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Title: A BAC POOLING STRATEGY: POWERFUL TOOL FOR THE MAIZE INTEGRATED GENETIC AND PHYSICAL MAP CONSTRUCTION

Author
item YIM, Y - UNIV OF MISSOURI
item MUSKET, T - UNIV OF MISSOURI
item SANCHEZ-VILLEDA, H - UNIV OF MISSOURI
item CLOSE, P - UNIV OF MISSOURI
item WING, R - CLEMSON UNIVERSITY
item MULLET, J - TEXAS A&M UNIV
item KLEIN, P - TEXAS A&M UNIV
item KLEIN, R - TEXAS A&M UNIV
item Coe Jr, Edward
item DAVIS, G - UNIV OF MISSOURI

Submitted to: Maize Genetics Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 3/14/2002
Publication Date: 3/14/2002
Citation: Yim, Y., Musket, T., Sanchez-Villeda, H., Close, P., Wing, R., Mullet, J., Klein, P., Klein, R., Coe Jr, E.H., Davis, G. 2002. A bac pooling strategy: powerful tool for the maize integrated genetic and physical map construction. Maize Genetics Conference Abstracts. V.44:84.

Interpretive Summary:

Technical Abstract: The construction of an integrated genetic and physical map of the maize genome (2500 Mbp) is the primary goal of our ongoing maize genome project. To accomplish this goal, we have used a BAC pooling strategy combined with a high-throughput PCR-based screening method to facilitate anchoring of the maize physical map to the genetic map. The BAC pooling strategy has been successfully demonstrated in sorghum, which has a genome size one-third of the maize genome. This is the first report demonstrating the usefulness and efficiency of this BAC pooling approach in maize despite its large genome size and high amount of repetitive DNA. About 6X haploid genome equivalents (110,592 maize BAC clones) were pooled in six different dimensions (plate, face, side, row, column, and diagonal) to create 288 pools of BAC DNA. The quality of the BAC DNA pools, and their utility for identifying BACs containing PCR-based markers, was tested using primers that amplify maize SSR markers. These markers have been mapped on the IBM Genetic Map and are dispersed across the maize genome. Amplified PCR bands from the pools were deconvoluted into individual BAC address using Resolve script. Results showed 1 to 13 positive BAC clones per SSR primer pair. On average, 5.45 BAC clones were identified with each SSR marker analyzed. Cross checking between our data and FPC fingerprinting data revealed that about 70% of the SSR markers identified BACs that were located in single contig. Among the remaining SSR markers, some identified BACs that were located in two different contigs created by fingerprinting, or BACs that were located in a contig and a pool of singleton BACs. These make our data extremely valuable in merging contigs or singletons and contigs. This information will be integrated with fingerprinting data generated by Clemson University Genomics Institute to assemble the BAC contigs using Fingerprint Contig Assembly and contribute to the process of physical map construction.