Sequencing the Maize Genome
Zea mays or maize is the highest-yielding crop worldwide and PGIR has also been involved in the maize genome projects. Several of those have been funded to prepare the sequencing of the genome, which at the time was difficult because of its size being larger than the human genome. The maize/sorghum collinearity project (PI, J. Messing, Rutgers University) sought to analyze the whole-genome duplication event that led to the formation of today’s maize genome. Because this project involved the sequencing of maize homoeologous regions, it also funded the construction of a BAC library (MboI) from the inbred B73. The Maize Mapping Project (MMP, PI, E. Coe Jr., University of Missouri) generated a genetic map from a recombinant inbred population derived from intermated B73 x Mo17 (IBM). It also included the construction of BAC libraries from inbred B73 (HindIII + EcoRI). BAC libraries from both sources consist of 458,905 clones covering the B73 genome of 2,365 Mb 29 times. In addition, the MMP sought to generate a physical map by DNA fingerprinting of the BAC libraries and linking them to the IBM map.
To further prepare for sequencing the entire genome, two additional projects were funded. The Sequencing the Maize Genome Project (STMG, PI, J. Messing, Rutgers University) sought to improve on the B73 physical map by High Information Content Fingerprinting (HICF) and by BAC end sequencing (BES). BESs serve as sequence tagged connectors (STCs) between sequences and the genetic map. They also represent a random comprehensive survey of genes and repeat elements of the maize genome. The third component of STMG was BAC sequencing from 100 random regions and to investigate assembly of shotgun reads, gene structure, and members of repetitive sequences. The second project, Consortium for Maize Genomics (CMG, PI, K. Schubert, Donald Danforth Plant Science Center), tested fractionation techniques of genomic regions containing only genes and not repetitive DNA elements. Both CMG and STMG have collaborated to sequence two homoeologous regions of the maize genome (7.8 Mb from Zm1S & 6.6 Mb from Zm9L, respectively) and to analyze maize genome structure and shotgun sequence assemblies of a larger interval. Based on a minimum tiling path generated from the maize map, the genome has been sequenced by the Washington University Genome Sequencing Center in collaboration with Arizona Genome Institute and Cold Spring Harbor Laboratory.
In addition to laying the foundation for the maize genome sequence, we also participated in a maize genome project focused on genes expressed in the endosperm of the maize seed with a consortium involving the laboratories of Don McCarty, Curt Hannah, Mark Settles, Karen Koch at the University of Florida at Gainesville, Phil Becraft at Iowa State University, and Brian Larkins at the University of Arizona, Tucson. This project also known as the uniformMu project used the transposable element mutator as a mutagen for gene-knockouts. We generated full-length cDNAs from endosperm of the same genetic background, inbred W22. We sequenced those and junction sequences of mutator insertions in the genome. Out of 23,348 high-quality cDNA sequence reads, we obtained 5,326 unigenes, reflecting the endosperm transcriptome. All the above projects have been National Science Foundation sponsored projects and ended in 2008.More recently, we received institutional support to use the maize genome data for evolutionary studies.
Additional information can be found on the Maize Genetics and Genomics Database.