The interplay between genetic and epigenetic variation is only partially understood. One form of epigenetic variation is methylation at CpG sites, which can be measured as methylation quantitative trait loci (meQTL). Here we report that in a panel of lymphocytes from 1,748 individuals, methylation levels at 1,919 CpG sites are correlated with at least one distal (trans) single-nucleotide polymo...

Even if considerable progress has been achieved towards the understanding of natural variation in plant systems, the contribution of transcript abundance variation to phenotypic diversity remains unappreciated. Over the last decade, efforts to characterise the genome-wide expression variation in natural accessions, structured populations and hybrids have improved our knowledge of the contributi...

Population scale studies combining genetic information with molecular phenotypes (for example, gene expression) have become a standard to dissect the effects of genetic variants onto organismal phenotypes. These kinds of data sets require powerful, fast and versatile methods able to discover molecular Quantitative Trait Loci (molQTL). Here we propose such a solution, QTLtools, a modular framewo...

The interaction between maternally provided environment and offspring genotype is a major determinant of offspring development and fitness in many organisms. Recent research has demonstrated that not only genetic effects, but also epigenetic effects may be subject to modifications by the maternal environment. Genomic imprinting resulting in parent-of-origin-dependent gene expression is among th...

Epigenetics has become one of the major areas of biological research. However, the degree of phenotypic variability that is explained by epigenetic processes still remains unclear. From a quantitative genetics perspective, the estimation of variance components is achieved by means of the information provided by the resemblance between relatives. In a previous study, this resemblance was describ...

Study Hypothesis Less than 2% of human DNA codes for proteins, whereas the vast majority of DNA in the human genome consists of sequences with unknown function. A substantial portion of the noncoding sequences harbors regulatory motifs important for gene expression. Recent genome-wide association studies (GWAS) suggest that the majority of single nucleotide polymorphisms (SNPs) associated with ...

Conventional biparental quantitative trait locus (QTL) mapping has led to some successes in the identification of causal genes in many organisms. QTL likelihood intervals not only provide "prior information" for finer-resolution approaches such as GWAS but also provide better statistical power than GWAS to detect variants with low/rare frequency in a natural population. Here, we describe a new ...

In recent years, there has been a considerable amount of research on the use of regularization methods for inference and prediction in quantitative genetics. Such research mostly focuses on selection of markers and shrinkage of their effects. In this review paper, the use of ridge regression for prediction in quantitative genetics using single-nucleotide polymorphism data is discussed. In parti...

Salinity stress is one of the most severe abiotic stresses that affect agricultural production. Genome wide association study (GWAS) has been widely used to detect genetic variations in extensive natural accessions with more recombination and higher resolution. In this study, 206 barley accessions collected worldwide were genotyped with 408 Diversity Arrays Technology (DArT) markers and evaluat...

Genome-wide association studies (GWAS) have been successful in facilitating the understanding of genetic architecture behind human diseases, but this approach faces many challenges. To identify disease-related loci with modest to weak effect size, GWAS requires very large sample sizes, which can be computational burdensome. In addition, the interpretation of discovered associations remains diff...