|Coe Jr, Edward|
|Goicoechea, Jose Luis|
Submitted to: PLoS Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/5/2007
Publication Date: 7/20/2007
Citation: Wei, F., Coe Jr, E., Nelson, W., Engler, F., Bharti, A.K., Butler, E., Kim, H., Goicoechea, J., Lee, S., Fuks, G., Sanchez-Villeda, H., Schroeder, S., Fang, Z., Mcmullen, M.D., Davis, G., Bowers, J.E., Paterson, A.H., Schaeffer, M.L., Gardiner, J., Cone, K., Messing, J., Soderlund, C., Wing, R.A. 2007. Physical and Genetic Structure of the Maize Genome Reflects its Complex Evolutionary History. PLoS Genetics. 3(7):e123. Interpretive Summary: Corn (maize) is the most important crop in the United States and one of the most important plant model species for genetic and biological research. An essential resource to move forward with maize research is a complete genome sequence. One requirement for obtaining a complete sequence is the availability of an integrated genetic and physical map. In this manuscript we report on the development of a sequence ready, fingerprinted contig physical map that covers 93.5% of the maize genome. Analysis of the gene positions in the maize physical map relative to that of the rice genome provides evidence for both a recent and ancient polyploidy origin for the maize genome. These results are important to the maize research community as the physical map is the foundation of the current maize whole genome sequencing effort.
Technical Abstract: Maize (Zea mays L.) is one of the most important cereal crops and a model for the study of genetics, evolution, and domestication. To better understand maize genome organization and build a framework for genome sequencing, we constructed a sequence ready fingerprinted contig (FPC)-based physical map that covers 93.5% of the genome, of which 86.1% is aligned to the genetic map. The FPC map contains 23,954 gene-containing sequences that enabled us to align nearly 73% of the anchored maize genome to the rice genome. In collinear regions, 1 kb in rice corresponds to an average of 3.2 kb in maize, with the overall 6.2-fold genome size expansion in maize explained by most regions in rice corresponding to two regions of maize resulting from its recent polyploid origin. Inversions account for the majority of chromosome structural variations during subsequent maize diploidization. We also find clear evidence of ancient genome duplication predating the divergence of the progenitors of maize and rice. Reconstructing the paleoethnobotany of the maize genome indicates that the progenitors of modern maize contained 10 chromosomes.