Primate evolution has been argued to result, in part, from changes in how genes are regulated. However, we still know little about gene regulation in natural primate populations. We conducted an RNA sequencing (RNA-seq)-based study of baboons from an intensively studied wild population. We performed complementary expression quantitative trait locus (eQTL) mapping and allele-specific expression ...

MOTIVATION In most quantitative trait locus (QTL) mapping studies, phenotypes are assumed to follow normal distributions. Deviations from this assumption may affect the accuracy of QTL detection and lead to detection of spurious QTLs. To improve the robustness of QTL mapping methods, we replaced the normal distribution for residuals in multiple interacting QTL models with the normal/independent...

Expression quantitative trait locus (eQTL) analysis is rapidly moving from a cutting-edge concept in genomics to a mature area of investigation, with important connections to genome-wide association studies for human disease, pharmacogenomics and toxicogenomics. Despite the importance of the topic, many investigators must develop their own code or use tools not specifically suited for eQTL anal...

The genetic architecture of fitness-relevant traits in natural populations is a topic that has remained almost untouched by quantitative genetics. Given the importance of parasitism for the host's fitness, we used QTL mapping to study the genetic architecture of traits relevant for host-parasite interactions in the trypanosome parasite, Crithidia bombi and its host, Bombus terrestris. The three...

We develop a Bayesian multi-SNP Markov chain Monte Carlo approach that allows published functional significance scores to objectively inform single nucleotide polymorphism (SNP) prior effect sizes in expression quantitative trait locus (eQTL) studies. We developed the Normal Gamma prior to allow the inclusion of functional information. We partition SNPs into predefined functional groups and sel...

The determination of expression quantitative trait loci (eQTL) epistasis - a form of functional interaction between genetic loci that affect gene expression - is an important step toward the thorough understanding of gene regulation. Since gene expression has emerged as an "intermediate" molecular phenotype eQTL epistasis might help to explain the relationship between genotype and higher level ...

We applied a simple and efficient two-step method to analyze a family-based association study of gene expression quantitative trait loci (eQTL) in a mixed model framework. This two-step method produces very similar results to the full mixed model method, with our method being significantly faster than the full model. Using the Genetic Analysis Workshop 15 (GAW15) Problem 1 data, we demonstrated...

In the fast-developing field of expression quantitative traits loci (eQTL) studies, much interest has been concentrated on detecting genomic regions containing transcriptional regulators that influence multiple expression phenotypes (trans-hubs). In this paper, we develop statistical methods for eQTL mapping and propose a new procedure for investigating candidate trans-hubs. We use data from th...

Characterizing the collective regulatory impact of genetic variants on complex phenotypes is a major challenge in developing a genotype to phenotype map. Using expression quantitative trait locus (eQTL) analyses, we constructed bipartite networks in which edges represent significant associations between genetic variants and gene expression levels and found that the network structure informs reg...

There is considerable interest in the evolution of morphological traits, and morphometric studies in combination with the multivariate theory of quantitative genetics can provide a detailed understanding of the variation and evolutionary potential of these traits. For both morphometrics and quantitative genetics, new and improved techniques have been established recently (e.g., Dryden and Mardi...