Patrick S. Schnable1, Srinivas Aluru1, Robert A. Martienssen2, W. Richard McCombie2, Lincoln Stein2, Doreen Ware2, Richard Wilson3, and Rod A. Wing4. (1) Iowa State University, Center for Plant Genomics, 2035B Roy J Carver Co-Lab, Ames, IA 50011-3650, (2) Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, (3) Genome Sequencing Center, Washington University School of Medicine, St. Louis, MO 63108, (4) Arizona Genomics Institute, Tucson, AZ 85721
A project to generate a near-complete sequence of the genome of maize inbred B73 was initiated in November 2005. This effort, which expected to require three years, will utilize a minimal tiling path of approximately 19,000 mapped BAC clones, and will focus on producing high-quality sequence coverage of all identifiable gene-containing regions of the maize genome. These regions will be ordered, oriented and, along with all of the intergenic sequences, anchored to the extant physical and genetic maps of the maize genome. Important features of the project include immediate release of preliminary and high-quality sequence assemblies, and the development of a genome browser that will facilitate user interaction with sequence and map data. Several examples of the types of insight that will be gained from analysis of the genome sequence will be presented. For example, mining an assembly of over 3,000,000 maize genomic sequences has identified ~350 expressed “orphan genes” (i.e., those that lack hits to any other species) and established that ~1% of maize genes have a NIP (Nearly Identical Paralog; >98% identical), many of which exhibit differential expression patterns. Temperature Gradient Capillary Electrophoresis (TGCE) has been used to identify dozens of highly conserved genes that may have been involved in the domestication of maize. A genetic map that contains ~9,000 markers has been created and used to anchor the physical map. The combination of Laser Capture Microdissection (LCM) and 454 transcript sequencing has annotated thousands of rare and potentially cell-type specific genes. Comparisons of ~250,000 ESTs from each of two inbreds (B73 and Mo17) identified thousands of putative SNPs, a sample of which have been validated using Sequenom mass spectrometry technology and have been placed on the genetic map.