The polyploid origin of maize

Handbook of Maize: Genetics and Genomics

Volumn , Issue , 2009, Pages 221-238

  Messing, Joachim ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84876730439     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-0-387-77863-1_11     Document Type: Chapter

References (51)

1. Ahn, S., and Tanksley, S. D. (1993). Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA 90, 7980-7984.
2. Anderson, E., and Cutler, H. C. (1942). Races of Zea Mays: I. Their Recognition and Classification. Annals of the Missouri Botanical Garden 29, 69-88.
3. Arabidopsis-Genome-Initiative. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
4. Bennett, M. D., and Leitch, I. J. (2005). Nuclear DNA amounts in angiosperms: progress, problems and prospects. Ann Bot (Lond) 95, 45-90.
5. Clausius, R. (1868). On the Mechanical Theory of Heat. Philos Mag 40, 122.
6. Du, C., Swigonova, Z., and Messing, J. (2006). Retrotranspositions in orthologous regions of closely related grass species. BMC Evol Biol 6, 62.
7. Falkow, S. (2004). Molecular Koch's postulates applied to bacterial pathogenicity-a personal recollection 15 years later. Nat Rev Microbiol 2, 67-72.
8. Gaut, B. S., and Doebley, J. F. (1997). DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci U S A 94, 6809-6814.
9. Goodman, M. M., and Brown, W. L. (1988). Races of corn. In Corn and corn improvement, G. F. Sprague and J. W. Dudley, eds (Madison: Amer. Soc. Agron), pp. pp. 33-79.
10. Goodman, M. M., Stuber, C. W., Newton, K., and Weissinger, H. H. (1980). Linkage Relationships of 19 Enzyme Loci in Maize. Genetics 96, 697-710.
11. Gregory, T. R. (2005). The C-value enigma in plants and animals: a review of parallels and an appeal for partnership. Ann Bot (Lond) 95, 133-146.
12. Griffiths, S., Sharp, R., Foote, T. N., Bertin, I., Wanous, M., Reader, S., Colas, I., and Moore, G. (2006). Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature 439, 749-752.
13. Guo, M., and Birchler, J. A. (1994). Trans-Acting Dosage Effects on the Expression of Model Gene Systems in Maize Aneuploids. Science 1999-2002.
14. Haberer, G., Young, S., Bharti, A. K., Gundlach, H., Raymond, C., Fuks, G., Butler, E., Wing, R. A., Rounsley, S., Birren, B., Nusbaum, C., Mayer, K. F., and Messing, J. (2005). Structure and architecture of the maize genome. Plant Physiol 139, 1612-1624.
15. Heidecker, G., and Messing, J. (1986). Structural Analysis of Plant Genes. Annual Review of Plant Physiology 37, 439-466.
16. Helentjaris, T., Weber, D., and Wright, S. (1988). Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphism. Genetics 118, 353-363.
17. International-Rice-Genome-Sequencing-Project. (2005). The map-based sequence of the rice genome. Nature 436, 793-800.
18. Jaenicke-Despres, V., Buckler, E. S., Smith, B. D., Gilbert, M. T., Cooper, A., Doebley, J., and Paabo, S. (2003). Early allelic selection in maize as revealed by ancient DNA. Science 302, 1206-1208.
19. Kapitonov, V. V., and Jurka, J. (2001). Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci U S A 98, 8714-8719.
20. Kashkush, K., Feldman, M., and Levy, A. A. (2003). Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet 33, 102-106.
21. Kellis, M., Birren, B. W., and Lander, E. S. (2004). Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428, 617-624.
22. Kim, H., San Miguel, P., Nelson, W., Collura, K., Wissotski, M., Walling, J. G., Kim, J. P., Jackson, S. A., Soderlund, C., and Wing, R. A. (2007). Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type). Genetics 176, 379-390.
23. Lai, J., Ma, J., Swigonova, Z., Ramakrishna, W., Linton, E., Llaca, V., Tanyolac, B., Park, Y. J., Jeong, O. Y., Bennetzen, J. L., and Messing, J. (2004). Gene loss and movement in the maize genome. Genome Res 14, 1924-1931.
24. Liu, B., Brubaker, C. L., Mergeai, G., Cronn, R. C., and Wendel, J. F. (2001). Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 44, 321-330.
25. Matzke, M. A., and Birchler, J. A. (2005). RNAi-mediated pathways in the nucleus. Nat Rev Genet 6, 24-35.
26. McClintock, B. (1930). A cytological demonstration of the location of an interchange between two non-homologous chromosomes of Zea mays. Proc Natl Acad Sci U S A 16, 791-796.
