Bayesian hierarchical shrinkage methods have been widely used for quantitative trait locus mapping. From the computational perspective, the application of the Markov chain Monte Carlo (MCMC) method is not optimal for high-dimensional problems such as the ones arising in epistatic analysis. Maximum a posteriori (MAP) estimation can be a faster alternative, but it usually produces only point esti...

We propose a method to detect the existence of quantitative trait loci (QTL) in a backcross population using a score test. Since the score test only uses the MLEs of parameters under the null hypothesis, it is computationally simpler than the likelihood ratio test (LRT). Moreover, because the location parameter of the QTL is unidentifiable under the null hypothesis, the distribution of the maxi...

A SAS macro package for performing multipoint QTL mapping using the DeFries-Fulker multiple regression method is presented.

A statistical method is presented for detecting quantitative trait loci (QTLs), based on the linear model. Unlike methods able to detect a few well separated QTLs and to estimate their effects and positions, this method considers the genome as a whole and enables the detection of chromosomal segments involved in the differences between two homozygous lines, and their backcross, doubled haploid,...

a The data in the first two rows correspond to the simulated scenario (2) of Cordell (2004) and are based on 10,000 replicates. For all other data, a normally distributed additive QTL was simulated, and results are averages from 1,000 replicates. b dT is the average difference between the test statistic achieved when uninformative pairs are removed from the analysis and the one achieved when th...

Dissection of cytonuclear interactions is fundamentally important for understanding the genetic architecture of complex traits. Here we propose a mating design based on reciprocal crosses and extend the existing QTL mapping method to evaluate the contribution of cytoplasm and QTL x cytoplasm interactions to the phenotypic variation. Efficiency of the design and method is demonstrated via simula...

Molecular markers have been used to map quantitative trait loci. However, they are rarely used to evaluate effects of chromosome segments of the entire genome. The original interval-mapping approach and various modified versions of it may have limited use in evaluating the genetic effects of the entire genome because they require evaluation of multiple models and model selection. Here we presen...