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Genetic Mapping and Maps

  • Karen C. Cone
  • Edward H. Coe

Early genetic analyses of maize were rooted in genetic mapping, and mapping continues to be an important tool for contemporary maize geneticists. Mapping is extraordinarily easy in maize; consequently many maps have been made. The first genetic map published for maize in 1935 contained 62 loci defined by morphological variants. Current genetic maps contain thousands of loci defined by morphological, biochemical, cytogenetic, and molecular polymorphic variants. These maps serve critically important functions in linking genes to traits, facilitating comparative evolutionary studies, enabling positional cloning, and anchoring the physical map for genome sequencing. Sequencing in turn now makes it possible to derive the map locations of sequenced genes by matching to genomic sequences that have been anchored to the physical map.

Keywords

Bacterial Artificial Chromosome Bacterial Artificial Chromosome Clone Bacterial Artificial Chromosome Library Maize Genome Recombination Nodule 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. Anderson, E. (1935) Chromosomal interchanges in maize. Genetics 200: 70– 83.Google Scholar
  2. Anderson, E. (1945) The following tables are compiled for the benefit of those using or wanting to use the sugary and waxy series of translocations for the study of economic or other characters in maize. MNL 19: 5– 8.Google Scholar
  3. Anderson, L. K., A. Lai, S. M. Stack, C. Rizzon and B. S. Gaut (2006) Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes. Genome Res. 16: 115– 122.PubMedCrossRefGoogle Scholar
  4. Anderson, L. K., N. Salameh, H. W. Bass, L. C. Harper, W. Z. Cande, G. Weber and S. M. Stack (2004) Integrating genetic linkage maps with pachytene chromosome structure in maize. Genetics 166: 1923– 1933.PubMedCrossRefGoogle Scholar
  5. Basten, C., B. S. Weir and Z.-B. Zeng (1997) QTL Cartographer: A reference manual and tutorial for QTL mapping. http://statgen.ncsu.edu/qtlcart/. Raleigh, N.C., Department of Statistics, North Carolina State University.
  6. Beckett, J. B. (1991) Cytogenetic, genetic and plant breeding applications of B-A translocations in maize. In Chromosome Engineering in Plants: Genetics Breeding, Evolution. (P. Gupta and T. Tsuchiya, ed.) Elsevier Science Publishers, New York, pp. 493– 529.Google Scholar
  7. Bennetzen, J. L. and M. Freeling (1997) The unified grass genome: Synergy in synteny. Genome Res. 7: 301– 306.PubMedGoogle Scholar
  8. Bi, I. V., M. D. McMullen, H. Sanchez-Villeda, S. Schroeder, J. Gardiner, M. Polacco, C. Soderlund, R. Wing, Z. Fang and E. H. Coe (2006) Single nucleotide polymorphisms and insertion-deletions for genetic markers and anchoring the maize fingerprint contig physical map. Crop Sci. 46: 12– 21.CrossRefGoogle Scholar
  9. Bortiri, E., G. Chuck, E. Vollbrecht, T. Rocheford, R. Martienssen and S. Hake (2006a) ramosa2 encodes a LATERAL ORGAN BOUNDARY domain protein that determines the fate of stem cells in branch meristems of maize. Plant Cell 18: 574– 585.CrossRefGoogle Scholar
  10. Bortiri, E., D. Jackson and S. Hake (2006b) Advances in maize genomics: the emergence of positional cloning. Curr. Op. Plant Biology 9: 164– 171.CrossRefGoogle Scholar
  11. Buckler, E. S., B. S. Gaut and M. D. McMullen (2006) Molecular and functional diversity of maize. Curr. Op. Plant Biology 9: 172– 176.CrossRefGoogle Scholar
