A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps

Persistent Link:
http://hdl.handle.net/10150/610399
Title:
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-Sun; Moak, 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, USA; Institute 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
Publisher:
BioMed Central
Citation:
BMC Genomics 2007, 8:47 doi:10.1186/1471-2164-8-47
Journal:
BMC Genomics
Rights:
© 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:
1471-2164
DOI:
10.1186/1471-2164-8-47
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2164/8/47

Full metadata record

DC FieldValue Language
dc.contributor.authorYim, Young-Sunen
dc.contributor.authorMoak, Patriciaen
dc.contributor.authorSanchez-Villeda, Hectoren
dc.contributor.authorMusket, Theresaen
dc.contributor.authorClose, Pamelaen
dc.contributor.authorKlein, Patriciaen
dc.contributor.authorMullet, Johnen
dc.contributor.authorMcMullen, Michaelen
dc.contributor.authorFang, Zheiweien
dc.contributor.authorSchaeffer, Maryen
dc.contributor.authorGardiner, Jacken
dc.contributor.authorCoe, Edwarden
dc.contributor.authorDavis, Georgiaen
dc.date.accessioned2016-05-20T09:05:58Z-
dc.date.available2016-05-20T09:05:58Z-
dc.date.issued2007en
dc.identifier.citationBMC Genomics 2007, 8:47 doi:10.1186/1471-2164-8-47en
dc.identifier.doi10.1186/1471-2164-8-47en
dc.identifier.urihttp://hdl.handle.net/10150/610399-
dc.description.abstractBACKGROUND: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.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/8/47en
dc.rights© 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)en
dc.titleA BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical mapsen
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentDivision of Plant Sciences, University of Missouri, 1-31 Agriculture, Columbia, MO, USAen
dc.contributor.departmentInstitute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USAen
dc.contributor.departmentUSDA-ARS, PGRU, 210 Curtis Hall, Columbia, MO, USAen
dc.contributor.departmentDepartment of Plant Sciences, 303 Forbes Hall, University of Arizona, Tucson, AZ, USAen
dc.identifier.journalBMC Genomicsen
dc.description.collectioninformationThis 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.en
dc.eprint.versionFinal published versionen
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