Construction and analysis of a transgenomic cytogenetic sorghum (Sorghum propinquum) BAC FISH map of maize (Zea mays L.) pachytene chromosome 9

Large-scale cytogenetic mapping in maize has been a major challenge primarily due to fact that the maize genome has a low gene density and an abundance of repetitive sequence elements. Using a unique combination of biological and genome resources for maize, sorghum, and oat, we have solved this problem and produced a cytogenetic FISH map of maize pachytenestage chromosome 9 with 32 maize markers. The genetically mapped markers used are distributed along the linkage maps at an average spacing of 5 centiMorgans. Each locus was mapped by means of multicolor direct FISH with a fluorescently labeled probe mix containing a whole chromosome paint, a single sorghum BAC clone, and the centromeric sequence, CentC. A maize-chromosome-addition line of oat was used for bright unambiguous identification of the maize 9 fiber within pachytene chromosome spreads. The locations of the sorghum BAC FISH signals were determined, and each new cytogenetic locus was assigned a centiMcClintock position on the short (9S) or long (9L) arm. Nearly all of the markers appeared in the same order on linkage and cytogenetic maps but at different relative positions on the two. The CentC FISH signal was localized between tda66 (at 9S.03) and cdo17 (at 9L.03). Several regions of genome hyperexpansion on maize chromosome 9 were found by comparative analysis of relative marker spacing in maize and sorghum. This transgenomic cytogenetic FISH map creates anchors between various maps of maize and sorghum integrating genetic markers, BAC fingerprints, and BAC hybridization data. It will provide tools for validating sequenced genomes, a foundation for exploring genomic diversity among related species, and a framework for comparative mapping of other plants with large and complex genomes.