RJ, Gaut B, Geller L, Glaubitz JC, Gore M, Guill KE, Holland J, Hufford MB, Lai J, Li M, Liu X, Lu Y, McCombie R, Nelson R, Poland J, Prasanna BM, Pyhajarvi T, Rong T, Sekhon RS, Sun Q, Tenaillon MI, Tian F, Wang J, Xu X, Zhang Z, Kaeppler SM, Ross-Ibarra J, McMullen MD, Buckler ES, Zhang G, Xu Y, Ware D (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet 44:803–807PubMedGoogle Scholar
  50. Chilcoat D, Liu Z-B, Sander J (2017) Use of CRISPR/Cas9 for crop improvement in maize and soybean. Prog Mol Biol Transl Sci 149:27–46PubMedGoogle Scholar
  51. Chojnacki S, Cowley A, Lee J, Foix A, Lopez R (2017) Programmatic access to bioinformatics tools from EMBL-EBI update: 2017. Nucleic Acids Res 45:W550–W553PubMedPubMedCentralGoogle Scholar
  52. Chourey PS, Schwartz D (1971) Ethyl methanesulfonate-induced mutations of the Sh1 protein in maize. Mutat Res 12:151–157PubMedGoogle Scholar
  53. Ci X, Li M, Liang X, Xie Z, Zhang D, Li X, Lu Z, Ru G, Bai L, Xie C, Hao Z, Zhang S (2011) Genetic contribution to advanced yield for maize hybrids released from 1970 to 2000 in China. Crop Sci 51:13–20Google Scholar
  54. Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4:265–270PubMedGoogle Scholar
  55. Coe EH Jr, Sarkar KR (1964) The detection of haploids in maize. Heredity 555:231–233Google Scholar
  56. Coe EH, Sarkar KR (1966) Preparation of nucleic acids and a genetic transformation attempt in maize. Crop Sci 6:432–435Google Scholar
  57. Coe E, Cone K, McMullen M, Chen SS, Davis G, Gardiner J, Liscum E, Polacco M, Paterson A, Sanchez-Villeda H, Soderlund C, Wing R (2002) Access to the maize genome: an integrated physical and genetic map. Plant Physiol 128:9–12PubMedPubMedCentralGoogle Scholar
  58. Comstock RE, Robinson HF, Harvey PH (1949) A breeding procedure designed to make maximum use of both general and specific combining ability. Agron J 41:360–367Google Scholar
  59. Cone KC, McMullen MD, Bi IV, Davis GL, Yim YS, Gardiner JM, Polacco ML, Sanchez-Villeda H, Fang Z, Schroeder SG, Havermann SA, Bowers JE, Paterson AH, Soderlund CA, Engler FW, Wing RA, Coe EH Jr (2002) Genetic, physical, and informatics resources for maize. On the road to an integrated map. Plant Physiol 130:1598–1605PubMedPubMedCentralGoogle Scholar
  60. Cooper M, Podlich DW (2002) The E(NK) model: extending the NK model to incorporate gene by environment interactions and epistasis for diploid genomes. Compexity 7:31–47Google Scholar
  61. Cooper M, Podlich DW, Micallef KP, Smith OS, Jensen NM et al. (2002) Complexity, quantitative traits and plant breeding: a role for simulation modeling in the genetic improvement of crops. In: Kang MS (ed) Quantitative genetics, genomics and plant breeding. CABGoogle Scholar
  62. Cooper M, Gho C, Leafgren R, Tang T, Messina C (2014) Breeding drought-tolerant maize hybrids for the US corn-belt: discovery to product. J Exp Bot 65:6191–6204PubMedGoogle Scholar
  63. Cress CE (1967) Reciprocal recurrent selection and modifications in simulated populations. Crop Sci 7:561–567Google Scholar
  64. Crow JF (1998) 90 years ago: the beginning of hybrid maize. Genetics 148:923–928PubMedPubMedCentralGoogle Scholar
  65. Crow JF (1999) Dominance and overdominance. In: Coors JG, Pandey S (eds) The genetics and exploitation of heterosis in crops. ASA, CSSA, Madison, pp 49–58Google Scholar
  66. Daetwyler HD, Pong-Wong R, Villanueva B, Woolliams JA (2010) The impact of genetic architecture on genome-wide evaluation methods. Genetics 185:1021–1031PubMedPubMedCentralGoogle Scholar
  67. Darrah DL, Zuber MS (1986) 1985 United States farm maize germplasm base and commercial breeding strategies. Crop Sci 26:1109–1113Google Scholar
  68. Davenport CB (1908) Degeneration, albinism and inbreeding. Science 28:454–455PubMedGoogle Scholar
  69. De Beukelaer H, De Meyer G, Fack V (2015) Heuristic exploitation of genetic structure in marker-assisted gene pyramiding problems. BMC Genet 16:2–16PubMedPubMedCentralGoogle Scholar
  70. Desta ZA, Ortiz R (2014) Genomic selection: genome-wide prediction in plant improvement. Trends Plant Sci 19:592–601PubMedGoogle Scholar
  71. Dicke FF, Guthrie WD (1988) The most important corn insects. In: Sprague GF, Dudley JW (eds) Corn and corn improvement, 3rd edn. American Society of Agronomy, Madison, pp 767–868Google Scholar
  72. Doebley J, Wendel JF, Smith JSC, Stuber CW, Goodman MM (1988) The origin of Cornbelt maize: the isozyme evidence. Econ Bot 42:120–131Google Scholar
  73. Dollinger EJ (1954) Studies on induced mutation in maize. Genetics 39:750–766PubMedPubMedCentralGoogle Scholar
  74. Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, Oggioni M, Dunning Hotopp JC, Hu FZ, Riley DR, Covacci A, Mitchell TJ, Bentley SD, Kilian M, Ehrlich GD, Rappuoli R, Moxon ER, Masignani V (2010) Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol 11:R107PubMedPubMedCentralGoogle Scholar
  75. Dong Q, Roy L, Freeling M, Walbot V, Brendel V (2003) ZmDB, an integrated database for maize genome research. Nucleic Acids Res 31:244–247PubMedPubMedCentralGoogle Scholar
  76. Dubreuil P, Dufour P, Krejci E, Causse M, deVienne D, Gallais A, Charcosset A (1996) Organization of RFLP diversity among inbred lines of maize representing the most significant heterotic groups. Crop Sci 36:790–799Google Scholar
  77. Duvick DN (1965) Cytoplasmic pollen sterility in corn. Adv Genet 13:1–56Google Scholar
  78. Duvick DN (1984) Genetic diversity in major farm crops on the farm and in reserve. Econ Bot 38:161–178Google Scholar
  79. Duvick DN (2005a) Genetic progress in yield of United States maize (Zea mays L.). Maydica 50:193–202Google Scholar
  80. Duvick DN (2005b) The contribution of breeding to yield advances in maize (Zea mays L.). Adv Agron 86:83–145Google Scholar
  81. Duvick DN, Cassman KG (1999) Post-green revolution trends in yield potential of temperate maize in the north-central United States. Crop Sci 39:1622–1630Google Scholar
  82. East EM (1908) Inbreeding in corn. Rep Conn Agric Exp Stn 1907:419–428Google Scholar
  83. Eberhart SA (1970) Factors affecting efficiencies of breeding methods. Afr Soils 15:669–680Google Scholar
  84. Eder J, Chalyk ST (2002) In vivo haploid induction in maize. Theor Appl Genet 104:703–708PubMedGoogle Scholar
  85. Edmeades GO, Trevisan W, Prasanna BM, Campos H (2017) Tropical maize (Zea mays L.). In: Campos H, Caligari PDS (eds) Genetic improvement of tropical crops. Springer, New York, pp 57–109Google Scholar
  86. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma C, Marks P, Maxham M, Murphy D, Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J, Turner S (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138PubMedGoogle Scholar
  87. Einset J (1942) Chromosome length in relation to transmission frequency in maize trisomes. Genetics 28:349–364Google Scholar
  88. Eisenstein M (2015) Startups use short-read data to expand long-read sequencing market. Nat Biotechnol 33:433–435PubMedGoogle Scholar
  89. Emerson RA (1917) Genetical studies of variegated pericarp in maize. Genetics 2:1–35PubMedPubMedCentralGoogle Scholar
  90. Eynard SE, Croiseau P, Laloe D, Fritz S, Calus MPL, Restoux G (2018) Which individuals to choose to update the reference population? Minimizing the loss of genetic diversity in animal genomic selection programs. G3 8:113–121PubMedGoogle Scholar
