Research in the Dooner Lab Focuses on Three Main Areas:

1. Transposons
Transposons are the main consitutents of the maize genome. We study their structures and interactions and use them as genetic tools to elucidate the function of genes. We have identified several new genetically active transposons, including Jittery and Mx, which are new autonomous members of the Mutator and hAT superfamilies, respectively. Maize appears to have several noninteracting elements in each superfamily, suggesting that new transposon specificities have arisen frequently. In our functional genomics project, we have generated an Ac insertion library which yielded many new interesting phenotypes, such as defective pollen grains with corkscrew pollen tube and seedings unable to produce volatile chemicals to defend themselves agains insects. This latter finding has prompted us to examine the function of orthologous gene pairs in defense responses. We are currently optimizing the use of Ac-Ds transposons as gene-searching engines in maize. We are developing a set of transgenic lines carrying a uniquely marked Ds element which should integrate at multiple locations in the genome and greatly facilitate the isolation of the interrupted gene.

2. Genome variability
Maize is the most variable plant species known. This variability manifests itself at all levels, ranging from variations in plant shape to polymorphisms in genome structure. We recently discovered that allelic regions of the genome can vary by as much as 70% of their DNA, mostly in the make-up of intergenic retrotransposon clusters, but also by the presence/absence of gene fragments borne on novel transposons known as Helitrons. Because Helitrons lack the typical structural features of other DNA elements, identifying them is a challenge. Therefore, we developed and implemented a heuristic searching algorithm to identify Helitrons in the maize genome database and empirically validated a subset. We are presently characterizing the bz region in the genome of different inbreds, land races, and wild relatives of maize in order to further document the extent of this genome stucture variation.

3. Homologous recombination
We have found that meitoic recombination in maize is restricted to genes, which comprise only 5% or less of the genome. We continue to use the bronze locus of maize, a uniquely advantageous system, to attempt to obtain answers to basic questions regarding the process of homologous meiotic recombination in plants. A main question that we are addressing is the effect of the highly polymorphic intergenic retrotransposon clusters on recombination. Given our finding that the number of genes in the bz region can vary among lines, we are also testing if the number of Helitron-borne gene fragments between two sites in the region affects recombination between them.