Polyploidization widely occurs in the evolutionary history of eukaryotes, especially for flowering plants. Exploring the evolutionary and agricultural important role by polyploidy is mystery and challenging job. In the first chapter of this thesis, I developed a quantitative genetics model based on orthogonal contrast scales, which would provide theoretical basis for any further bi-allelic QTL analysis in autotetraploid species. In the next chapter, I developed an interval mapping method for QTL mapping in outbred population for autotetraploid, considering both bivalent and quadrivalent pairing during meiosis. Extensive simulation work has been implemented to demonstrate the reliability of this method. This work would provide practical tools for breeding the world’s third most important crop, the cultivated potato. To give some insight into the evolutionary important role played by polyploidization, I developed a statistical method for inferring crossover interference based on three-locus analysis in autotetraploids in the third chapter and a method to predict genome-wide crossover rate for autotetraploid yeast in the final chapter.