Display Settings:


Send to:

Choose Destination
See comment in PubMed Commons below
Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):9161-6. Epub 2001 Jul 24.

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

Author information

  • 1Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA.


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.

[PubMed - indexed for MEDLINE]
Free PMC Article

Images from this publication.See all images (3)Free text

Figure 1
Figure 2
Figure 3

Publication Types, MeSH Terms, Substances, Secondary Source ID

Publication Types

MeSH Terms


Secondary Source ID

PubMed Commons home

PubMed Commons

How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire Icon for PubMed Central Icon for Faculty of 1000
    Loading ...
    Write to the Help Desk