A recombination hotspot in the maize A1 intragenic region.

We find that recombination between two alleles of the maize A1 locus that contain transposon insertions at known molecular positions can occur at 0.04-0.08 cM per kbp (centimorgan per kilobase pair), which is two orders of magnitude higher than the recombination rate for the whole maize genome. It is however, close to the rates found within the bronze locus, another maize structural gene for which both genetic and molecular data are available. This observation supports the idea that the genome consists of regions that are highly recombinogenic - in some cases, at least, structural genes - interspersed with regions that are less recombinogenic.