Distribution of genes, recombination, and repetitive elements in the maize genome

A high-density genetic map of maize (Zea mays U, integrated with a high-resolution bacterial artificial chromosome (BAC) contig mop compiled from two inbred lines, B73 and Mo17, was used to determine gene density and recombination frequency along chromosomes and to compare the distribution of these features as a function of physical distance. Recombination frequency is well correlated with gene density for each chromosome (r= 0.767-0.960), although in centromeric regions, recombination is more depressed than a strict correlation with gene density would indicate. In addition, the distribution of major retrotransposon classes and of Mu and Helitron insertion sites were examined . Overall retrotransposon density is equal at all maize chromosomes (r = 0.996), although different classes of retrotransposons display preferential insertion into different chromosome regions. Cinful, Zeon, and Prem are more common near the centromere, while Opie, A and Huck preferentially reside at the subtelomeric segments of chromosomes. Grande does not show preference in distribution relative to physical location on the chromosome. Comparison of the distribution of genic overgo probe hybridization-positive BACs from maize inbred line B73 to those of the inbred Mo17 indicates that nonshored genic segments, many of which correspond to pseudogenes carried by the Helitron elements, tend to be less common in the centromeric region. As previously reported, Mu transposons seem to preferentially insert in the vicinity of genes, as indicated by their paucity in centromeric regions, and moderate correlation (r= 0.759) with gene density.