Genetics, Vol. 162, 1401-1413, November 2002, Copyright © 2002

Patterns of Diversity and Recombination Along Chromosome 1 of Maize (Zea mays ssp. mays L.)

Maud I. Tenaillona, Mark C. Sawkinsa, Lorinda K. Andersonb, Stephen M. Stackb, John Doebleyc, and Brandon S. Gauta
a Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92612,
b Department of Biology, Colorado State University, Fort Collins, Colorado 80523
c Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706

Corresponding author: Brandon S. Gaut, University of California, 321 Steinhaus Hall, Irvine, CA 92612., bgaut{at}uci.edu (E-mail)

Communicating editor: D. CHARLESWORTH

We investigate the interplay between genetic diversity and recombination in maize (Zea mays ssp. mays). Genetic diversity was measured in three types of markers: single-nucleotide polymorphisms, indels, and microsatellites. All three were examined in a sample of previously published DNA sequences from 21 loci on maize chromosome 1. Small indels (1–5 bp) were numerous and far more common than large indels. Furthermore, large indels (>100 bp) were infrequent in the population sample, suggesting they are slightly deleterious. The 21 loci also contained 47 microsatellites, of which 33 were polymorphic. Diversity in SNPs, indels, and microsatellites was compared to two measures of recombination: C (=4Nc) estimated from DNA sequence data and R based on a quantitative recombination nodule map of maize synaptonemal complex 1. SNP diversity was correlated with C (r = 0.65; P = 0.007) but not with R (r = -0.10; P = 0.69). Given the lack of correlation between R and SNP diversity, the correlation between SNP diversity and C may be driven by demography. In contrast to SNP diversity, microsatellite diversity was correlated with R (r = 0.45; P = 0.004) but not C (r = -0.025; P = 0.55). The correlation could arise if recombination is mutagenic for microsatellites, or it may be consistent with background selection that is apparent only in this class of rapidly evolving markers.




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