The differences between maximum-likelihood (ML) and regression (REG) interval mapping in the analysis of quantitative trait loci (QTL) are investigated analytically and numerically by simulation. The analytical investigation is based on the comparison of the solution sets of the ML and REG methods in the estimation of QTL parameters. Their differences are found to relate to the similarity betwe...

The biological and statistical advantages of functional mapping result from joint modeling of the mean-covariance structures for developmental trajectories of a complex trait measured at a series of time points. While an increased number of time points can better describe the dynamic pattern of trait development, significant difficulties in performing functional mapping arise from prohibitive c...

In linkage analysis, it is often necessary to include covariates such as age or weight to increase power or avoid spurious false positive findings. However, if a covariate term in the model is specified incorrectly (e.g., a quadratic term misspecified as a linear term), then the inclusion of the covariate may adversely affect power and accuracy of the identification of quantitative trait loci (...

Drought and low nitrogen are the most common abiotic stresses limiting rice productivity in the rainfed rice areas of Asia and Africa. Development and adoption of green super rice (GSR) varieties with greatly improved drought tolerance (DT) and low nitrogen tolerance (LNT) are the most efficient way to resolve this problem. In this study, using three sets of trait-specific introgression lines (...

Many statistical methods have been developed to map multiple quantitative trait loci (QTL) in experimental cross populations. Among these methods, multiple-interval mapping (MIM) can map QTL with epistasis simultaneously. However, the previous implementation of MIM is for continuously distributed traits. In this study we extend MIM to ordinal traits on the basis of a threshold model. The method...

The rapid progression of farm animal genomics has introduced novel technologies capable of presenting global descriptions of biological systems at the level of gene and protein expression and protein interaction. To fully benefit from these developments, experimental designs have to be adapted to these new technologies, and important considerations must be made in the choice of technologies and...

The aim of many genetic studies is to locate the genomic regions (called quantitative trait loci, QTL) that contribute to variation in a quantitative trait (such as body weight). Confidence intervals for the locations of QTL are particularly important for the design of further experiments to identify the gene or genes responsible for the effect. Likelihood support intervals are the most widely ...

Multipoint linkage analysis of quantitative-trait loci (QTLs) has previously been restricted to sibships and small pedigrees. In this article, we show how variance-component linkage methods can be used in pedigrees of arbitrary size and complexity, and we develop a general framework for multipoint identity-by-descent (IBD) probability calculations. We extend the sib-pair multipoint mapping appr...