  91. FAOSTAT (2018) Crop data. FAO United Nations, Rome.
  92. Fehr, WR (1991) Maximizing genetic improvement. In: Principles of cultivar development: theory and technique. Macmillian, USA, pp. 219–246Google Scholar
  93. Feng L, Sebastian S, Smith S, Cooper M (2006) Temporal trends in SSR allele frequencies associated with long-term selection for yield of maize. Maydica 51:293–300Google Scholar
  94. Feng PC, Qi Y, Chiu T, Stoecker MA, Schuster CL, Johnson SC, Fonseca AE, Huang J (2014) Improving hybrid seed production in corn with glyphosate-mediated male sterility. Pest Manag Sci 70:212–218PubMedGoogle Scholar
  95. Fernandez J, Toro MA (1999) The use of mathematical programming to control inbreeding in selection schemes. J Anim Breed Genet 116:447–466Google Scholar
  96. Fischer T, Byerlee D, Edmeades G (2014) Crop yields and global food security: will yield increase continue to feed the world? ACIAR monograph no. 158. Australian Centre for International Agricultural Research, Canberra, xxii + 634 ppGoogle Scholar
  97. Fisher RA (1930) The fundamental theorem of natural selection. The genetical theory of natural selection. Oxford University Press, Oxford, pp 22–47Google Scholar
  98. Flint-Garcia SA, Buckler ES, Tiffin P, Ersoz E, Springer NM (2009) Heterosis is prevalent for multiple traits in diverse maize germplasm. PLoS ONE 4:e7433PubMedPubMedCentralGoogle Scholar
  99. Frame BR, Shou H, Chikwamba RK, Zhang Z, Xiang C, Fonger TM, Pegg SE, Li B, Nettleton DS, Pei D, Wang K (2002) Agrobacterium tumefaciens-mediated transformation of maize embryos using a standard binary vector system. Plant Physiol 129:13–22PubMedPubMedCentralGoogle Scholar
  100. Fraser AS, Burnell DG (1970) Computer models in genetics. McGraw-Hill, San FransciscoGoogle Scholar
  101. Frisch M, Bohn M, Melchinger AE (1999) Comparison of selection strategies for marker-assisted backcrossing of a gene. Crop Sci 39:1295–1301Google Scholar
  102. Fromm ME, Taylor LP, Walbot V (1986) Stable transformation of maize after gene transfer by electroporation. Nature 319:791–793PubMedGoogle Scholar
  103. Fu H, Dooner HK (2002) Intraspecific violation of genetic colinearity and its implications in maize. Proc Natl Acad Sci USA 99:9573–9578PubMedGoogle Scholar
  104. Gabay-Laughnan S, Laughnan JR (1994) The male sterility and restorer genes in maize. In: Freeling M, Walbot V (eds) The maize handbook. Springer, New York, pp 418–423Google Scholar
  105. Gaffney J, Anderson J, Franks C, Collinson S, MacRobert J, Woldemariam W, Albertsen MC (2016) Robust seed systems, emerging technologies and hybrid crops for Africa. Food Secur. 9:36–44Google Scholar
  106. Gama EEG, Hallauer AR (1977) Relation between inbred and hybrid traits in maize. Crop Sci 17:703–706Google Scholar
  107. Ganal MW, Durstewitz G, Polley A, Berard A, Buckler ES, Charcosset A, Clarke JD, Graner EM, Hansen M, Joets J, Le Paslier MC, McMullen MD, Montalent P, Rose M, Schon CC, Sun Q, Walter H, Martin OC, Falque M (2011) 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 6:28334Google Scholar
  108. Gao C (2018) The future of CRISPR technologies in agriculture. Nat Rev Mol Cell Biol 19:275–276PubMedGoogle Scholar
  109. Garcia AAF, Wang S, Melchinger AE, Zeng Z-B (2008) Quantitative trait loci mapping and the genetic basis of heterosis in maize and rice. Genetics 180:1707–1724PubMedPubMedCentralGoogle Scholar
  110. Gardiner JM, Coe EH, Melia-Hancock S, Hoisington DA, Chao S (1993) Development of a core RFLP map in maize using an immortalized F2 population. Genetics 134:917–930PubMedPubMedCentralGoogle Scholar
  111. Gardner CA (2012) Maize diversification by capturing useful alleles from exotic germplasm. In: Proceedings 48th Annual Illinois Corn Breeding School, March 5–6, 2012. Urbana-Champaign, IL, p 172Google Scholar
  112. Garing F (2000) Inbred corn plant 90QDD1 and seeds thereof. United States Patent No. US 6,034,305. US Patent Office, Washington, DCGoogle Scholar
  113. Gaynor RC, Gorjanc G, Bentley AR, Ober ES, Howell P, Jackson R, Mackay IJ, Hickey JM (2017) A two-part strategy for using genomic selection to develop inbred lines. Crop Sci 57:2372–2386Google Scholar
  114. Geiger HH (2009) Doubled haploids. Maize handbook—volume ii: genetics and genomics. Springer, New York, pp 641–657Google Scholar
  115. Geiger HH, Braun MD, Gordillo GA, Koch S, Jesse J, Krutzfeldt BAE (2006) Variation for female fertility among haploid maize lines. Maize Genet Newsl 80:28–29Google Scholar
  116. Georges F, Ray H (2017) Genome editing of crops: a renewed opportunity for food security. GM Crops & Food 8:1–12Google Scholar
  117. Gibson PB, Brink RA, Stahmann MA (1950) The mutagenic action of mustard gas on Zea mays. J Hered 41:232–238PubMedGoogle Scholar
  118. Giraud H, Lehermeier C, Bauer E, Falque M, Segura V, Bauland C, Camisan C, Campo L, Meyer N, Ranc N, Schipprack W, Flament P, Melchinger AE, Menz M, Moreno-González J, Ouzunova M, Charcosset A, Schön C, Moreau L (2014) 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 198:1717–1734PubMedPubMedCentralGoogle Scholar
  119. Giraud H, Bauland C, Falque M, Madur D, Combes V, Jamin P, Monteil C, Laborde J, Palaffre C, Gaillard A, Blanchard P, Charcosset A, Moreau L (2017) Reciprocal genetics: identifying QTLs for general and specific combining abilities in hybrids between multiparental populations from two maize (Zea mays L.) heterotic groups. Genetics 207:1167–1180PubMedPubMedCentralGoogle Scholar
  120. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100PubMedGoogle Scholar
  121. Golicz AA, Batley J, Edwards D (2016) Towards plant pangenomics. Plant Biotechnol J 14:1099–1105PubMedGoogle Scholar
  122. Golovkin MV, Abraham M, Morocz S, Bottka S, Feder A, Dudits D (1993) Production of transgenic maize plants by direct DNA uptake into embryogenic proroplasts. Plant Sci 90:41–52Google Scholar
  123. Gonzalez VH, Tollenaar M, Bowman A, Good B, Lee EA (2018) Maize yield potential and density tolerance. Crop Sci 58:472–485Google Scholar
  124. Goodman MM (1978) A brief survey of the races of maize and current attempts to infer racial relationships. In: Walden DB (ed) Maize breeding and genetics, pp143–184Google Scholar
  125. Goodman MM (1999) Broadening the genetic diversity in maize breeding by use of exotic germplasm. In: Coors JG, Pandey S (eds) The genetics and exploitation of heterosis in crops, pp139–148Google Scholar
  126. Goodman MM (2005) Broadening the U.S. maize germplasm base. Maydica 50:203–214Google Scholar
  127. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178–D1186PubMedGoogle Scholar
  128. Gordillo GA, Geiger HH (2008) Optimization of DH-line based recurrent selection procedures in maize under a restricted annual loss of genetic variance. Euphytica 161:141–154Google Scholar
  129. Gordon-Kamm WJ, Spencer TM, Mangano ML, Adams TR, Daines RJ, Start WG, O’Brien JV, Chambers SA, Adams WR Jr, Willets NG, Rice TB, Mackey CJ, Krueger RW, Kausch AP, Lemaux PG (1990) Transformation of maize cells and regeneration of fertile transgenic plants. Plant Cell 2:603–618PubMedPubMedCentralGoogle Scholar
  130. Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES (2009) A first-generation haplotype map of maize. Science 326:1115–1117PubMedGoogle Scholar
  131. Gorjanc G, Gaynor RC, Hickey JM (2018) Optimal cross selection for long-term genetic gain in two-part programs with rapid recurrent genomic selection. Theor Appl Genet 131:1953–1966PubMedCentralGoogle Scholar
  132. Gowen JW (1952) Heterosis. Iowa State College Press, AmesGoogle Scholar
  133. Graham GI, Wolff DW, Stuber CW (1997) Characterization of a yield quantitative trait locus on chromosome five of maize by fine mapping. Crop Sci 37:1601Google Scholar
  134. Grimsley N, Hohn T, Davies JW, Hohn B (1987) Agrobacterium mediated delivery of infectious maize streak virus into maize plants. Nature 325:177–179Google Scholar
  135. Gurian-Sherman D (2009) Failure to yield: evaluating the performance of genetically engineered crops. Union of Concerned Scientists.–to–yield.pdf