  12. Burr, B. and F. A. Burr (1991) Recombinant inbreds for molecular mapping in maize: theoretical and practical considerations. Trends Genet. 7: 55– 60.PubMedGoogle Scholar
  13. Burr, B., F. A. Burr, K. H. Thompson, M. C. Albertson and C. W. Stuber (1988) Gene mapping with recombinant inbreds in maize. Genetics 118: 519– 526.PubMedGoogle Scholar
  14. Carson, C., J. Robertson and E. Coe (2004) High-volume mapping of maize mutants with simple sequence repeat markers. Plant Mol. Biol. Rep. 22: 131– 143.CrossRefGoogle Scholar
  15. Casa, A., C. Brouwer, A. Nagel, L. Wang, Q. Zhang, S. Kresovich and S. Wessler (2000) The MITE family heartbreaker (Hbr): molecular markers in maize. Proc. Natl. Acad. Sci. USA 97:10083– 10089PubMedCrossRefGoogle Scholar
  16. Casa, A., A. Nagel and S. Wessler (2004) MITE display. Methods Mol. Biol. 260: 175– 188.PubMedGoogle Scholar
  17. Chuck, G., A. Cigan, K. Saeteurn and S. Hake (2007) The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA. Nat. Genet. 39: 544– 549.PubMedCrossRefGoogle Scholar
  18. Coe, E. (1993) Gene list and working maps. MNL 67.Google Scholar
  19. Coe, E., K. Cone, M. McMullen, S. S. Chen, G. Davis, J. Gardiner, E. Liscum, M. Polacco, A.Paterson, H. Sanchez– Villeda, C. Soderlund and R. Wing (2002) Access to the maize genome: An integrated physical and genetic map. Plant Physiol. 128: 9– 12.PubMedCrossRefGoogle Scholar
  20. Coe, E., D. J. Hancock, S. Kowalewski and M. Schaeffer (1995) Gene list and working maps.MNL 69M: 191– 256.Google Scholar
  21. Coe, E. and M. Neuffer (1977) The genetics of corn. In: Corn and Corn Improvement. (G. Sprague,ed.) American Society of Agronomy, Madison, WI, pp. 111– 223.Google Scholar
  22. Coe, E., M. Neuffer and D. A. Hoisington (1988) The genetics of corn. In: Corn and Corn Improvement. (G. Sprague and J. Dudley, ed.) American Society of Agronomy, Madison, WI,pp. 81– 258.Google Scholar
  23. Coe, E. and M. Schaeffer (2005) Genetic, physical, maps, and database resources for maize. Maydica 50: 285– 303.Google Scholar
  24. Cone, K. C., M. D. McMullen, I. V. Bi, G. L. Davis, Y. S. Yim, J. M. Gardiner, M. L. Polacco, H.Sanchez-Villeda, Z. W. Fang, S. G. Schroeder, S. A. Havermann, J. E. Bowers, A. H. Paterson,C. A. Soderlund, F. W. Engler, R. A. Wing and E. H. Coe (2002) Genetic, physical, and informatics resources for maize: on the road to an integrated map. Plant Physiol. 130: 1598– 1605.PubMedCrossRefGoogle Scholar
  25. Davis, G. L., M. D. McMullen, C. Baysdorfer, T. Musket, D. Grant, M. Staebell, G. Xu, M. Polacco, L. Koster, S. Melia-Hancock, K. Houchins, S. Chao and E. H. Coe (1999) A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map. Genetics 152: 1137– 1172.PubMedGoogle Scholar
  26. Devos, K. M. and M. D. Gale (1997) Comparative genetics in the grasses. Plant Mol. Biol. 35: 3– 15.PubMedCrossRefGoogle Scholar
  27. Draye, X., Y. Lin, X. Qian, J. E. Bowers, G. Burow, P. Morell, D. Peterson, G. Presting, S. Ren, R. Wing and A. Paterson (2001) Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation. Plant Physiol. 125: 1325– 1341.PubMedCrossRefGoogle Scholar
  28. Emerson, R., G. Beadle and A. Fraser (1935) A summary of linkage studies in maize. Cornell Univ. Agric. Exp. Stn. Memoir 180: 1– 83.Google Scholar
  29. Evola, S., F. A. Burr and B. Burr (1986) The suitability of restriction fragment length polymorphisms as genetic markers in maize. Theor. Appl. Genet. 71: 765– 771.CrossRefGoogle Scholar
