Intellectual merit. Homologous meiotic recombination is an important process because it creates new genotypes by shuffling chromosomal segments that otherwise would be inherited as blocks and promotes fertility by ensuring that chromosomes segregate properly. Maize is the species with the most diverse genome structure known. In many chromosomal segments, different inbred lines share just the gene sequences, but none of the surrounding repetitive DNA. The latter consists of transposons, retrotransposons making up more than half of the genome. This high level of structural variation affects recombination and, possibly, gene expression. This project aims to analyze those effects.
The genetic system used is the bz locus, which has unique advantages for studies of recombination. Previous work showed that genome structural variation affects the frequency and distribution of recombination events in maize in multiple ways. Although recombination is limited to genes, its distribution is highly nonuniform: some genes are hotspots and others are coldspots. Genes in Helitron transposons fail to recombine. Whether a sequence recombines or not depends on its C-methylation status and transposons are highly methylated. The presence of a retrotransposon block in only one homolog, a common situation in hybrids, inhibits recombination in adjacent genes. Recombination not associated with crossing over, called gene conversion, shows a strong polarity: bz mutations at both ends of the gene convert (i.e., recombine) more frequently than central ones. This project will continue to exploit the power of genetic analysis in the bz region. It will elucidate the pattern of recombination within a plant gene and will use recombination as a tool in the genetic analysis of gene expression differences. Its specific objectives are to: 1. Test whether genomic structural variation (+/- intergenic retrotransposons) impacts the frequency and polarity of conversion in an adjacent gene. 2. Determine if the stretch of DNA transferred from one homolog to another (conversion tract) at the bz 5 high conversion end extends into the adjacent gene. 3. Investigate whether conversion tracts are generally shorter when the recombining DNAs differ at only two sites than when they differ at many, as in the heterozygotes commonly studied. 4. Measure recombination and crossing-over interference in heterozygotes between identical chromosomes, i.e., an inbred, and contrast with values obtained from standard maize F1 heterozygotes, i.e., hybrids. 5. Define all genes in the sh-bz interval of two well studied lines and use recombinants to dissect the contribution of genomic structural variation to allelic expression differences.
Broader impacts. This project will train a graduate student in plant genetics and provide summer employment and training for students, including those from a predominantly undergraduate institution with which the Principal Investigator collaborates. It will incorporate several members of underrepresented groups and will help the Principal Investigator to maintain ongoing collaborations with investigators in developing countries. The project is relevant to the long-term improvement of U.S. agriculture in that it studies recombination, a cornerstone of genetics and the basis of most plant and animal breeding, and it utilizes maize, an excellent model organism and a crop of economic importance. Much of the proposed work is based on an earlier discovery in the Principal Investigator's lab of an unprecedented level of maize genome structure variation. The project aims to study how recombination and gene expression are affected by it.