  136. Haegele JW, Cook KA, Nichols DM, Below FE (2013) Changes in nitrogen use traits associated with genetic improvement for grain yield of maize hybrids released in different decades. Crop Sci 53:1256–1268Google Scholar
  137. Hallauer AR, Miranda F (1981) Quantitative genetics in maize breeding. Iowa State University Press, AmesGoogle Scholar
  138. Hallauer AR, M. J. Carena, Filho JBM (2010) Selection: experimental results. In: Quantitative genetics in maize breeding. Handbook of plant breeding, vol 6. Springer, New York, pp 291–383Google Scholar
  139. Han Y, Cameron JN, Wang L, Beavis WD (2017) The predicted cross value for genetic introgression of multiple alleles. Genetics 205:1409–1423PubMedPubMedCentralGoogle Scholar
  140. Häntzschel KR, Weber G (2010) Blockage of mitosis in maize root tips using colchicine-alternatives. Protoplasma 241:99–104PubMedGoogle Scholar
  141. Hazel LN (1943) The genetic basis for constructing selection indices. Genetics 28:476–490PubMedPubMedCentralGoogle Scholar
  142. Heady EO (1954) Simplified presentation and logical aspects of linear programming technique. J Farm Econ 36:1035–1048Google Scholar
  143. Heather JM, Chain B (2016) The sequence of sequencers: the history of sequencing DNA. Genomics 107:1–8PubMedPubMedCentralGoogle Scholar
  144. Heffner EL, Sorrells ME, Jannink J-L (2009) Genomic selection of crop improvement. Crop Sci 49:1–12Google Scholar
  145. Helentjaris T, Slocum M, Wright S, Schaefer A, Nienhuis J (1986) Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphisms. Theor Appl Gen 72:761–769Google Scholar
  146. Henderson CR (1975) Best linear unbiased estimation and prediction under a selection model. Biometrics 31:423–447PubMedGoogle Scholar
  147. Herzog E, Frisch M (2011) Selection strategies for marker-assisted backcrossing with high-throughput marker systems. Theor Appl Genet 123:251–260PubMedGoogle Scholar
  148. Herzog E, Falke KC, Presterl T, Scheuermann D, Ouzunova M, Frisch M (2014) Selection strategies for the development of maize introgression populations. PLoS ONE 9:e92429PubMedPubMedCentralGoogle Scholar
  149. Heslot N, Yang H-P, Sorrells ME, Jannink J-L (2012) Genomic selection in plant breeding: a comparison of models. Crop Sci 52:146–152Google Scholar
  150. Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38:226–231PubMedGoogle Scholar
  151. Hillel J, Schaap T, Haberfeld A, Jeffreys AJ, Plotzky Y, Cahaner A, Lavi U (1990) DNA fingerprints applied to gene introgression in breeding programs. Genetics 124:783–789PubMedPubMedCentralGoogle Scholar
  152. Hirsch CN, Foerster JM, Johnson JM, Sekhon RS, Muttoni G, Vaillancourt B, Penagaricano F, Lindquist E, Pedraza MA, Barry K, de Leon N, Kaeppler SM, Buell CR (2014) Insights into the maize pan-genome and pan-transcriptome. Plant Cell 26:121–135PubMedPubMedCentralGoogle Scholar
  153. Holland JB (2004) Breeding: incorporation of exotic germplasm. In: Goodman RM (ed) Encyclopedia of plant and crop science. Marcel Dekker, New York, pp 222–224Google Scholar
  154. Holland J, Nyquist WE, Cervantes-Martinez CT (2003) Estimating and interpreting heritability for plant breeding: an update. Plant Breed Rev 22:9–112Google Scholar
  155. Hospital F (2001) Size of donor chromosome segments around introgressed loci and reduction of linkage drag in marker-assisted backcross programs. Genetics 158:1363–1379PubMedPubMedCentralGoogle Scholar
  156. Hospital F, Charcosset A (1997) Marker-assisted introgression of quantitative trait loci. Genetics 147:1469–1485PubMedPubMedCentralGoogle Scholar
  157. Hospital F, Chevalet C, Mulsant P (1992) Using markers in gene introgression breeding programs. Genetics 132:1199–1210PubMedPubMedCentralGoogle Scholar
  158. Howard R, Carriquiry AL, Beavis WD (2014) Parametric and nonparametric statistical methods for genomic selection of traits with additive and epistatic genetic architectures. G3 (Bethesda) 4:1027–1046Google Scholar
  159. Howard JT, Pryce JE, Baes C, Maltecca C (2017) Invited review: inbreeding in the genomics era: inbreeding, inbreeding depression, and management of genomic variability. J Dairy Sci 100:6009–6024PubMedGoogle Scholar
  160. Huang CR, Burns KH, Boeke JD (2012) Active transposition in genomes. Annu Rev Genet 46:651–675PubMedPubMedCentralGoogle Scholar
  161. Hufford MB, Lubinksy P, Pyhäjärvi T, Devengenzo MT, Ellstrand NC, Ross-Ibara J (2013) Correction: the genomic signature of crop-wild introgression in maize. PLOS Genetics. PubMedGoogle Scholar
  162. Hull RH (1945) Recurrent selection and specific combining ability in corn. J Am Soc Agron 37:134–145Google Scholar
  163. Inghelandt DV, Melchinger AE, Lebreton C, Stich B (2010) Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers. Theor Appl Genet 120:1289–1299PubMedPubMedCentralGoogle Scholar
  164. Initiative AG (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815Google Scholar
  165. ISAAA (2017) Global status of commercialized Biotech/GM Crops in 2017: biotech crop adoption surges as economic benefits accumulate in 22 years. ISAAA Brief no. 53, ISAAA: Ithaca, NYGoogle Scholar
  166. Ishida Y, Saito H, Ohta SH, Hiei Y, Komari T, Kumashiro T (1996) High efficiency transformation of maize (Zea mays L.) mediated by Agrobacterium tumefaciens. Nat Biotechnol 14:745–750PubMedGoogle Scholar
  167. Ishii T, Yonezawa K (2007) Optimization of the marker-based procedures for pyramiding genes from multiple donor lines: I. Schedule of crossing between the donor lines. Crop Sci 47:537–547Google Scholar
  168. Jannink J-L (2010) Dynamics of long-term genomic selection. Genet Sel Evol 42:11Google Scholar
  169. Jeffrey B, Lübberstedt T (2014) Molecular breeding of bioenergy traits. In: Corn S, Goldman (ed.) Compendium of bioenergy plantsscience. Publishers/Taylor & Francis/CRC PRESS, Boca Raton, FL, USA, pp.198–215Google Scholar
  170. Jenkins MT (1940) The segregation of genes affecting yield of grain in maize. J Am Soc Agron 32:55–63Google Scholar
  171. Jiao Y, Zhao H, Ren L, Song W, Zeng B, Guo J, Wang B, Liu Z, Chen J, Li W, Zhang M, Xie S, Lai J (2012) Genome-wide genetic changes during modern breeding of maize. Nat Genet 44:812–815PubMedGoogle Scholar
  172. Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin CS, Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR, Springer NM, Antoniou E, McCombie WR, Presting GG, McMullen M, Ross-Ibarra J, Dawe RK, Hastie A, Rank DR, Ware D (2017) Improved maize reference genome with single-molecule technologies. Nature 546:524–527PubMedGoogle Scholar
  173. Johnson I, Eldredge J (1953) Performance of recovered popcorn inbred lines derived from outcrosses to dent corn. Agron J 45:105–110Google Scholar
  174. Johnson B, Gardner CO, Wrede KC (1988) Application of an optimization model to multi-trait selection programs. Crop Sci 28:723–728Google Scholar
  175. Jones DF (1917) Dominance of linked factors as a means of accounting for heterosis. Genetics 2:466–479PubMedPubMedCentralGoogle Scholar
  176. Jugenheimer RJ (1985) Corn improvement, seed production and uses. RE Krieger, Malabar, p 794Google Scholar
  177. Kadam DC, Potts SM, Bohn MO, Lipka AE, Lorenz AJ (2016) Genomic prediction of single crosses in the early stages of a maize hybrid breeding pipeline. G3(6):3443–3453Google Scholar
  178. Kaeppler S (2012) Heterosis: many genes, many mechanisms—end the search for an undiscovered unifying theory. ISRN Bot 2012:1–12Google Scholar
  179. Karush W (1939) Minima of functions of several variables with inequalities as side constraints. University of Chicago, ChicagoGoogle Scholar
  180. Kassie GT, Erenstein O, Mwangi W, La Rovere R, Setimela P, Langyintuo A (2012) Characterization of maize production in southern Africa: synthesis of CIMMYT/DTMA household level farming system surveys in Angola, Malawi, Mozambique, Zambia and Zimbabwe. Socio-economics program working paper 4. CIMMYT, Mexico, D.FGoogle Scholar
  181. Kato A (2002) Chromosome doubling of haploid maize seedling using nitrous oxide gas at the flower primordial stage. Plant Breed 1215:370–377Google Scholar
  182. Kelliher T, Starr D, Richbourg L, Chintamanani S, Delzer B, Nuccio ML, Green J, Chen Z, McCuiston J, Wang W, Liebler T, Bullock P, Martin B (2017) MATRILINEAL, a sperm-specific phospholipase, triggers maize haploid induction. Nature 542:105–109PubMedGoogle Scholar