27. McClintock, B. (1984). The significance of responses of the genome to challenge. Science 226, 792-801.
28. Messing, J., Bharti, A. K., Karlowski, W. M., Gundlach, H., Kim, H. R., Yu, Y. Wei, F., Fuks, G., Soderlund, C. A., Mayer, K. F., and Wing, R. A. (2004). Sequence composition and genome organization of maize. Proc Natl Acad Sci U S A 101, 14349-14354.
29. Meyers, B. C., Tingey, S. V., and Morgante, M. (2001). Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res 11, 1660-1676.
30. Molina, M.d. C., and Naranjo, C. A. (1987). Cytogenetic studies in the genus Zea. TAG Theoretical and Applied Genetics 73, 542-550.
31. Moore, G., Devos, K., Wang, Z., and Gale, M. D. (1995). Grasses, line up and form a circle. Curr Biol 5, 737-739.
32. Nelson, W. M., Bharti, A. K., Butler, E., Wei, F., Fuks, G., Kim, H.-R., Wing, R. A., Messing, J., and Soderlund, C. (2005). Whole-Genome Validation of High-Information-Content Fingerprinting. Plant Physiol. 139, 27-38.
33. Rice-Chromosomes-11-and-12-Sequencing-Consortia. (2005). The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biol 3, 20.
34. Roman, H. (1947). Mitotic Nondisjunction in the Case of Interchanges Involving the B-Type Chromosome in Maize. Genetics 32, 391-409.
35. Sanmiguel, P., and Bennetzen, J. L. (1998). Evidence that a Recent Increase in Maize Genome Size was Caused by the Massive Amplification of Intergene Retrotransposons. Annals of Botany 82, 37.
36. San Miguel, P., Gaut, B. S., Tikhonov, A., Nakajima, Y. and Bennetzen, J. L. (1998). The paleontology of intergene retrotransposons of maize. Nat Genet 20, 43-45.
37. Song, R., and Messing, J. (2002). Contiguous genomic DNA sequence comprising the 19-kD zein gene family from maize. Plant Physiol 130, 1626-1635.
38. Song, R., and Messing, J. (2003). Gene expression of a gene family in maize based on noncollinear haplotypes. Proc Natl Acad Sci U S A 100, 9055-9060.
39. Song, R., Llaca, V., and Messing, J. (2002). Mosaic organization of orthologous sequences in grass genomes. Genome Res 12, 1549-1555.
40. Song, R., Llaca, V. Linton, E., and Messing, J. (2001). Sequence, regulation, and evolution of the maize 22-kD alpha zein gene family. Genome Res 11, 1817-1825.
41. Swigonova, Z., Bennetzen, J. L., and Messing, J. (2005). Structure and evolution of the r/b chromosomal regions in rice, maize and sorghum. Genetics 169, 891-906.
42. Swigonova, Z., Lai, J., Ma, J., Ramakrishna, W., Llaca, V. Bennetzen, J. L., and Messing, J. (2004). Close split of sorghum and maize genome progenitors. Genome Res 14, 1916-1923.
43. Thuriaux, P. (1977). Is recombination confined to structural genes on the eukaryotic genome? Nature 268, 460-462.
44. Wei, F., Coe, E., Nelson, W., Bharti, A. K., Engler, F., Butler, E., Kim, H., Goicoechea, J. L., Chen, M., Lee, S., Fuks, G., Sanchez-Villeda, H., Schroeder, S., Fang, Z., McMullen, M., Davis, G., Bowers, J. E., Paterson, A. H., Schaeffer, M., Gardiner, J., Cone, K., Messing, J., Soderlund, C., and Wing, R. A. (2007). Physical and Genetic Structure of the Maize Genome Reflects Its Complex Evolutionary History. PLoS Genet 3, e123.
45. Wendel, J. F., Stuber, C. W., Edwards, M. D., and Goodman, M. M. (1986). Duplicated chromosomal segments in Zea mays L.: Further evidence from Hexokinase isozymes. Theor Appl Genet 72, 178-185.
46. Whitkus, R., Doebley, J., and Lee, M. (1992). Comparative genome mapping of Sorghum and maize. Genetics 132, 1119-1130.
47. Wilson, C. M., Spraque, G. F., and Nelsen, T. C. (1989). Linkages among zein genes determined by isoelectric focusing. Theor. Appl. Genet. 77, 217-226.
48. Wolfe, K. H. (2001). Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet 2, 333-341.
49. Xu, J. H., and Messing, J. (2006). Maize haplotype with a helitron-amplified cytidine deaminase gene copy. BMC Genet 7, 52.
50. Xu, J. H., and Messing, J. (2008). Organization of the prolamin gene family provides insight into the evolution of the maize genome and gene duplications in grass species. Proc Natl Acad Sci U S A 105, 14330-14335.
51. Zupan, J., Muth, T. R., Draper, O., and Zambryski, P. (2000). The transfer of DNA from agrobacterium tumefaciens into plants: a feast of fundamental insights. Plant J 23, 11-28.