ARS | Publication request: The Physical and Genetic Framework of the B73 Maize Genome

Submitted to: PLoS Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 12, 2009
Publication Date: November 20, 2009
Citation: Wei, F., Zhang, J., Zhou, S., He, R., Schaeffer, M.L., Collura, K., Kudrna, D., Faga, B., Wissotski, M., Golser, W., Fulton, L., Courtney, W., Fronick, C., Fulton, B., Coe, E., Schwartz, D.C., Ware, D., Clifton, S., Wilson, R.K., Wing, R.A. 2009. The Physical and Genetic Framework of the B73 Maize Genome. PLoS Genetics. 5(11):e1000715.

Interpretive Summary: Corn (Maize) is a major cereal crop and an important model system for basic biological research. Knowledge gained from maize research can also be used to improve its grass relatives such as sorghum, wheat, rice. The primary objective of the Maize Genome Sequencing Consortium (MGSC) was to generate a reference genome sequence for the US inbred line B73. This is used by both plant breeders and basic researchers to locate candidate genes and favorable alleles for agronomic traits and biologically interesting functions. The B73 genome has 10 different chromosomes, and 2,300,000,000 nucleotides. To facilitate the sequencing of a genome this size, the project relied on the selection of 17,000 overlapping pieces (clones), that represented 93% of the B73 genome. This report describes how the clones were selected, ordered and linked to genetic maps coordinates. The genetic map locations are essential to make the sequence useful to plant breeders and basic researchers.

Technical Abstract: Corn (Maize) is a major cereal crop and an important model system for basic biological research. Knowledge gained from maize research can also be used to genetically improve its grass relatives such as sorghum, wheat, rice. The primary objective of the Maize Genome Sequencing Consortium (MGSC) was to generate a reference genome sequence that was integrated with both the physical and genetic maps. Using a previously published integrated genetic and physical map, combined with in-coming maize genomic sequence, new sequence-based genetic markers, and an optical map, we dynamically picked a minimum tiling path (MTP) of 16,910 bacterial artificial chromosome (BAC) and fosmid clones that were used by the MGSC to sequence the maize genome. The final MTP resulted in a significantly improved physical map that reduced the number of contigs from 721 to 435, incorpored a total of 8,315 mapped markers, and ordered and oriented the majority of FPC contigs. The new integrated physical and genetic map covered 2120 Mb (93%) of the 2300-Mb genome, of which 405 contigs were anchored to the genetic map, totaling 2103.4 Mb (99.2% of the 2120 Mb physical map). More importantly, 336 contigs, comprising 94.0% of the physical map (~1993 Mb), were ordered and oriented. Finally we used all available physical, sequence, genetic and optical data to generate a golden path (AGP) of chromosome-based pseudomolecules, herein referred to as the B73 Reference Genome Sequence version 1 (B73 RefGen_v1).