  183. Kermicle JL (1969) Androgenesis conditioned by a mutation in maize. Science 166:1422–1424PubMedGoogle Scholar
  184. Kermicle JL (1994) Indeterminate gametophyte ig biology and use. In: Freeling M, Walbot V (eds) The maize handbook. Springer, New York, pp 388–393Google Scholar
  185. Kinghorn BP (1998) Mate selection by groups. J Dairy Sci 81:55–63PubMedGoogle Scholar
  186. Kingsbury N (2009) Hybrid: the history and science of plant breeding. The University of Chicago Press, ChicagoGoogle Scholar
  187. Kleiber D, Prigge V, Melchinger AE, Burkard F, San Vicente F, Palomino G, Gordillo GA (2012) Haploid fertility in temperate and tropical maize germplasm. Crop Sci 52:623–630Google Scholar
  188. Klein RR, Mullet JE, Jordan DR, Miller FR, Rooney WI, Menz MA, Franks CD, Klein PE (2008) The effect of tropical sorghum conversion and inbred development on genome diversity as revealed by high-resolution genotyping. Crop Sci 48:12Google Scholar
  189. Klein RR, Miller FR, Bean S, Klein PE (2016) Registration of 40 converted germplasm sources from the reinstated sorghum conversion program. J Plant Regist 10:57Google Scholar
  190. Kremling KAG, Chen S-Y, Su M-H, Lepak NK, Romay MC, Swarts KL, Lu F, Lorant A, Bradbury PJ, Buckler ES (2018) Dysregulation of expression correlates with rare-allele burden and fitness loss in maize. Nature 555:520–523PubMedGoogle Scholar
  191. Kuhn HW, Tucker AW (1951) Nonlinear programming. In: Proceedings of 2nd Berkeley symposium, pp 481–492Google Scholar
  192. Kumar GR, Sakthivel K, Sundaram RM, Neeraja CN, Balachandran S, Rani NS, Viraktamath B, Madhav M (2010) Allele mining in crops: prospects and potentials. Biotechnol Adv 28:451–461PubMedGoogle Scholar
  193. Kump KL, Bradbury PJ, Wisser RJ, Buckler ES, Belcher AR, Oropeza-Rosas MA, Zwonitzer JC, Kresovich S, McMullen MD, Ware D, Balint-Kurti PJ, Holland JB (2011) Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43:163–168PubMedGoogle Scholar
  194. Laborda PR, Oliveira KM, Garcia AF, Paterniani MEAG, Souza AP (2005) Tropical maize germplasm: what can we say about its genetic diversity in the light of molecular markers? Theor Appl Genet 111:1288–1299PubMedGoogle Scholar
  195. Lanza LLB, de Souza CL Jr, Ottoboni LMM, Vieira MLC, de Souza AP (1997) Genetic distance of inbred lines and prediction of maize single-cross performance using RAPD markers. Theor Appl Genet 94:1023–1030Google Scholar
  196. Larkins JR (2000) Inbred corn plant RQAA8 and seeds thereof. U.S. Patent No 6,143,961. US Patent Office, Washington DCGoogle Scholar
  197. Lawrence CJ, Harper LC, Schaeffer ML, Sen TZ, Seigfried TE, Campbell DA (2008) MaizeGDB: the maize model organism database for basic, translational, and applied research. Int J Plant Genom 2008:496957Google Scholar
  198. Le Clerc V, Bazante F, Baril C, Guiard J, Zhang D (2005) Assessing temporal changes in genetic diversity of maize varieties using microsatellite markers. Theor Appl Genet 110:294–302PubMedGoogle Scholar
  199. Leakey ADB, Uribelarrea M, Ainsworth EA, Naidu SLO, Rogers A, Ort DR, Long SP (2006) Photosynthesis, productivity, and yield of maize are not affected by open-air elevation of CO2 concentration in the absence of drought. Plant Physiol 140:779–790PubMedPubMedCentralGoogle Scholar
  200. Lee M, Phillips RL (1987) Genomic rearrangements in maize induced by tissue culture. Genome 29:123–128Google Scholar
  201. Lee M, Sharopova N, Beavis WD, Grant D, Katt M, Blair D, Hallauer A (2002) Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population. Plant Mol Biol 48:453–461PubMedGoogle Scholar
  202. Leung H, Raghavan C, Zhou B, Oliva R, Choi IR, Lacorte V, Jubay ML, Cruz CV, Gregorio G, Singh RK (2015) Allele mining and enhanced genetic recombination for rice breeding. Rice 8:1Google Scholar
  203. Li Y, Ma X, Wang T, Li Y, Liu C, Liu Z, Sun B, Shi Y, Song Y, Carlone M, Bubeck D, Bhardwaj H, Whitaker D, Wilson W, Jones E, Wright K, Sun S, Niebur W, Smith S (2011) Increasing maize productivity in China by planting hybrids with germplasm that responds favorably to higher planting densities. Crop Sci 51:2391–2400Google Scholar
  204. Li X, Zhu C, Wang J, Yu J (2012a) Computer simulation in plant breeding. Adv Agron 116:219–264Google Scholar
  205. Li X, Zhu C, Yeh CT, Wu W, Takacs EM, Petsch KA, Tian F, Bai G, Buckler ES, Muehlbauer GJ, Timmermans MC, Scanlon MJ, Schnable PS, Yu J (2012b) Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Res 22:2436–2444PubMedPubMedCentralGoogle Scholar
  206. Li YH, Zhou G, Ma J, Jiang W, Jin LG, Zhang Z, Guo Y, Zhang J, Sui Y, Zheng L, Zhang SS, Zuo Q, Shi XH, Li YF, Zhang WK, Hu Y, Kong G, Hong HL, Tan B, Song J, Liu ZX, Wang Y, Ruan H, Yeung CK, Liu J, Wang H, Zhang LJ, Guan RX, Wang KJ, Li WB, Chen SY, Chang RZ, Jiang Z, Jackson SA, Li R, Qiu LJ (2014) De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol 32:1045–1052PubMedGoogle Scholar
  207. Li R, Hsieh CL, Young A, Zhang Z, Ren X, Zhao Z (2015) Illumina synthetic long read sequencing allows recovery of missing sequences even in the “Finished” C. elegans Genome. Sci Rep 5:10814PubMedPubMedCentralGoogle Scholar
  208. Li YX, Li C, Bradbury PJ, Liu X, Lu F, Romay CM, Glaubitz JC, Wu X, Peng B, Shi Y, Song Y, Zhang D, Buckler ES, Zhang Z, Li Y, Wang T (2016) Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population. Plant J 86:391–402PubMedGoogle Scholar
  209. Li H, Rasheed A, Hickey LT, He Z (2018) Fast-forwarding genetic gain. Trends Plant Sci 23:184–186PubMedGoogle Scholar
  210. Liang Z, Zhang K, Chen K, Gao C (2014) Targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system. J Genet Genom 41:63–68Google Scholar
  211. Liu K, Goodman M, Muse S, Smith JS, Buckler E, Doebley J (2003) Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165:2117–2128PubMedPubMedCentralGoogle Scholar
  212. Liu F, Zhu Y, Yi Y, Lu N, Zhu B, Hu Y (2014) Comparative genomic analysis of Acinetobacter baumannii clinical isolates reveals extensive genomic variation and diverse antibiotic resistance determinants. BMC Genom 15:1163Google Scholar
  213. Liu Z, Ren J, Trampe B, Frei UK, Lübberstedt T (2016) Doubled haploids: from obscure phenomenon to key technology of current maize breeding programs. Plant Breed Rev 40:123–166Google Scholar
  214. Liu C, Li X, Meng D, Zhong Y, Chen C, Dong X, Xu X, Chen B, Li W, Li L, Tian X, Zhao H, Song W, Luo H, Zhang Q, Lai J, Jin W, Yan J, Chen S (2017) A 4-bp insertion at ZmPLA1 encoding a putative phospholipase A generates haploid induction in maize. Mol Plant 10:520–522PubMedGoogle Scholar
  215. Longin CFH, Utz HF, Reif JC, Wegenast T, Schipprack W, Melchinger AE (2007) Hybrid maize breeding with doubled haploids: III. Efficiency of early testing prior to doubled haploid production in two-stage selection for tescross performance. Theor Appl Genet 115:519–527PubMedGoogle Scholar
  216. Longin CFH, Mi X, Wurschum T (2015) Genomic selection in wheat: optimum allocation of test resources and comparison of breeding strategies for line and hybrid breeding. Theor Appl Genet 128:1297–1306PubMedGoogle Scholar
  217. Lowe K, Wu E, Wang N, Hoerster G, Hastings C, Cho MJ, Scelonge C, Lenderts B, Chamberlin M, Cushatt J, Wang L, Ryan L, Khan T, Chow-Yiu J, Hua W, Yu M, Banh J, Bao Z, Brink K, Igo E, Rudrappa B, Shamseer PM, Bruce W, Newman L, Shen B, Zheng P, Bidney D, Falco C, Register J, Zhao ZY, Xu D, Jones T, Gordon-Kamm W (2016) Morphogenic regulators Baby boom and Wuschel improve monocot transformation. Plant Cell 28:1998–2015PubMedPubMedCentralGoogle Scholar
  218. Lu Y, Yan J, Guimaraes CT, Taba S, Hao Z, Gao S, Chen S, Li J, Zhang S, Vivek BS, Magorokosho C, Mugo S, Makumbi D, Parentoni SN, Shah T, Rong T, Crouch JH, Xu Y (2009) Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms. Theor Appl Genet 120:93–115PubMedGoogle Scholar
  219. Lu Y, Shah T, Hao Z, Taba S, Zhang S, Gao S, Liu J, Cao M, Wang J, Bhanu Pralash A, Rong TXuY (2011) Comparative SNP and haplotype analysis reveals a higher genetic diversity and rapider LD decay in tropical than temperate germplasm in maize. PLoS ONE 6(9):e24861PubMedPubMedCentralGoogle Scholar
