Identification of the Genomic Locations of Duplicate Nucleotide Sequences in Maize by Analysis of Restriction Fragment Length Polymorphisms

INVESTIGATIONS

Identification of the Genomic Locations of Duplicate Nucleotide Sequences in Maize by Analysis of Restriction Fragment Length Polymorphisms

T. Helentjaris, D. Weber and S. Wright
Molecular Biology Group, NPI, Salt Lake City, Utah 84108

While preparing a linkage map for maize based upon loci detected through the use of restriction fragment length polymorphisms (RFLPs), it was found that 62 of the 217 cloned maize sequences tested (29%) detected more than one fragment on genomic Southern blots. Thus, more than one nucleotide sequence is present within the maize genome which is in part homologous to each of these cloned sequences. The genomic locations of these ``duplicate'' sequences were determined and it was found that they usually originated from different chromosomes. The process which produced them did not operate randomly as some pairs of chromosomes share many duplicate sequences while many other pairs share none. Furthermore, these shared duplicate sequences are generally arrayed in an ordered arrangement along these chromosomes. It is believed that chromosomal segments which contain several duplicate loci in a generally ordered arrangement must have had a common origin. The presence of these duplicated segments supports the idea that allopolyploidy may have been involved in the evolution of maize. Nevertheless, the duplicate loci do not primarily involve five pairs of chromosomes and thus, five pairs of homeologous chromosomes are not currently present within the maize genome. The data clearly indicate that maize is not a recent allotetraploid produced by hybridization between two individuals with similar genomic structures; however, the data are also consistent with the possibility of these shared duplicate chromosomal segments having been generated through internal duplication.

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				H. W. Bass, J. E. Krawetz, G. R. OBrian, C. Zinselmeier, J. E. Habben, and R. S. Boston Maize ribosome-inactivating proteins (RIPs) with distinct expression patterns have similar requirements for proenzyme activation J. Exp. Bot., October 1, 2004; 55(406): 2219 - 2233. [Abstract] [Full Text] [PDF]

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				E. A. Kellogg What happens to genes in duplicated genomes PNAS, April 15, 2003; 100(8): 4369 - 4371. [Full Text] [PDF]

				A. P. Dias, E. L. Braun, M. D. McMullen, and E. Grotewold Recently Duplicated Maize R2R3 Myb Genes Provide Evidence for Distinct Mechanisms of Evolutionary Divergence after Duplication Plant Physiology, February 1, 2003; 131(2): 610 - 620. [Abstract] [Full Text] [PDF]

				D. T. Morishige, K. L. Childs, L. D. Moore, and J. E. Mullet Targeted Analysis of Orthologous Phytochrome A Regions of the Sorghum, Maize, and Rice Genomes using Comparative Gene-Island Sequencing Plant Physiology, December 1, 2002; 130(4): 1614 - 1625. [Abstract] [Full Text] [PDF]

				G. Chuck, M. Muszynski, E. Kellogg, S. Hake, and R. J. Schmidt The Control of Spikelet Meristem Identity by the branched silkless1 Gene in Maize Science, November 8, 2002; 298(5596): 1238 - 1241. [Abstract] [Full Text] [PDF]

				S. J. Szalma, M. E. Snook, B. S. Bushman, K. E. Houchins, and M. D. McMullen Duplicate Loci as QTL: The Role of Chalcone Synthase Loci in Flavone and Phenylpropanoid Biosynthesis in Maize Crop Sci., September 1, 2002; 42(5): 1679 - 1687. [Abstract] [Full Text] [PDF]