Restriction Site Variation in the Zea Chloroplast Genome

J. Doebley ¹, W. Renfroe ¹, and A. Blanton ¹

¹ Department of Biology. Texas A&M University, College Station, Texas 77843

Nineteen accessions selected from the four species and three subspecies of the genus Zea and one accession from the related genus Tripsacum were surveyed for variation with 21 restriction endonucleases. In all, 580 restriction sites were assayed in each chloroplast (cp)DNA, this representing 2.2% of the genome. Twenty-four of the 580 sites were variable in one or more of the cpDNAs. The number of nucleotide substitutions per site (p) between Zea and Tripsacum (0.0056) approximates that between other closely related angiosperm genera. The range in values of p among Zea species (0.0003-0.0024) is on the lower end of the range reported for other angiosperm genera. Analysis of the distribution of restriction site mutations throughout the genome indicated that the inverted repeat evolves more slowly than either the small or large unique sequence regions. Parsimony phylogenetic analysis of the restriction site data produced a tree consistent with isoenzymatic and morphological measures of affinity among the species. Chloroplast DNA analysis was not useful in discriminating the subspecies within Zea mays. The lack of any detectable differences between the cpDNA of maize (Z. mays subsp. mays) and some teosintes (Z. mays subsps. mexicana and parviglumis ) is consistent with the hypothesis that maize is a domesticated form of teosinte. Comparison of the degree of sequence divergence for Z. mays cpDNA and the Adh1 locus suggests the latter may be evolving at 10 times the rate of the former. Comparison of rates of sequence evolution for the mitochondrial and chloroplast genomes was inconclusive and could not clarify whether these two genomes have dissimilar rates of sequence evolution.

This article has been cited by other articles:

				K. Fukunaga, J. Hill, Y. Vigouroux, Y. Matsuoka, J. Sanchez G., K. Liu, E. S. Buckler, and J. Doebley Genetic Diversity and Population Structure of Teosinte Genetics, April 1, 2005; 169(4): 2241 - 2254. [Abstract] [Full Text] [PDF]

				J. O. Allen Effect of Teosinte Cytoplasmic Genomes on Maize Phenotype Genetics, February 1, 2005; 169(2): 863 - 880. [Abstract] [Full Text] [PDF]

				P. Tiffin, R. Hacker, and B. S. Gaut Population Genetic Evidence for Rapid Changes in Intraspecific Diversity and Allelic Cycling of a Specialist Defense Gene in Zea Genetics, September 1, 2004; 168(1): 425 - 434. [Abstract] [Full Text] [PDF]

				P. Tiffin and B. S. Gaut Sequence Diversity in the Tetraploid Zea perennis and the Closely Related Diploid Z. diploperennis: Insights From Four Nuclear Loci Genetics, May 1, 2001; 158(1): 401 - 412. [Abstract] [Full Text]

				K. M. Olsen and B. A. Schaal Microsatellite variation in cassava (Manihot esculenta, Euphorbiaceae) and its wild relatives: further evidence for a southern Amazonian origin of domestication Am. J. Botany, January 1, 2001; 88(1): 131 - 142. [Abstract] [Full Text]

				H. Hilton and B. S. Gaut Speciation and Domestication in Maize and Its Wild Relatives: Evidence From the Globulin-1 Gene Genetics, October 1, 1998; 150(2): 863 - 872. [Abstract] [Full Text]

				A. Eyre-Walker, R. L. Gaut, H. Hilton, D. L. Feldman, and B. S. Gaut Investigation of the bottleneck leading to the domestication of maize PNAS, April 14, 1998; 95(8): 4441 - 4446. [Abstract] [Full Text] [PDF]