  220. Lu F, Romay MC, Glaubitz JC, Bradbury PJ, Elshire RJ, Wang T, Li Y, Li Y, Semagn K, Zhang X, Hernandez AG, Mikel MA, Soifer I, Barad O, Buckler ES (2015) High-resolution genetic mapping of maize pan-genome sequence anchors. Nat Commun 6:6914PubMedPubMedCentralGoogle Scholar
  221. Magorokosho C (2006) Genetic diversity and performance of maize varieties from Zimbabwe, Zambia and Malawi. PhD thesis Texas A&M University, College Station, TX, 179 ppGoogle Scholar
  222. Makarevitch I, Waters AJ, West PT, Stitzer M, Hirsch CN, Ross-Ibarra J, Springer NM (2015) Transposable elements contribute to activation of maize genes in response to abiotic stress. PLoS Genet 11:e1004915PubMedPubMedCentralGoogle Scholar
  223. Mangelsdorf PC (1961) Introgression in maize. Euphytica 10:157–168Google Scholar
  224. Mariani C, De Beuckeleer M, Truettner J, Leemans J, Goldberg RB (1990) Induction of male sterility in plants by a chimaeric ribonuclease gene. Nature 347:737–741Google Scholar
  225. Markelz RJ, Strellner RS, Leakey ADB (2011) Impairment of C4 photosynthesis by drought is exacerbated by limiting nitrogen and ameliorated by elevated CO2 in maize. J Exp Bot 62:3235–3246PubMedGoogle Scholar
  226. Marulanda JJ, Mi X, Melchinger AE, Xu JL, Wurschum T, Longin CF (2016) Optimum breeding strategies using genomic selection for hybrid breeding in wheat, maize, rye, barley, rice and triticale. Theor Appl Genet 129:1901–1913PubMedGoogle Scholar
  227. Mastrodomenico AT, Hendrix CC, Below FE (2018) Nitrogen use efficiency and the genetic variation of maize expired plant variety protection germplasm. Agric Agric 8:3Google Scholar
  228. Masuka B, Atlin GN, Olsen M, Magorokosho C, Labuschagne M, Crossa J, Banziger M, Pixley KV, Vivek B, Biljon A, MacRobert JF, Alvarado G, Prasanna BM, Makumbi D, Makumbi D, Tarekegne AT, Das B, Zaman-Allah M, Cairns JE (2017a) Gains in maize genetic improvement in Eastern and Southern Africa : I. CIMMYT hybrid breeding pipeline. Crop Sci 57:168–179Google Scholar
  229. Masuka B, Magorokosho C, Olsen M, Atlin GN, Bänziger M, Pixley KV, Vivek BS, Labuschagne M, Matemba-Mutasa R, Burgueño J, Macrobert J, Prasanna BM, Das B, Makumbi D, Tarekegne A, Crossa J, Zaman-Allah M, van Biljon A, Cairns JE (2017b) Gains in maize genetic improvement in Eastern and Southern Africa: II. CIMMYT open-pollinated variety breeding pipeline. Crop Sci 57:180–191Google Scholar
  230. Matsuoka Y, Vigouroux Y, Goodman MM, Sanchez J, Buckler E, Doebley J (2002) A single domestication for maize shown by multilocus microsatellite genotyping. Proc Natl Acad Sci USA 99:6080–6084PubMedGoogle Scholar
  231. May BP, Liu H, Vollbrecht E, Senior L, Rabinowicz PD, Roh D, Pan X, Stein L, Freeling M, Alexander D, Martienssen R (2003) Maize-targeted mutagenesis: a knockout resource for maize. Proc Natl Acad Sci USA 100:11541–11546PubMedGoogle Scholar
  232. McCarty DR, Suzuki M, Hunter C, Collins J, Avigne WT, Koch KE (2013) Genetic and molecular analyses of UniformMu transposon insertion lines. Methods Mol Biol 1057:157–166PubMedGoogle Scholar
  233. McClintock B (1950) The origin and behavior of mutable loci in maize. Proc Natl Acad Sci USA 36:344–355PubMedGoogle Scholar
  234. MCGC (2016) Maize crop germplasm committee. USDA-ARS GRIN. Vulnerability statement recommendations. Accessed 12 Dec 2016
  235. Melchinger AE, Geiger HH, Schnell FW (1986) Epistasis in maize (Zea mays L.). Theor Appl Genet 72:231–239PubMedGoogle Scholar
  236. Melchinger AE, Schipprack W, Mi X, Mirdita V (2015) Oil content is superior to oil mass for identification of haploid seeds in maize produced with high-oil inducers. Crop Sci 55:188–195Google Scholar
  237. Merrill WL, Hard RJ, Mabry JB, Fritz GJ, Adams KR, Roney JR, MacWilliams AC (2009) The diffusion of maize to the southwestern United States and its impact. Proc Natl Acad Sci USA 106:21019–21026PubMedGoogle Scholar
  238. Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829PubMedPubMedCentralGoogle Scholar
  239. Mi X, Utz HF, Technow F, Melchinger AE (2014) Optimizing resource allocation for multistage selection in plant breeding with R package. Crop Sci 54:1413Google Scholar
  240. Mikel MA, Dudley JW (2006) Evolution of North American dent corn from public to proprietary germplasm. Crop Sci 46:1193–1205Google Scholar
  241. Mir C, Zerjal T, Combes V, Dumas F, Madur D, Bedoya C, Dreisigacker S, Franco J, Grudloyma P, Hao P, Hearne S, Jampatong C, Laloë D, Muthamia Z, Nguyen T, Prasanna B, Taba S, Xie C, Yunus M, Zhang S, Warburton M, Charcosset A (2013) Out of America: tracing the genetic footprints of the global diffusion of maize. Theor Appl Genet 126:2671–2682PubMedGoogle Scholar
  242. National Corn Growers Association (2018) World corn production, National Corn Growers Association (sourced from USDA, FAS Grain: World Markets and Trade) Accessed 12 Jan 2018
  243. Nelson PT, Goodman MM (2008) Evaluation of elite exotic maize inbreds for use in temperate breeding. Crop Sci 48:85–92Google Scholar
  244. Nelson PT, Krakowsky MD, Coles ND, Holland JB, Bubeck DM, Smith JSC, Goodman MM (2016) Genetic characterization of the North Carolina State University maize lines. Crop Sci 56:259–275Google Scholar
  245. Neuffer MG (1957) Additional evidence on the effect of X-ray and ultraviolet radiation on mutation in maize. Genetics 42:273–282Google Scholar
  246. Neuffer MG (1994) Mutagenesis. In: Freeling M, Walbot V (eds) The maize handbook. Springer, New York, pp 212–218Google Scholar
  247. Neuffer MG, Coe EH (1978) Paraffin oil technique for treating mature corn pollen with chemical mutagens. Maydica 23:21–28Google Scholar
  248. Neuffer MG, Fiscor G (1963) Mutagenic action of ethyl methanesulfonate in maize. Science 139:1296–1297PubMedGoogle Scholar
  249. Neuffer MG, Johal G, Chang MT, Hake S (2009) Mutagenesis—the key to genetic analysis. In: Bennetzen JL, Hake S (eds) The maize handbook. Springer, New York, pp 63–84Google Scholar
  250. Niu X, Xie R, Liu X, Zhang F, Li S, Gao S (2013) Maize yield gains in Northeast China in the last six decades. J Integr Agric 12:630–637Google Scholar
  251. NRC (1972) Committee on genetic vulnerability of major crops. (1972) Genetic vulnerability of major crops. Natl Acad Sci Washington DC, 307 ppGoogle Scholar
  252. NRC (1993) Committee on managing global genetic resources: agricultural imperatives. Board on agriculture. Natl Res Council National Academy Press, Washington DCGoogle Scholar
  253. Pace J, Gardner C, Romay C, Ganapathsybrumanian B, Lübberstedt T (2015) Genome-wide association analysis of seedling root development in maize. BMC Genom 16:47Google Scholar
  254. Paten B, Novak AM, Eizenga JM, Garrison E (2017) Genome graphs and the evolution of genome inference. Genome Res 27:665–676PubMedPubMedCentralGoogle Scholar
  255. Peccoud J, Velden KV, Podlich D, Winkler C, Arthur L, Cooper M (2004) The selective values of alleles in a molecular network model are context dependent. Genetics 166:1715–1725PubMedPubMedCentralGoogle Scholar
  256. Peiffer JA, Romay MC, Gore MA, Flint-Garcia SA, Zhang Z, Millard MJ, Gardner CA, McMullen MD, Holland JB, Bradbury PJ, Buckler ES (2014) The genetic architecture of maize height. Genetics 196:1337–1356PubMedPubMedCentralGoogle Scholar
  257. Peng T, Sun X, Mumm RH (2014a) Optimized breeding strategies for multiple trait integration: I Minimizing linkage drag in single event introgression. Mol Breed 33:89–104PubMedGoogle Scholar
  258. Peng T, Sun C, Mumm RH (2014b) Optimized breeding strategies for multiple trait integration: II Process efficiency in event pyramiding and trait fixation. Mol Breed 33:105–115PubMedGoogle Scholar
  259. Peterson P (1953) A mutable pale green locus in maize. Genetics 38:682–683Google Scholar
  260. Piepho H-P (2009) Ridge regression and extensions for genomewide selection in maize. Crop Sci 49:1165–1176Google Scholar
  261. Piperno DR, Ranere AJ, Holst I, Inarte J, Dickau R (2009) Starch grain and phytolith evidence for early ninth millennium B.P. maize from the Central Balsas River Valley. Mexico. Proc Natl Acad Sci USA 106:5019–5024PubMedGoogle Scholar
