Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.)

doi:10.1073/pnas.151244298

Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.)

^*Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697; and ^‡Department of Genetics, University of Wisconsin, Madison, WI 53706

Communicated by M. T. Clegg, University of California, Riverside, CA (received for review March 2, 2001)

Abstract

We measured sequence diversity in 21 loci distributed along chromosome 1 of maize (Zea mays ssp. mays L.). For each locus, we sequenced a common sample of 25 individuals representing 16 exotic landraces and nine U.S. inbred lines. The data indicated that maize has an average of one single nucleotide polymorphism (SNP) every 104 bp between two randomly sampled sequences, a level of diversity higher than that of either humans or Drosophila melanogaster. A comparison of genetic diversity between the landrace and inbred samples showed that inbreds retained 77% of the level of diversity of landraces, on average. In addition, Tajima's D values suggest that the frequency distribution of polymorphisms in inbreds was skewed toward fewer rare variants. Tests for selection were applied to all loci, and deviations from neutrality were detected in three loci. Sequence diversity was heterogeneous among loci, but there was no pattern of diversity along the genetic map of chromosome 1. Nonetheless, diversity was correlated (r = 0.65) with sequence-based estimates of the recombination rate. Recombination in our sample was sufficient to break down linkage disequilibrium among SNPs. Intragenic linkage disequilibrium declines within 100–200 bp on average, suggesting that genome-wide surveys for association analyses require SNPs every 100–200 bp.

Footnotes

↵ † M.I.T. and M.C.S. contributed equally to this work.
↵ § To whom reprint requests should be addressed at: Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, University of California, Irvine, CA 92697-2525. E-mail: bgaut{at}uci.edu.
Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. AF377345–AF377864).
Abbreviations:

SNP,

single nucleotide polymorphism;

LD,

linkage disequilibrium;

RFLP,

restriction fragment length polymorphism;

HKA test,

Hudson–Kreitman–Aguade test;

cM,

centimorgan