Slide 1: High-Resolution Physical Mapping of the Apple Genome by BAC Fingerprinting Schuyler Korban & Jonathan Beever University of Illinois at Urbana-Champaign USDA-CSREES NRI Award #2005-35300-15538
Slide 2: Apple: One of the Three Pillars of the Rosaceae Model System • Apple is a diploid with 2n= 34 • A relatively small size genome: 750 Mb or 1.54 pg DNA/2C • Availability of genetic linkage maps with ~ 840 molecular markers (RAPDs, AFLPs, and SSRs) • Map-based cloning strategies have been successful • Efficient systems for apple transformation and regeneration of transgenic lines for multiple apple cvs. • Availability of bacterial artificial chromosome (BAC) libraries • Availability of over 200,000 expressed sequence tags (ESTs) in the public database
Slide 3: Overall Goal • Generate a whole-genome map for the apple Rationale Although availability of molecular markers and several genetic linkage maps have contributed to our genetic knowledge of qualitative as well complex traits, developing a whole-genome clone-based physical map, consisting of ordered recombinant genomic clones spanning the entire genome, is essential for large-scale genome sequencing, efficient positional cloning of major genes and QTL, target DNA marker development, and provides a powerful platform for high-throughput EST physical mapping
Slide 4: Objectives • Construct a genome-wide framework for a highresolution physical map of the apple genome by BAC fingerprinting • Create a panel of BAC DNA pools for PCRbased screening of ~10X coverage of the apple genome • Discover, characterize, and map EST-SSRs • Anchor BAC-fingerprinted contigs to current genetic and physical marker maps by STS content mapping
Slide 5: Overall Strategy Develop a BAC-based physical map using an agarose gelbased fingerprinting method of 70,000 BAC clones Fingerprinting data will be used to cluster highly-related clones, further refined by manual clustering, and followed by merging of contigs of related clones to assemble the BAC map In parallel, will use the apple EST database to develop ESTderived SSRs, and integrate them into a genetic map Use all genetic markers to anchor apple BAC contigs to the apple genetic map, apple EST unigenes will be anchored to BAC contigs, and a comprehensive apple transcript map will be developed A BAC tiling path will be determined, and a set of BACs with minimal overlap will be established
Slide 6: Project Deliverables • A preliminary physical map will be generated by the second year of the project • A final genetic and physical map of the apple genome will be completed by the end of the third year • Provide several thousand nucleation points suitable for fine mapping, positional cloning, and sequence-based identification of genome regions containing QTL
Slide 7: Project Team Schuyler Korban, PI Jonathan Beever, Co-PI Yuepeng Han, Postdoc Research Assoc Ksenija Gasic, Postdoc Research Assoc Bioinformatics/ Data Management Lei Liu, Collaborator Jyothi Thimmapuram, Collaborator Dorrie Main, Collaborator