  262. Pixley KV (2006) Hybrid and open-pollinated varieties in modern agriculture. In: Lamkey KR, Lee M (eds) Plant breeding: the Arnel R. Hallauer international symposium. Blackwell Publishing, AmesGoogle Scholar
  263. Podlich DW, Cooper M (1998) Qu-GENE: a simulation platform for quantitative analysis of genetic models. Bioinformatics 14:632–653PubMedGoogle Scholar
  264. Poland JA, Bradbury PJ, Buckler ES, Nelson RJ (2011) Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc Natl Acad Sci USA 108:6893–6898PubMedGoogle Scholar
  265. Pollacsek M (1992) Management of the ig gene for haploid induction in maize. Agronomie 12:247–251Google Scholar
  266. Pong-Wong R, Woolliams JA (2007) Optimisation of contribution of candidate parents to maximise genetic gain and restricting inbreeding using semidefinite programming. Genet Sel Evol 39:3–25PubMedPubMedCentralGoogle Scholar
  267. Prasanna BM (2012) Diversity in global maize germplasm: characterization and utilization. J Biosci 37:843–855PubMedGoogle Scholar
  268. Puchta H, Hohn B (2010) Breaking news: plants mutate right on target. Proc Natl Acad Sci USA 107:1165–11658Google Scholar
  269. Putnam NH, O’Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, Troll CJ, Fields A, Hartley PD, Sugnet CW, Haussler D, Rokhsar DS, Green RE (2016) Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res 26:342–350PubMedPubMedCentralGoogle Scholar
  270. Qin X, Feng F, Li Y, Xu S, Siddique KHM, Liao Y (2016) Maize yield improvements in China: past trends and future directions. Plant Breed 135:166–176Google Scholar
  271. Randolph LF (1940) Note on haploid frequencies. Maize Genet Coop Newsl 14:23–24Google Scholar
  272. Ray DK, Ramankutty N, Mueller ND, West PC, Foley JA (2012) Recent patterns of crop yield growth and stagnation. Nat Commun 3:1293PubMedGoogle Scholar
  273. Reif JC, Melchinger AE, Xia XC, Warburton ML, Hoisington DA, Vasal SK, Beck S, Bohn M, Frisch M (2003) Use of SSRs for establishing heterotic groups in subtropical maize. Theor Appl Genet 107:947–957PubMedGoogle Scholar
  274. Reif JC, Fischer S, Schrag TA, Lamkey KR, Klein D, Dhillon BS, Utz HF, Melchinger AE (2010) Broadening the genetic base of European maize heterotic pools with US Cornbelt germplasm using field and molecular marker data. Theor Appl Genet 120:301–310PubMedGoogle Scholar
  275. Ren J, Wu P, Tian X, Lübberstedt T, Chen SJ (2017) Fine mapping of quantitative trait locus qhmf4 causing haploid male fertility in maize based on segregation distortion. Theor Appl Genet 130:1349–1359PubMedGoogle Scholar
  276. Rendel JM, Robertson A (1950) Estimation of gnetic gain in milk yield by selection ina closed herd of dairy cattle. Journal of Genetics 50:1–8PubMedGoogle Scholar
  277. Rhoades M (1931) Cytoplasmic inheritance of male sterility in Zea mays. Science 73:340–341PubMedGoogle Scholar
  278. Rhoades MM (1938) Effect of Dt gene on the mutability of the a1 allele in maize. Genetics 23:377–397PubMedPubMedCentralGoogle Scholar
  279. Rhodes CA, Pierce DA, Mettler IJ, Mascarenhas D, Detmer JJ (1988) Genetically transformed maize plants from protoplasts. Science 240:204–207PubMedGoogle Scholar
  280. Robertson A (1957) Optimum group size in progeny testing and family selection. Biometrics 13:442–450Google Scholar
  281. Robertson A (1960) A theory of limits in artificial selection. Proc R Soc Lond 153:234–249Google Scholar
  282. Rogers DL, McGuire PE (2015) Genetic erosion: context is key. In: Ahuja MR, Jain SM (eds) Genetic diversity and erosion in plants. Springer, New York, pp 1–24Google Scholar
  283. Romay MC, Millard MJ, Glaubitz JC, Peiffer JA, Swarts KL, Casstevens TM, Elshire RJ, Acharya CB, Mitchell SE, Flint-Garcia SA, McMullen MD, Holland JB, Buckler ES, Gardner CA (2013) Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol 14:R55PubMedPubMedCentralGoogle Scholar
  284. Romero Navarro JA, Willcox M, RomayC Swarts K, Trachsel S, Preciado E, Terron A, Delgado HV, Vidal V, OrtegaA Banda AE, Montiel NO, Ortiz-Monasterio I, Vicente FS, EspinozaAG Atlin G, WenzlP Hearne S, Buckler S (2017) A study of allelic diversity underlying flowering-time adaptation in maize landraces. Nat Genet 49:476–480PubMedGoogle Scholar
  285. Ronaghi M, Uhlen M, Nyren P (1998) A sequencing method based on real-time pyrophosphate. Science 281(363):365Google Scholar
  286. Rotarenco VA, Dicu G, State D, Fuia S (2010) New inducers of maternal haploids in maize. Maize Genet Coop Newslett 84:1–7Google Scholar
  287. Sanchez D, Liu S, Ibrahim R, Blanco M, Lübberstedt T (2018) Association mapping of seedling root traits in exotic derived doubled haploid lines of maize. Plant Sci 268:30–38PubMedGoogle Scholar
  288. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467PubMedGoogle Scholar
  289. Sarvella P, Grogan CO (1967) The mutagenic effects of gamma rays on Zea mays in relation to ear location. Radiat Bot 7:107–111Google Scholar
  290. Schnable JC, Freeling M (2011) Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize. PLoS ONE 6:e17855PubMedPubMedCentralGoogle Scholar
  291. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115PubMedGoogle Scholar
  292. Schneerman MC, Charbonneau M, Weber DF (2000) A survey of ig containing materials. Maize Genet Coop Newslett 74:92–93Google Scholar
  293. Schrag TA, Westhues M, Schipprack W, Seifert F, Thiemann A, Scholten S, Melchinger AE (2018) Beyond genomic prediction: combining different types of omics data can improve prediction of hybrid performance in maize. Genetics 208:1373–1385PubMedGoogle Scholar
  294. Schwartz DC, Li X, Hernandez LI, Ramnarain SP, Huff EJ, Wang YK (1993) Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262:110–114PubMedGoogle Scholar
  295. Segerman B (2012) The genetic integrity of bacterial species: the core genome and the accessory genome, two different stories. Front Cell Infect Microbiol 2:116PubMedPubMedCentralGoogle Scholar
  296. Servin B, Martin OC, Mezard M, Hospital F (2004) Toward a theory of marker-assisted gene pyriamiding. Genetics 168:513–523PubMedPubMedCentralGoogle Scholar
  297. Shi J, Gao H, Wang H, Lafitte R, Archibald RL, Yang M, Hakimi SH, Mo H, Habben J (2017) ARGOS8 variants generated by CRISPR-Cas9 improve maize grain under field drought stress conditions. Plant Biotechnol J 15:2017–2216Google Scholar
  298. Shukla VP, Doyon Y, Miller JC, DeKelver RC, Moehle EA, Worden SE, Mitchell JC, Arnold NL, Gopalan S, Meng X, Choi VM, Rock JM, Wu YY, Katibah GE, Zhifang G, McCaskill D, Simpson MA, Blakeslee B, Greenwalt SA, Butler HJ, Hinkley SJ, Zhang L, Rebar EJ, Gregory PD, Urnov FD (2009) Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459:437–441PubMedGoogle Scholar
  299. Shull GH (1908) The composition of a field of maize. Am Breeders Assoc Rep 4:296–301Google Scholar
  300. Singleton WR (1941) Hybrid vigor and its utilization in sweet corn breeding. Am Nat 75:48–60Google Scholar
  301. Smith HF (1936) A discriminant function for plant selections. Ann Eugenetics 7:240–250Google Scholar
  302. Smith OS (1986) Covariance between line per se and testcross performance. Crop Sci 26:540–543Google Scholar
  303. Smith JSC, Smith OS (1991) Restriction fragment length polymorphisms can differentiate among U.S. maize hybrids. Crop Sci 31:893–899Google Scholar
  304. Smith DR, White DG (1988) Diseases of corn. In: Sprague GF, Dudley JW (eds) Corn and corn improvement, III edn. American Society of Agronomy, Madison, pp 687–766Google Scholar
  305. Smith JSC, Smith OS, Wright S, Wall SJ, Walton W (1992) Diversity of U.S. hybrid maize germplasm as revealed by restriction fragment length polymorphisms. Crop Sci 32:598–604Google Scholar
  306. Smith S, Cooper M, Gogerty J, Löffler C, Borcherding D, Wright K (2014) Maize. In: Smith et al (ed) Yield gains in major U.S. field crops. CSSA Spec. Publ. 33. ASA, CSSA, and SSSA, Madison, pp 125–171Google Scholar
  307. Smith JS, Gardner CA, Costich DE (2017) Ensuring the genetic diversity of maize and its wild relatives. In: Watson D (ed) Achieving sustainable cultivation of maize. Burleigh Dodds, CambridgeGoogle Scholar