  30. Feuillet, C. and B. Keller (2002) Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann. Bot. 89: 3– 10.PubMedCrossRefGoogle Scholar
  31. Fu, Y., T. J. Wen, Y. I. Ronin, H. D. Chen, L. Guo, D. I. Mester, Y. J. Yang, M. Lee, A. B. Korol,D. A. Ashlock and P. S. Schnable (2006) Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize. Genetics 174: 1671– 1683.PubMedCrossRefGoogle Scholar
  32. Gardiner, J., S. Schroeder, M. L. Polacco, H. Sanchez-Villeda, Z. W. Fang, M. Morgante, T. Landewe, K. Fengler, F. Useche, M. Hanafey, S. Tingey, H. Chou, R. Wing, C. Soderlund and E. H. Coe (2004) Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization. Plant Physiol. 134: 1317– 1326.PubMedCrossRefGoogle Scholar
  33. Gardiner, J. M., E. H. Coe, S. Melia-Hancock, D. A. Hoisington and S. Chao (1993) Development of a core RFLP map in maize using an immortalized-F2 population. Genetics 134: 917– 930.PubMedGoogle Scholar
  34. Hayes, H. and F. Immer (1942). Methods of Plant Breeding, McGraw-Hill, New York.Google Scholar
  35. Helentjaris, T., M. Slocum, S. Wright, A. Schaefer and J. Nienhuis (1986) Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphisms. Theor. Appl. Genet. 72: 761– 769.CrossRefGoogle Scholar
  36. Helentjaris, T., D. Weber and S. Wright (1988) Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. Genetics 118: 353– 363.PubMedGoogle Scholar
  37. Kato, A., J. Vega, F. Han, J. Lamb and J. Birchler (2005) Advances in plant chromosome identification and cytogenetic techniques. Curr. Op. Plant Biology 8: 148– 154.CrossRefGoogle Scholar
  38. Kim, S. and A. Misra (2007) SNP genotyping: technologies and biomedical applications. Annu. Rev. Biomed. Eng. 9: 289– 320.PubMedCrossRefGoogle Scholar
  39. Koumbaris, G. and H. W. Bass (2003) A new single-locus cytogenetic mapping system for maize (Zea mays L.): overcoming FISH detection limits with marker-selected sorghum (S. propinq-uum L.) BAC clones. Plant J. 35: 647– 659.PubMedCrossRefGoogle Scholar
  40. Kynast, R. G., R. J. Okagaki, M. W. Galatowitsch, S. R. Granath, M. S. Jacobs, A. O. Stec, H. W. Rines and R. L. Phillips (2004) Dissecting the maize genome by using chromosome addition and radiation hybrid lines. Proc. Natl. Acad. Sci. USA 101: 9921– 9926.PubMedCrossRefGoogle Scholar
  41. Lai, J. S., Y. B. Li, J. Messing and H. K. Dooner (2005) Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc. Natl. Acad. Sci. USA 102: 9068– 9073.PubMedCrossRefGoogle Scholar
  42. Lamb, J., T. Danilova, M. Bauer, J. Meyer, J. Holland, M. Jensen and J. Birchler (2007) Single-gene detection and karyotyping using small-target fluorescence in situ hybridization on maize somatic chromosomes. Genetics 175: 1047– 1058.PubMedCrossRefGoogle Scholar
  43. Lander, E. S., P. Green, J. Abrahamson, A. Barlow, M. Daley, S. Lincoln and L. Newburg (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174– 181.PubMedCrossRefGoogle Scholar
  44. Lawrence, C., T. Seigfried, H. Bass and L. K. Anderson (2006) Predicting chromosomal locations of genetically mapped loci in maize using the Morgan2McClintock translator. Genetics 172: 2007– 2009.PubMedCrossRefGoogle Scholar
  45. Lee, M., N. Sharopova, W. D. Beavis, D. Grant, M. Katt, D. Blair and A. Hallauer (2002) Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population. Plant Mol. Biol. 48(5): 453– 461.PubMedCrossRefGoogle Scholar
  46. Lincoln, S., M. Daley and E. S. Lander (1992) Mapping genes controlling quantitative traits. http://www.broad.mit.edu/genome_software/other/qtl.html, Whitehead Institute Technical Report. 2007.
