High resolution physical mapping of the maize genome and sequencing a part thereof

Arvind K. Bharti¹, Fusheng Wei², Ed Butler², Yeisoo Yu², Jose L. Goicoechea², HyeRan Kim², Galina Fuks¹, Will Nelson³, Jamie Hatfield³, Heidrun Gundlach⁴, Wojciech M. Karlowski⁴, Christina Raymond⁵, Sarah Towey⁵, David Jaffe⁵, Chad Nusbaum⁵, Bruce Birren⁵, Klaus Mayer⁴, Cari Soderlund³, Rod A. Wing² and Joachim Messing¹

¹The Plant Genome Initiative at Rutgers, Waksman Institute, Rutgers University, Piscataway, NJ; ²Arizona Genomics Institute, ³Arizona Genomics Computational Laboratory, University of Arizona, Tucson, AZ; ⁴Munich Information Center for Protein Sequences, Institut für Bioinformatik, Neuherberg, Germany; ⁵MIT/Broad Institute Center for Genome Research, Cambridge, MA

Due to its economic significance, maize (>2 Gb) is likely to be the next cereal to be sequenced after rice (0.4 Gb). Sequencing the maize genome will present a new challenge not only because it is 5-times larger but also because it contains many gene families, tandemly arrayed and nested repeat sequences. To establish a framework to sequence maize, we are developing a high information-content fingerprinting (HICF)/BAC sequence tagged connector (STC)-based physical map. This map will be fully integrated with the genetic map and is complementary to previous work by the NSF funded Maize Mapping Project (www.genome.arizona.edu/fpc/maize). MMP generated a genetically anchored BAC-based physical map by fingerprinting three deep coverage BAC libraries (HindIII, EcoRI, and MboI) using a lower resolution “agarose” method. The HICF method builds upon the MMP physical map by generating HICF fingerprints of the identical libraries, which allows for a more precise determination of a minimum tiling path of BAC clones across the entire genome. The current success rate of HICF is ~86%, which has already yielded 382,696 successful fingerprints. Preliminary investigation suggests that many HICF mega-contigs are likely to join two or more agarose-based contigs and thus should result in the reduction of the total number of contigs. Additional contigs are expected to be anchored based on alignments of STCs to the rice genome. To evaluate the MTP generated by the HICF/agarose physical map, 56 BACs are being sequenced from a ~5 Mb mega-contig, in addition to 100 randomly selected BACs (>10 Mb). All sequence information generated from this project, from both BAC ends and whole BACs, is being annotated, which will provide invaluable data on the sequence organization of the maize genome.