significance test and genome selection in bayesian shrinkage analysis显著性检验在贝叶斯收缩和基因组选择分析.pdfVIP

Hindawi Publishing Corporation International Journal of Plant Genomics Volume 2010, Article ID 893206, 11 pages doi:10.1155/2010/893206 Research Article Significance Test and Genome Selection in Bayesian Shrinkage Analysis Xiaohong Che1 and Shizhong Xu2 1 Department of Statistics, University of California, Riverside, California 92521, USA 2 Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA Correspondence should be addressed to Shizhong Xu, shizhong.xu@ Received 16 November 2009; Revised 5 February 2010; Accepted 27 March 2010 Academic Editor: Yunbi Xu Copyright © 2010 X. Che and S. Xu. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Bayesian shrinkage analysis is the state-of-the-art method for whole genome analysis of quantitative traits. It can estimate the genetic effects for the entire genome using a dense marker map. The technique is now called genome selection. A nice property of the shrinkage analysis is that it can estimate effects of QTL as small as explaining 2% of the phenotypic variance in a typical sample size of 300–500 individuals. In most cases, QTL can be detected with simple visual inspection of the entire genome for the effect because the false positive rate is low. As a Bayesian method, no significance test is needed. However, it is still desirable to put some confidences on the estimated QTL effects. We proposed to use the permutation test to draw empirical thresholds to declare significance of QTL under a predetermined genome wide type I error. With the permutation test, Bayesian shrinkage analysis can be routinely used for QTL detection. 1.