Statistical Issues in the Analysis of Quantitative Traits in Combined Crosses

Statistical Issues in the Analysis of Quantitative Traits in Combined Crosses

Fei Zou^a, Brian S. Yandell^a, and Jason P. Fine^a
^a Department of Statistics, University of Wisconsin, Madison, Wisconsin 53706

Corresponding author: Fei Zou, Department of Statistics, 1210 W. Dayton St., Madison, WI 53706., feizou{at}stat.wisc.edu (E-mail)

Communicating editor: Z-B. ZENG

We consider some practical statistical issues in QTL analysiswhere several crosses originate in multiple inbred parents.Our results show that ignoring background polygenic variationin different crosses may lead to biased interval mapping estimatesof QTL effects or loss of efficiency. Threshold and power approximationsare derived by extending earlier results based on the Ornstein-Uhlenbeckdiffusion process. The results are useful in the design andanalysis of genome screen experiments. Several common designsare evaluated in terms of their power to detect QTL.

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