1. Evolution of bz Orthologous Regions in the Genus Zea and Relatives in the Andropogoneae Qinghua Wang and Hugo K. Dooner Waksman Institute, Rutgers University, Piscataway, NJ 08854 Abstract Genome structure exhibits remarkable variation within Zea mays. To examine how haplotype structure has evolved within the Andropogoneae tribe, we have analyzed the bz gene-rich region of seven species, including maize, the teosintes Zea mays ssp. mexicana, Zea luxurians and Zea diploperennis, Tripsacum dactyloides, Coix lacryma-jobi, and Sorghum propinquum. We have sequenced and annotated 10 BAC clones from these species and reannotated the orthologous S. bicolor and Brachypodium regions. Our analysis has revealed the following: Gene colinearity in the bz region is well conserved within the genus Zea. However, the orthologous regions of Coix and Sorghum exhibit several micro-rearrangements relative to Zea, including addition, truncation, and deletion of genes. The pattern of interspersion of genes and retrotransposons varies between Sorghum bicolor and Sorghum propinquum, as it does among and within the Zeas. The stc1 gene, involved in the production of a terpenoid insect defense signal, is evolving particularly fast. It is mutated in Tripsacum, truncated in Coix, and deleted to barely detectable fragments in the two Sorghum haplotypes. Analysis of the remaining stc1 fragments in Sorghum suggests that the progressive disappearance of a gene from the genome occurs by microhomology-mediated recombination. The average divergence time between maize and Tripsacum, Coix and Sorghum is around 8.5, 12.1, and 12.4 million years ago (MYA), respectively, and that between Coix and Sorghum is 9.3 MYA. Common transposon insertion sites are seen among haplotypes belonging to different Zea mays subspecies, but not outside of the species. As in maize, very few solo LTRs occur in these Andropogoneae, suggesting that genome size reduction by homologous recombination between LTR repeats may be rare in the tribe. A comparison of the bz orthologous regions of Zea, Sorghum, and Coix with those of Oryza and Brachypodium shows how the region has evolved by the addition and deletion of genes in the approximately 50 MY since these genera diverged from a common progenitor. Supported by NSF grants MCB-0212785 and DBI-0320683 Figure 1. Organization of bz haplotypes among Zea relatives. The Ns on the left and right mark the NotI cut sites. Genes are shown as pentagons pointing in the direction of transcription; exons are in bronze and introns in yellow. The same symbols are used for gene fragments carried by Helitrons (Hels), which are represented as bidirectional arrows below or above the line for each haplotype. Retrotransposons are indicated by solid triangles of different colors. DNA transposons are indicated by open triangles in different colors. Only the genes have been drawn to scale. Figure 2. Organization of bz haplotypes among nonZea relatives, maize chromosome 6L, Brachypodium, and rice. The same symbols are used as in Fig. 1. Figure 3. A. Putative organization of the bz haplotype in the last common ancestor of rice and maize. B. Diagram of the evolution of the bz region in Oryza, Brachypodium, Setaria and the Andropogoneal clade Coix, Sorghum and Zea. Red arrows: gene loss; blue arrows: gene gain.