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

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.

Figure 1

θ̂_silent for each locus, with a 95% confidence interval, on the genetic map of chromosome 1. Values were calculated on the combined inbred and landrace samples.

Figure 2

Correlation between the intragenic recombination rate, estimated by 4Nc, and θ̂_total. The regression line is given.

Figure 3

Thin gray lines represent ρ², the expected value of r², for each of 20 loci, based on complete data sets. One thick black line represents ρ² averaged among loci, based on combined landrace and inbred data; the second thick black line represents an averaged ρ² curve for inbred data only.