  308. Springer NM, Stupar RM (2007) Allelic variation and heterosis in maize: how do two halves make more than a whole? Genome Res 17:264–275PubMedGoogle Scholar
  309. Springer N, Anderson SN, Andorf C, Ahern K, Bai F, Barad O, Barbazuk WB, Bass HW, Baruch K, Ben-Zvi G, Buckler ES, Bukowski R, Campbell MS, Cannon EKS, Chomet P, Dawe RK, Davenport R, Dooner HK, Du LH, Du C, Easterling KA, Gault C, Guan J-C, Jander G, Hunter CT, Jiao Y, Koch KE, Kol G, Kudo T, Li Q, Lu F, Mayfield-Jones D, Mei W, McCarty DR, Noshay J, Ronen G, Settles MA, Shem-Tov D, Shi J, Soifer I, Stein JC, Suzuki M, Vera DL, Vollbrecht E, Vrebalov JT, Ware D, Wei X, Wimalanathan K, Woodhouse MR, Xiong W, Brutnell TP (2018) The W22 genome: a foundation for maize functional genomics and transposon biology. Nat Genet 50(9):1282–1288PubMedGoogle Scholar
  310. St Martin SA, Skavaril RV (1984) Computer simulation as a tool in teaching introductory plant breeding. J Agron Educ 13:43–47Google Scholar
  311. Stadler LJ (1949) A note on haploidy in maize (unpublished)Google Scholar
  312. Stadler LJ, Sprague GF (1936) Genetic effects of ultra-violet radition in maize. II. Filtered raditions. Genetics 22:579–583Google Scholar
  313. Stadler LJ, Uber F (1942) Genetic effects of ultra-violet radiation in maize.IV. Comparison of monochromatic radiations. Genetics 27:84–118PubMedPubMedCentralGoogle Scholar
  314. Stuber CW, Lincoln SE, Wolff DW, Helentjaris T, Lander ES (1992) Identification of genetic factors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers. Genetics 132:823–839PubMedPubMedCentralGoogle Scholar
  315. Sun X, Peng T, Mumm RH (2011) The role and basics of computer simulation in support of critical decision in plant breeding. Mol Breed 28:421–436Google Scholar
  316. Sun C, Hu Z, Zheng T, Lu K, Zhao Y, Wang W, Shi J, Wang C, Lu J, Zhang D, Li Z, Wei C (2017) RPAN: rice pan-genome browser for approximately 3000 rice genomes. Nucleic Acids Res 45:597–605PubMedGoogle Scholar
  317. Sun S, Zhou Y, Chen J, Shi J, Zhao H, Zhao H, Song W, Zhang M, Cui Y, Dong X, Liu H, Ma X, Jiao Y, Wang B, Wei X, Stein JC, Glaubitz JC, Lu F, Yu G, Liang C, Fengler K, Li B, Rafalski A, Schnable PS, Ware DH, Buckler ES, Lai J (2018) Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nat Genet 50:1289–1295PubMedGoogle Scholar
  318. Svitashev S, Young JK, Schwartz C, Gao H, Falco SC, Cigan MA (2015) Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 guide RNA. Plant Physiol 169:931–945PubMedPubMedCentralGoogle Scholar
  319. Svitashev S, Schwartz C, Lenderts B, Young JK, Cigan MA (2016) Genome editing in maize by CRISPR-Cas9 ribonucleoprotein complexes. Nat Commun 7:13274PubMedPubMedCentralGoogle Scholar
  320. Swarts K, Gutaker RM, Benz B, Blake M, Bukowski R, Holland J, Kruse-Peeples M, Lepak N, Prim L, Cinta Romay M, Ross-Ibarra J, de Jesus Sanchez-Gonzalez J, Schmidt C, Schuenemann VJ, Krause J, Matson RG, Weigel D, Buckler ES, Burbano HA (2017) Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science 357:512–515PubMedGoogle Scholar
  321. Technow F, Messina CD, Totir LR, Cooper M (2015) Integrating crop growth models with whole genome prediction through approximate Bayesian computation. PLoS ONE 10:e0130855PubMedPubMedCentralGoogle Scholar
  322. Tello-Ruiz MK, Naithani S, Stein JC, Gupta P, Campbell M, Olson A, Wei S, Preece J, Geniza MJ, Jiao Y, Lee YK, Wang B, Mulvaney J, Chougule K, Elser J, Al-Bader N, Kumari S, Thomason J, Kumar V, Bolser DM, Naamati G, Tapanari E, Fonseca N, Huerta L, Iqbal H, Keays M, Munoz-Pomer Fuentes A, Tang A, Fabregat A, D’Eustachio P, Weiser J, Stein LD, Petryszak R, Papatheodorou I, Kersey PJ, Lockhart P, Taylor C, Jaiswal P, Ware D (2018) Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res 46:D1181–D1189PubMedGoogle Scholar
  323. Tenaillon MI, Charcosset A (2011) A European perspective on maize history. CR Biol 334:221–228Google Scholar
  324. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O’Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci USA 102:13950–13955PubMedGoogle Scholar
  325. Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43:159–162PubMedGoogle Scholar
  326. Till BJ, Reynolds SH, Weil C, Springer N, Burtner C, Young K, Bowers E, Codomo CA, Enns LC, Odden AR, Greene EA, Comai L, Henikoff S (2004) Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 4:12PubMedPubMedCentralGoogle Scholar
  327. Tinker NA, Mather DE (1993) GREGOR: software for genetic simulation. J Hered 84:237Google Scholar
  328. Troyer AF (1999) Background of U.S. hybrid corn. Crop Sci 39:601–626Google Scholar
  329. Troyer AF (2006) Adaptedness and heterosis in corn and mule hybrids. Crop Sci 46:528–543Google Scholar
  330. Troyer AF, Wellin EJ (2009) Heterosis decreasing in hybrids: yield test inbreds. Crop Sci 49:1969–1976Google Scholar
  331. Unterseer S, Pophaly SD, Peis R, Westermeier P, Manfred M, Seidel MA, Haberer G, Mayer KFX, Ordas B, Pausch H, Tellier A, Bauer E, Schon C-C (2016) A comprehensive study of the genomic differentiation between temperate Dent and Flint maize. Genome Biol 17:137PubMedPubMedCentralGoogle Scholar
  332. Unterseer S, Seidel MA, Bauer E, Haberer G, Hochholdinger F, Opitz N, Marcon C, Baruch K, Spannagl M, Mayer KFX, Schön C-C (2017) European Flint reference sequences complement the maize pan-genome. bioRxiv
  333. van Heerwaarden J, Doebley J, Briggs WH, Glaubitz JC, Goodman MM, de Jesus Sanchez Gonzalez J, Ross-Ibarra J (2011) Genetic signals of origin, spread, and introgression in a large sample of maize landraces. Proc Natl Acad Sci USA 108:1088–1092PubMedGoogle Scholar
  334. van Heerwaarden J, Hufford MB, Ross-Ibarra J (2012) Historical genomics of North American maize. Proc Natl Acad Sci USA 109:12420–12425PubMedGoogle Scholar
  335. Vanous A, Gardner C, Blanco M, Martin-Schwarze A, Flint-Garcia S, Bohn M, Edwards J, Lübberstedt T (2018) Association mapping of flowering and plant height traits in germplasm enhancement of maize doubled haploid (GEM-DH) lines. The Plant Genome 11:170083Google Scholar
  336. Vernikos G, Medini D, Riley DR, Tettelin H (2015) Ten years of pan-genome analyses. Curr Opin Microbiol 23:148–154PubMedGoogle Scholar
  337. Vigouroux Y, Glaubitz JC, Matsuoka Y, Goodman MM, Sánchez GJ, Doebley J (2008) Population structure and genetic diversity of New World maize races assessed by DNA microsatellites. Am J Bot 95:1240–1253PubMedGoogle Scholar
  338. Visscher PM, Haley CS, Thompson R (1996) Marker-assisted introgression in backcross breeding programs. Genetics 144:1923–1932PubMedPubMedCentralGoogle Scholar
  339. Voelkerding KV, Dames SA, Durtschi JD (2009) Next-generation sequencing: from basic research to diagnostics. Clin Chem 55:641–658PubMedGoogle Scholar
  340. Vollbrecht E, Duvick J, Schares JP, Ahern KR, Deewatthanawong P, Xu L, Conrad LJ, Kikuchi K, Kubinec TA, Hall BD, Weeks R, Unger-Wallace E, Muszynski M, Brendel VP, Brutnell TP (2010) Genome-wide distribution of transposed Dissociation elements in maize. Plant Cell 22:1667–1685PubMedPubMedCentralGoogle Scholar
  341. Voss-Fels K, Snowdon RJ (2016) Understanding and utilizing crop genome diversity via high-resolution genotyping. Plant Biotechnol J 14:1086–1094PubMedGoogle Scholar
  342. Wallace JG, Bradbury PJ, Zhang N, Gibon Y, Stitt M, Buckler ES (2014) Association mapping across numerous traits reveals patterns of functional variation in maize. PLoS Genetics 10:e1004845PubMedPubMedCentralGoogle Scholar
  343. Wang Q, Dooner HK (2006) Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proc Natl Acad Sci USA 103:17644–17649PubMedGoogle Scholar
  344. Wang AS, Evans RA, Altendorf PR, Hanten JA, Doyle MC, Rosichan JL (2000) A mannose selection system for production of fertile transgenic maize plants from protoplasts. Plant Cell Rep 19:654–660PubMedGoogle Scholar
  345. Wang K, Frame B, Marcell L (2003a) Maize genetic transformation. In: Jaiwal PK, Singh RP (eds) Plant genetic engineering, vol 2. Improvement of food crops. Sci-Tech Publication, Houston, pp 175–217Google Scholar