  47. Manly, K. F. and J. M. Olson (1999) Overview of QTL mapping software and introduction to map manager QT. Mammal. Genome 10: 327– 334.CrossRefGoogle Scholar
  48. McMullen, M. (2003) Quantitative trait locus analysis as a gene discovery tool. In: Methods in Molecular Biology: Plant Functional Genomics Methods and Protocols. (E. Grotewold, ed.) Humana Press, Inc., Totowa, NJ, 236: pp. 141– 154.CrossRefGoogle Scholar
  49. Messing, J., A. K. Bharti, W. M. Karlowski, H. Gundlach, H. R. Kim, Y. Yu, F. S. Wei, G. Fuks, C. A. Soderlund, K. F. X. Mayer and R. A. Wing (2004) Sequence composition and genome organization of maize. Proc. Natl. Acad. Sci. USA 101: 14349– 14354.PubMedCrossRefGoogle Scholar
  50. Messing, J. and H. K. Dooner (2006) Organization and variability of the maize genome. Curr. Op. Plant Biology 9: 157– 163.CrossRefGoogle Scholar
  51. Michelmore, R. W., I. Paran and R. V. Kessell (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segegrating populations. Proc. Natl. Acad. Sci. USA 88: 9828– 9832.PubMedCrossRefGoogle Scholar
  52. Moore, G., K. M. Devos, Z. Wang and M. D. Gale (1995) Cereal genome evolution — grasses, line up and form a circle. Curr. Biol. 5: 737– 739.PubMedCrossRefGoogle Scholar
  53. Morgante, M., S. Brunner, G. Pea, K. Fengler, A. Zuccolo and A. Rafalski (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat. Genet. 37: 997– 1002.PubMedCrossRefGoogle Scholar
  54. Morgante, M. and F. Salamini (2003) From plant genomics to breeding practice. Curr. Op.Biotech. 14: 214– 219.CrossRefGoogle Scholar
  55. Nelson, W. M., A. K. Bharti, E. Butler, F. S. Wei, G. Fuks, H. Kim, R. A. Wing, J. Messing and C. Soderlund (2005) Whole-genome validation of high-information-content fingerprinting.Plant Physiol. 139: 27– 38.PubMedCrossRefGoogle Scholar
  56. Neuffer, M. (1960) Linkage maps of maize chromosomes. MNL 40: 167– 172.Google Scholar
  57. Neuffer, M. and E. Coe, Jr (1975) Corn (Maize). In: Handbook of Genetics. (R. King, ed.) Plenum Press, New York, 2: pp. 3– 30.Google Scholar
  58. Neuffer, M., L. Jones and M. Zuber (1968). The Mutants of Maize. Crop Science Society of America, Madison, WI.Google Scholar
  59. Neuffer, M., E. Coe and S. Wessler (1997). Mutants of Maize. Cold Spring Harbor Laboratory,Cold Spring Harbor, NY.Google Scholar
  60. Okagaki, R. J., R. G. Kynast, S. M. Livingston, C. D. Russell, H. W. Rines and R. L. Phillips (2001) Mapping maize sequences to chromosomes using oat-maize chromosome addition materials. Plant Physiol. 125: 1228– 1235.PubMedCrossRefGoogle Scholar
  61. Rhoades, M. (1942) Inasmuch as the writer was assigned chromosome 2 he has from time to time collected additional data on the location of certain genes placed in the map by two-point tests. MNL 16: 4.Google Scholar
  62. Rhoades, M. (1950) Meiosis in maize. J. Heredity 41: 58– 67.Google Scholar
  63. Rhoades, M. (1955) The cytogenetics of maize. In: Corn and Corn Improvement. (G. Sprague,ed.) Academic Press, New York: pp. 123– 220.Google Scholar
  64. Rhoades, M. and B. McClintock (1935) The cytogenetics of maize. Bot. Rev. 10: 292– 325.CrossRefGoogle Scholar
  65. Roman, H. (1947) Mitotic nondisjunction in the case of interchanges involving the B-type chromosome in maize. Genetics 320: 391– 409.Google Scholar
  66. Salvi, S., G. Sponza, M. Morgante, D. Tomes, X. Niu, K. A. Fengler, R. Meeley, E. V. Ananiev,S. Svitashev, E. Bruggemann, B. Li, C. F. Hainey, S. Radovic, G. Zaina, J. A. Rafalski, S. V.Tingey, G. H. Miao, R. L. Phillips and R. Tuberosa (2007) Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus m maize. Proc. Natl. Acad.Sci. USA 104: 11376– 11381.PubMedCrossRefGoogle Scholar
  67. Sanchez-Villeda, H., S. Schroeder, M. Polacco, M. McMullen, S. Havermann, G. Davis, I.Vroh-Bi, K. Cone, N. Sharopova, Y. Yim, L. Schultz, N. Duru, T. Musket, K. Houchins, Z.Fang, J. Gardiner and E. Coe (2003) Development of an integrated laboratory information management system for the maize mapping project. Bioinformatics 19: 2022– 2030.PubMedCrossRefGoogle Scholar
