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United States Department of Agriculture

Agricultural Research Service

Title: Characterization and Physical Mapping of Maize Bac Libraries Using High Density Bac Filter Hybridization

Authors
item Yim, Y - UNIV OF MISSOURI
item Duru, N - UNIV OF MISSOURI
item Musket, T - UNIV OF MISSOURI
item Soderlund, C - CLEMSON UNIVERSITY
item Schaeffer, Mary
item Davis, G - UNIV OF MISSOURI

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: January 10, 2002
Publication Date: January 10, 2002

Technical Abstract: A HindIII and an EcoRI maize BAC library have been constructed from maize inbred line B73. Use of both libraries to make a physical map should minimize the under representation of certain genomic regions caused by the use of a particular restriction enzyme. High-density filter sets from the two libraries containing six filters equivalent to 6X (HindIII) and 7X (EcoRI) haploid genome coverage, respectively, were evaluated with a set of complex probes. The complex probes will provide information on chromosome architecture and organellar DNA content. Probes in this set include the 185bp knob repeat, ribosomal DNA, two telomere-associated-repeat sequences, four-centromere repeat sequences, mitochondrial DNA, lambda, and a chloroplast DNA cocktail. A very low percentage of the HindIII and EcoRI libraries consisted of chloroplast, lambda, and mitochondrial clones, <0.69% and <1.09% respectively. Centromeric repeats gives similar results in both libraries. However, the number of positives for telomere repeat sequences and rDNA were increased in the EcoRI library by four- and seven-fold, respectively. A second set of probes containing 90 maize RFLP core markers were hybridized to the HindIII library. The RFLP core markers will be utilized to facilitate the anchoring process of genetic map to physical map. These core markers have been extensively used to generate genetic maps in maize and provide a framework to anchor BAC contigs screened by hybridizations with the IBM map and function as bin delimiters. Twenty three of the single-copy-number core markers identified an average of 7.2 ± 3.10 positive clones with a range of 3 to 15 positive clones. Forty-two markers with two to three copies gave 3 to 23 positive BAC clones. The wide range of positive signals identified between probes may be indicative of the effects of preferential cloning obtained from the use of the HindIII restriction enzyme. This information has been 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.

Last Modified: 12/22/2014
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