Abstract
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, and 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, incorporated a total of 8,315 mapped markers, and ordered and oriented the majority of FPC contigs. The new integrated physical and genetic map covered 2,120 Mb (93%) of the 2,300-Mb genome, of which 405 contigs were anchored to the genetic map, totaling 2,103.4 Mb (99.2% of the 2,120 Mb physical map). More importantly, 336 contigs, comprising 94.0% of the physical map (∼1,993 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).
Highlights
Maize is an important crop and a model biological system
By utilizing maize genome sequence and genetic map information we were able to significantly improve the physical map by performing new contig merges, breaking mis-assembled contigs and anchoring additional FPC contigs to the maize genetic map
Using individual bacterial artificial chromosome (BAC) assemblies, over 8,300 sequence-based genetic markers, and the optical map, we significantly improved the integrated genetic
Summary
Maize is an important crop and a model biological system. With global climate change and increasing caloric and raw material demands, the development of higher yielding and more stressresistant maize cultivars is a major challenge facing 21st century breeders. We describe our progress in integrating new and more complex resources into the physical map to better guide the generation, validation and annotation of a reference genome sequence for maize These processes included the use of maize genome sequence and optical map information to merge, break, anchor and orient FPC contigs. Upon completion of the shotgun sequencing and sequence improvement of most large-insert clones, we combined all available evidence (i.e. sequence, physical, genetic, and optical map information) to construct a golden path (AGP) of pseudomolecules across the maize genome, hereinafter referred to as the ‘‘B73 RefGen_v1’’. To sequence the maize genome (B73), we employed a clone-byclone approach and selected a minimum tiling path of BACs across the integrated genetic and physical map. The AGP and maize B73 RefGen_v1 are available at: http://www2.genome.arizona.edu/genomes/maize
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