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

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 sampl e of 25 individuals representing 16 exotic landraces and nine U.S. inbred l ines. The data indicated that maize has an average of one single nucleotide polymorphism (SNP) every 104 by between two randomly sampled sequences, a level of diversity higher than that of either humans or Drosophila melanoga ster. A comparison of genetic diversity between the landrace and inbred sam ples showed that inbreds retained 77% of the level of diversity of landrace s, on average. In addition, Tajima's D values suggest that the frequency di stribution of polymorphisms in inbreds was skewed toward fewer rare variant s. Tests for selection were applied to all loci, and deviations from neutra lity were detected in three loci. Sequence diversity was heterogeneous amon g loci, but there was no pattern of diversity along the genetic map of chro mosome 1. Nonetheless, diversity was correlated (r = 0.65) with sequence-ba sed estimates of the recombination rate. Recombination in our sample was su fficient to break down linkage disequilibrium among SNPs. Intragenic linkag e disequilibrium declines within 100-200 by on average, suggesting that gen ome-wide surveys for association analyses require SNPs every 100-200 bp.