作物学报Issue(1)：1-11,11.DOI:10.3724/SP.J.1006.2013.00001
QTL作图中零假设检验统计量分布特征及LOD临界值估计方法
Properties of the Test Statistic under Null Hypothesis and the Calculation of LOD Threshold in Quantitative Trait Loci (QTL) Mapping
摘要
Abstract
Selecting an appropriate LOD threshold is of great interest in QTL mapping studies. Many approaches can be consid-ered to calculate the critical value throughout a genome, such as simulation-based method, analytical approximation, and empiri-cal method based on permutation test. Many tests are conducted in QTL mapping, which are not mutually independent because the linkage relationship of adjacent markers on chromosomes. In order to declare a significant QTL at a genome-wide significance level, it is necessary to understand the behavior of test statistic under null hypothesis in QTL mapping and to deal with the de-pendent multiple-test problem arising in the genome-wide test. Our objectives in this study were (1) to investigate the properties of LRT (likelihood ratio test) statistic of one-point scanning under null hypothesis in QTL mapping, (2) to determine the factors affecting the cumulative distribution of maximum LOD score, and (3) to identify the relationship between the effective number of independent tests and the length of chromosome by simulation method. Results indicated that the LRT test statistic in one-dimensional scanning of additive-dominant QTL and two-dimensional scanning of epistatic QTL followed chi-square distri-butions, and the degree of freedom (df) was equal to the number of genetic parameters to be estimated. For example, degree of freedom in recombinant inbred lines (RIL) population was equal to 1 in one dimensional or two dimensional scanning. Degree of freedom in F2 populations was equal to 2 in one-dimensional scanning and 4 in two-dimensional scanning. Number of chromo-some, population size and phenotyping error variance did not have any effect on the distribution of LRT under null hypothesis, and therefore will not affect the selection of LOD threshold. On the contrary, population type, genome size and marker density had significant impacts. For BC1, RIL, and F2 populations, the threshold was the smallest in BC1 population and the highest in F2 population. Higher marker density and longer chromosome resulted in higher LOD threshold. It was identified that the effective number of independent tests (Mef ) was proportional to the length of chromosome in one-dimensional scanning of addi-tive-dominant QTL. In two-dimensional scanning of epistatic QTL, it was identified that Mef was in a squared relationship to the length of chromosome. With the help of Bonferroni correction, we could acquire the relationship between point-wise and ge-nome-wide significance levels. Therefore, it is convenient to calculate the threshold LOD in QTL mapping, given the ge-nome-wide significance level, the population type, marker density and genome size.关键词
QTL作图/似然比检验/LOD统计量/零假设/显著性水平/独立检验次数Key words
QTL mapping/Likelihood ratio test/LOD score/Null hypothesis/Significance level/Number of independent tests引用本文复制引用
孙子淇,李慧慧,张鲁燕,王建康..QTL作图中零假设检验统计量分布特征及LOD临界值估计方法[J].作物学报,2013,(1):1-11,11.基金项目
本研究由国家自然科学基金项目(31000540)资助 （31000540）
