Retrotransposon polymorphisms affect genic recombination in maize.

Maize exhibits a high degree of intraspecific variation in genome structure, most of which is due to intergenic retrotransposon polymorphsisms among unrelated varieties. For example, a comparison of eight haplotypes of the bronze1 (bz1) locus, which contains numerous retrotransposons, showed that sequence similarity between any two haplotypes ranged from 25 to 84% (Wang and Dooner, 2006). In this issue of The Plant Cell, Dooner and He (pages 249–258) investigate the extent to which heterozygosity for large retrotransposon insertions, which occur in every mapping population, might affect recombination in the adjacent genes. The authors compared the frequency of recombination between the adjacent bz1 and stc1 genomic regions in the heterozygous maize lines of McC crossed with B73 or W22, which differ in the presence (B73) or absence (McC and W22) of a 26-kb intergenic retrotransposon cluster. Recombinants were scored by the use of Ds and Ac markers that allowed recombinants to be identified based on seed pigmentation (see figure). It is shown that the presence of the transposon cluster decreased the genetic distance by reducing recombination between the adjacent bz1 and stc1 markers. Reduced recombination could be due to disruption of normal pairing of adjacent genic sequences in heterozygotes (because of large structural differences in the intergenic region) or to chromatin-mediated effects (dense packing of DNA in the highly heterochromatic transposon cluster interfering with recombination machinery acting in adjacent euchromatic regions). In addition, the authors show that recombination within the genes shuffled the adjacent retrotransposon blocks, creating novel chimeric haplotypes and either contracting or expanding the physical distance between markers. This study underscores the notion that retrotransposon polymorphisms can have a strong influence on estimates of genetic distance between closely linked markers because they reduce recombination between adjacent genes and add physical length to the intergenic region. The authors acknowledge that variations in centimorgan/kilobase ratios between different mapping populations may average out over longer genetic differences but urge caution in comparisons of local gene regions and genetic distances from the reference maize B73 sequence to various other inbreds that may lack the large retrotransposon cluster.