Collaborative Research: A Rapid and Inexpensive Whole-Genome Mapping Method for Arabidopsis Using CAPS Co-Dominant Ecotype-Specific PCR-Based Markers

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9405961 Abstract This proposal describes experiments that will generate a large set of mapping markers for Arabidopsis thaliana. Each marker will correspond to a mapped DNA fragment that contains an informative polymorphism for the restriction endonucleases AluI or Sau3A. This collaborative project will have the following goals: (1) to clone DNA fragments that contain the desired polymorphisms by RFLP and genomic subtraction, (2) to sequence the clones and synthesize PCR primers that will amplify the entire fragment, (3) to determine which of the amplified products contain the desired polymorphisms, (4) to use GenBank information to generate additional CAPS (co- dominant, cleaved amplified polymorphic sequences), (5) to map each of the CAPS using DNA from a recombinant inbred Columbia X Landsberg erecta population, and (6) to develop methods that will allow many genes to be mapped in an efficient manner. *** This work will generate a large set of mapping markers for the model plant, Arabidopsis thaliana. The sequences of the clones and of useful primers, as they are identified, will be provided to the community and efforts will be made to arrange for a commercial firm to synthesize sets of primes as inexpensive "mapping kits". If successful, this work should make mapping of any gene from either the Columbia or the Landsberg ecotype much, much faster and much less expensive. %%%