Linkage disequilibrium mapping of DNA polymorphisms that contribute to variation in abdominal and steronpleural bristle number in large samples of wild caught Drosophila will be carried out in order to test a number of hypotheses: i) Do DNA polymorphisms at candidate genes contribute to standing variation in continuous characters?. ii) What are the frequencies and effects (including epistasis) of these polymorphisms, iii) What is the molecular nature (coding versus regulatory) of standing variation in quantitative traits?, iv) Are factors identified by association mapping consistent with those identified by QTL mapping, v) Is association mapping capable of being used effectively in humans to identify polymorphisms which contribute to complex disease phenotypes? Assessing the applicability of disequilibrium mapping to natural populations is crucial if we wish such studies to serve as a model for identifying human disease causing polymorphisms. In order to detect associations between DNA polymorphisms and genetic factors contributing a small fraction to standing variation in a quantitative character a large number of individuals must be typed for a large number of polymorphic DNA markers through a candidate gene region. This project focuses on three candidate genes, Delta, Notch, and Enhancer if Split, which are of central importance in the development of the peripheral nervous system (bristles are sensilla), and are particularly well characterized at the molecular level. Typing will be accomplished by first sequencing twenty alleles at each of the candidate genes to identify genes to identify all common polymorphisms that could potentially affect bristle number. Then, allele specific oligonucleotides are designed and hybridized to high density membranes on which long PCR products from approximately 4000 wild caught individuals are spotted. Hybridization patterns over sequential oligonucleotide probings allows each individual to be genotyped for a large number of polymorphic sites. Data will be examined for associations between polymorphic DNA sites and variation in bristle number, and regions containing sites with significant associations will be further typed to saturation to identify candidate causative polymorphisms. The set of candidate causative polymorphism will allow the above hypotheses to be directly addressed.
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