A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps
Author
Yim, Young-SunMoak, Patricia
Sanchez-Villeda, Hector
Musket, Theresa
Close, Pamela
Klein, Patricia
Mullet, John
McMullen, Michael
Fang, Zheiwei
Schaeffer, Mary
Gardiner, Jack
Coe, Edward
Davis, Georgia
Affiliation
Division of Plant Sciences, University of Missouri, 1-31 Agriculture, Columbia, MO, USAInstitute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
USDA-ARS, PGRU, 210 Curtis Hall, Columbia, MO, USA
Department of Plant Sciences, 303 Forbes Hall, University of Arizona, Tucson, AZ, USA
Issue Date
2007
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BioMed CentralCitation
BMC Genomics 2007, 8:47 doi:10.1186/1471-2164-8-47Journal
BMC GenomicsRights
© 2007 Yim et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0).Collection Information
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.Abstract
BACKGROUND:Molecular markers serve three important functions in physical map assembly. First, they provide anchor points to genetic maps facilitating functional genomic studies. Second, they reduce the overlap required for BAC contig assembly from 80 to 50 percent. Finally, they validate assemblies based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy in combination with a high-throughput PCR-based screening method to anchor the maize genetic and physical maps.RESULTS:A total of 110,592 maize BAC clones (~ 6x haploid genome equivalents) were pooled into six different matrices, each containing 48 pools of BAC DNA. The quality of the BAC DNA pools and their utility for identifying BACs containing target genomic sequences was tested using 254 PCR-based STS markers. Five types of PCR-based STS markers were screened to assess potential uses for the BAC pools. An average of 4.68 BAC clones were identified per marker analyzed. These results were integrated with BAC fingerprint data generated by the Arizona Genomics Institute (AGI) and the Arizona Genomics Computational Laboratory (AGCoL) to assemble the BAC contigs using the FingerPrinted Contigs (FPC) software and contribute to the construction and anchoring of the physical map. A total of 234 markers (92.5%) anchored BAC contigs to their genetic map positions. The results can be viewed on the integrated map of maize 1,2].CONCLUSION:This BAC pooling strategy is a rapid, cost effective method for genome assembly and anchoring. The requirement for six replicate positive amplifications makes this a robust method for use in large genomes with high amounts of repetitive DNA such as maize. This strategy can be used to physically map duplicate loci, provide order information for loci in a small genetic interval or with no genetic recombination, and loci with conflicting hybridization-based information.EISSN
1471-2164Version
Final published versionAdditional Links
http://www.biomedcentral.com/1471-2164/8/47ae974a485f413a2113503eed53cd6c53
10.1186/1471-2164-8-47
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Except where otherwise noted, this item's license is described as © 2007 Yim et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0).