  346. Wang X, Van Ginkel M, Podlich D, Ye G, Trethowan R, Pfeiffer W, DeLacy IH, Cooper M, Rajaram S (2003b) Comparison of two breeding strategies by computer simulation. Crop Sci 43:1764–1773Google Scholar
  347. Wang J, van Ginkel M, Trethowan R, Ye G, DeLacy I, PodlichD Cooper M (2004) Simulating the effects of dominance and epistasis on selection response in the CIMMYT wheat breeding program using QuCim. Crop Sci 44:2006–2018Google Scholar
  348. Wang J, Chapman SC, Bonnett DG, Rebetzke GJ, Crouch J (2007) Application of population genetic theory and simulation models to efficiently pyramid multiple genes via marker-assisted selection. Crop Sci 47:582–590Google Scholar
  349. Watson A, Ghosh S, Williams M, Cuddy WS, Simmonds J, Rey M-D, Hatta MAM, Hinchlife A, Steed A, Reynolds D, Adamski N, Breakspear A, Korolev A, Rayner T, Dixon LE, Riaz A, Martin W, Ryan M, Edwards D, Batley J, Raman H, Rogers C, Domoney C, Moore G, Harwood W, Nicholson P, Dieters MJ, DeLacy IH, Zhou J, Uauy C, Boden SA, Park RF, Wulf BBH, Hickey LT (2017) Speed breeding: a powerful tool to accelerate crop research and breeding. Nat Plants 4:23–29Google Scholar
  350. Weber D, Helentjaris T (1989) Mapping RFLP loci in maize using B–A translocations. Genetics 121:583–590PubMedPubMedCentralGoogle Scholar
  351. Wei F, Zhang J, Zhou S, He R, Schaeffer M, Collura K, Kudrna D, Faga BP, Wissotski M, Golser W, Rock SM, Graves TA, Fulton RS, Coe E, Schnable PS, Schwartz DC, Ware D, Clifton SW, Wilson RK, Wing RA (2009) The physical and genetic framework of the maize B73 genome. PLoS Genet 5:e1000715PubMedPubMedCentralGoogle Scholar
  352. Wellhausen EJ, Roberts LM, Hernandez X, Mangelsdorf PC (1952) Races of maize in Mexico: their origin, characteristics and distribution. Bussey Inst Harvard Univ Cambridge, Mass, p 222Google Scholar
  353. Wen W, Araus JL, Shah T, Cairns J, Mahuku G, Bänziger M, Torres JL, Sánchez C, Yan J (2011) Molecular characterization of a diverse maize inbred line collection and its potential utilization for stress tolerance improvement. Crop Sci 51:2569–2581Google Scholar
  354. Westengen OT, Berg PR, Kent MP, Brysting AK (2012) Spatial structure and climatic adaptation in African maize revealed by surveying SNP diversity in relation to global breeding and landrace panels. PLoS ONE 7(10):e47832PubMedPubMedCentralGoogle Scholar
  355. Whittaker JC, Thompson R, Denham MC (2000) Marker-assisted selection using ridge regression. Genet Res 75:249–252PubMedGoogle Scholar
  356. Wilcox JR, Cavins JF (1995) Backcrossing high seed protein to a soybean cultivar. Crop Sci 35:1036–1041Google Scholar
  357. Williams ME (2016) Alternative mutagens for maize (Zea mays L.). Maize Genom Genet 7:1–8Google Scholar
  358. Winston WL, VenkataramananM, Goldberg JB (2003) Introduction to mathematical programming, vol 1. Operations Research, 4 edn. Brooks/Cole, Pacific Grove, CAGoogle Scholar
  359. Woodhouse MR, Schnable JC, Pedersen BS, Lyons E, Lisch D, Subramaniam S, Freeling M (2010) Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biol 8:e1000409PubMedPubMedCentralGoogle Scholar
  360. Woolliams JA, Berg P, Dagnachew BS, Meuwissen TH (2015) Genetic contributions and their optimization. J Anim Breed Genet 132:89–99PubMedGoogle Scholar
  361. Wu Y, Frei UK, Liu H, De La Fuente G, Huang K, Wei Y, Lübberstedt T (2015) Combining genomic selection and doubled haploid technology increases efficiency of maize breeding. In: Govil JN (ed) Recent developments in biotechnology, vol 2. Plant Biotechnology. Studium Press, pp 215–237Google Scholar
  362. Wu Y, Fox TW, Trimnell MR, Wang L, Xu RJ, Cigan AM, Huffman GA et al (2016) Development of a novel recessive genetic male sterility system for hybrid seed production in maize and other cross-pollinating crops. Plant Biotechnol J 14:1046–1054PubMedGoogle Scholar
  363. Wych RD (1988) Production of hybrid seed corn. In: Sprague GF (ed) Corn and corn improvement. American Society of Agronomy Inc, Crop Science Society of America, and Soil Science Society of America, Madison, pp 565–607Google Scholar
  364. Xing HL, Dong L, Wang ZP, Zhang HY, Han CY, Liu B, Wang XC, Chen QJ (2014) A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol 14:327PubMedPubMedCentralGoogle Scholar
  365. Xu Y (2016) Envirotyping for deciphering environmental impacts on crop plants. Theor Appl Genet 129:653–673PubMedPubMedCentralGoogle Scholar
  366. Xu P, Wang L, Beavis WD (2011) An optimization approach to gene stacking. Eur J Oper Res 214:168–178Google Scholar
  367. Xu Y, Li P, Zou C, Lu Y, Xie C, Zhang X, Prasanna BM, Olsen MS (2017) Enhancing genetic gain in the era of molecular breeding. J Exp Bot 68:2641–2666PubMedGoogle Scholar
  368. Yang N, Xu X-W, Wang R-R, Peng W-L, Cai L, Song J-M, Li W, Luo X, Niu L, Wang Y, Jin M, Chen L, Luo J, Deng M, Wang L, Pan Q, Liu F, Jackson D, Yang X, Chen L-L, Yan J (2017a) Contributions of Zea mays subspecies mexicana haplotypes to modern maize. Nat Commun 8:1874PubMedPubMedCentralGoogle Scholar
  369. Yang J, Mezmouk S, Baumgarten A, Buckler ES, Guill KE, McMullen MD, Mumm RH, Ross-Ibarra J (2017b) Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. PLoS Genet 13:e1007019PubMedPubMedCentralGoogle Scholar
  370. Ye G, Smith KF (2008) Marker-assisted gene pyramiding for inbred line development: basic principles and practical guidelines. Int J Plant Breed 2:1–10Google Scholar
  371. Yim YS, Davis GL, Duru NA, Musket TA, Linton EW, Messing JW, McMullen MD, Soderlund CA, Polacco ML, Gardiner JM, Coe EH Jr (2002) Characterization of three maize bacterial artificial chromosome libraries toward anchoring of the physical map to the genetic map using high-density bacterial artificial chromosome filter hybridization. Plant Physiol 130:1686–1696PubMedPubMedCentralGoogle Scholar
  372. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92PubMedGoogle Scholar
  373. Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178:539–555PubMedPubMedCentralGoogle Scholar
  374. Yu X, Li X, Guo T, Zhu C, Wu Y, Mitchell SE, Roozeboom KL, Wang D, Wang ML, Pederson GA, Tesso TT, Schnable PS, Bernardo R, Yu J (2016) Genomic prediction contributing to a promising global strategy to turbocharge gene banks. Nat Plants 2:16150PubMedGoogle Scholar
  375. Zabirova ER, Shatskaya OA, Shcherbak VS (1993) Line 613/2 as a source of a high frequency of spontaneous diploidization in corn. Maize Genet Coop Newsl 67:67Google Scholar
  376. Zhang X, Zhang H, Li L, Lan H, Ren Z, Liu D, Wu L, Liu H, Jaqueth J, Li B, Pan G, Gao S (2016) Characterizing the population structure and genetic diversity of maize breeding germplasm in Southwest China using genome-wide SNP markers. BMC Genom 17:697Google Scholar
  377. Zhang D, Wu S, An X, Xie K, Dong Z, Zhou Y, Xu L, Fang W, Liu S, Liu S, Zhu T, Li J, Rao L, Zhao J, Wan X (2018) Male-sterile line and hybrid seed production based on the ZmMs7 gene encoding a PHD-finger transcription factor. Plant Biotech J 16:459–471Google Scholar
  378. Zhao Z-Y, Gu W, Cai T, Tagliani L, Hondred D, Bond D, Schroeder S, Rudert M, Pierce D (2001) High throughput genetic transformation mediated by Agrobacterium tumefaciens in maize. Mol Breed 8:323–333Google Scholar
  379. Zhao Y, Mette MF, Reif JC (2015) Genomic selection in hybrid breeding. Plant Breed 134:1–10Google Scholar
  380. Zila CT, Ogut F, Romay MC, Gardner CA, Buckler ES, Holland JB (2014) Genome-wide association study of Fusarium ear rot disease in the. BMC Plant Biol 14:372PubMedPubMedCentralGoogle Scholar
  381. Zuber MS, Darrah DL (1981) 1979 U.S. corn germplasm base. In: Proceedings of the 35th Ann Corn and Sorghum Ind Res Conf. ,Washington DC American Seed Trade Association, pp 234–249Google Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Carson Andorf
    • 1
  • William D. Beavis
    • 2
  • Matthew Hufford
    • 3
  • Stephen Smith
    • 2
  • Walter P. Suza
    • 2
  • Kan Wang
    • 2
  • Margaret Woodhouse
    • 1
  • Jianming Yu
    • 2
  • Thomas Lübberstedt
    • 2
    Email author
  1. 1.USDA-ARSAmesUSA
  2. 2.Department of AgronomyIowa State UniversityAmesUSA
  3. 3.Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesUSA

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