Development of Pachytene Cytogenetic Fluorescence in Situ Hybridization (FISH) Maps for Six Maize Chromosomes

Plant cytogenetics has continued to flourish and make essential contributions to genomics projects by delineating marker order, defining contig gaps, and revealing genome rearrangements. Here we review the field of plant cytogenetics from its conception through the eras of molecular biology and genomics (Chapter 1). Significant advances in chromosome preparation, such as extended fiber-FISH, have greatly increased the axial resolution limits, while imaging and signal amplification technologies have improved our ability to detect small gene-sized probes. These advances are described, together with selected examples that illustrate the power of plant cytogenetics in guiding genome projects. The integration of genetic and physical maps of maize is progressing rapidly, but the cytogenetic maps lag behind, with the exception of the pachytene fluorescence in situ hybridization (FISH) maps of maize chromosome 9. We sought to produce integrated FISH maps of other maize chromosomes using the landmark Core Bin Marker loci. Because these 1 Kb restriction fragment length polymorphism (RFLP) probes are below the FISH detection limit, we used BACs from sorghum, a small-genome relative of maize, as surrogate clones for FISH mapping. We sequenced 151 maize RFLP probes and compared in silico BAC selection methods to that of library filter hybridization and found the latter to be the best. BAC library screening, clone verification, and single-clone selection criteria are presented in Chapter 2. The use of homologous sorghum BACs as representative FISH probes for the creation of cytogenetic FISH maps for six maize chromosomes as well as in the mapping of duplicate maize regions are presented in Chapters 3 and 4, respectively. Finally, in Chapter 5 we compare our pachytene cytogenetic maps as well as the high-density chromosome 9 FISH map to the maize genomic map (Schnable et al., 2009), the UMC98 genetic linkage map (Davis et al., 1999), and to recombination nodule-based predictions of meiotic cytological coordinates (Anderson et al., 2004; Lawrence et al., 2006).