  68. Schaeffer, M. (2006) Consensus quantitative trait maps in maize: a database strategy. Maydica 51:357– 367.Google Scholar
  69. Schaeffer, M., H. Sanchez-Villeda, M. McMullen and E. Coe (2006) IBM2 2005 Neighbors — 45,000 locus resource for maize. Plant and Animal Genome Conference Abstracts XIV: 200.Google Scholar
  70. Sharopova, N., M. D. McMullen, L. Schultz, S. Schroeder, H. Sanchez-Villeda, J. Gardiner, D.Bergstrom, K. Houchins, S. Melia-Hancock, T. Musket, N. Duru, M. Polacco, K. Edwards, T.Ruff, J. C. Register, C. Brouwer, R. Thompson, R. Velasco, E. Chin, M. Lee, W. Woodman-Clikeman, M. J. Long, E. Liscum, K. Cone, G. Davis and E. H. Coe (2002) Development and mapping of SSR markers for maize. Plant Mol. Biol. 48: 463– 481.PubMedCrossRefGoogle Scholar
  71. Snape, J. (1988) The detection and estimation of linkage using doubled haploid or single seed descent populations. Theor. Appl. Genet. 76: 125– 128.CrossRefGoogle Scholar
  72. Soderlund, C., I. Longden and R. Mott (1997) FPC: a system for building contigs from restriction fingerprinted clones. Comput. Appl. Biosci. 13: 523– 535.PubMedGoogle Scholar
  73. Stam, P. (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J. 3: 739– 744.CrossRefGoogle Scholar
  74. Taramino, G. and S. Tingey (1996) Simple sequence repeats for germplasm analysis and mapping in maize. Genome 39: 277– 287.PubMedCrossRefGoogle Scholar
  75. Tomkins, J. P., G. Davis, D. Main, Y. Yim, N. Duru, T. Musket, J. L. Goicoechea, D. A. Frisch, E.H. Coe and R. A. Wing (2002) Construction and characterization of a deep-coverage bacterial artificial chromosome library for maize. Crop Sci. 42: 928– 933.Google Scholar
  76. Tuberosa, R. and S. Salvi (2006) Genomics-based approaches to improve drought tolerance of crops. Trends Plant Sci. 11: 405– 412.PubMedCrossRefGoogle Scholar
  77. Vuylsteke, M., M. R, R. Antonise, E. Bastiaans, L. Senior, C. Stuber, A. Melchinger, T. Luebberstedt, X. Xia, P. Stam, M. Zabeau and M. Kuiper (1999) Two high-density AFLP linkage maps of Zea mays L. : analysis of distribution of AFLP markers. Theor. Appl. Genet. 99: 921– 935.CrossRefGoogle Scholar
  78. Wei, F., E. Coe, W. Nelson, A. K. Bharti, F. Engler, E. Butler, H. Kim, J. L. Goicoechea, M. Chen, S. Lee, G. Fuks, H. Sanchez-Villeda, S. Schroeder, Z. Fang, M. McMullen, G. Davis, J. E. Bowers, A. H. Paterson, M. Schaeffer, J. Gardiner, K. Cone, J. Messing, C. Soderlund and R. A. Wing (2007) Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLOS Genetics 3: 1254– 1263.CrossRefGoogle Scholar
  79. Wendel, J. F., M. M. Goodman, C. W. Stuber and J. B. Beckett (1988) New isozyme systems for maize (Zea mays L.): aconitate dehydratase, adenylate kinase, NADH dehydrogenase, and shikimate dehydrogenase. Biochem Genet 26: 421– 445.PubMedGoogle Scholar
  80. Winkler, C., N. Jensen, M. Cooper, D. Podlich and O. Smith (2003) On the determination of recombination rates in intermated recombinant inbred populations. Genetics 164: 741– 745.PubMedGoogle Scholar
  81. Yim, Y., G. Davis, N. Duru, T. Musket, E. Linton, J. Messing, M. McMullen, C. Soderlund, M. Polacco, J. Gardiner and E. Coe (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– 1696.PubMedCrossRefGoogle Scholar
  82. Yim, Y. S., P. Moak, H. Sanchez-Villeda, T. A. Musket, P. Close, P. E. Klein, J. E. Mullet, M. D. McMullen, Z. Fang, M. L. Schaeffer, J. M. Gardiner, E. H. Coe and G. L. Davis (2007) A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps. BMC Genomics 8:47.PubMedCrossRefGoogle Scholar

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© Springer Science + Business Media, LLC 2009

Authors and Affiliations

  • Karen C. Cone
    • 1
  • Edward H. Coe
    • 2
    • 3
  1. 1.Division of Biological SciencesUniversity of MissouriColumbia
  2. 2.Plant Genetics Research Unit, USDA-ARSUniversity of MissouriColumbia
  3. 3.Division of Plant SciencesUniversity of MissouriColumbia

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