Abstract
Natural variation provides a valuable resource to study the genetic regulation of quantitative traits. In quantitative trait locus (QTL) analyses this variation, captured in segregating mapping populations, is used to identify the genomic regions affecting these traits. The identification of the causal genes underlying QTLs is a major challenge for which the detection of gene expression differences is of major importance. By combining genetics with large scale expression profiling (i.e. genetical genomics), resulting in expression QTLs (eQTLs), great progress can be made in connecting phenotypic variation to genotypic diversity. In this review we discuss examples from human, mouse, Drosophila, yeast and plant research to illustrate the advances in genetical genomics, with a focus on understanding the regulatory mechanisms underlying natural variation. With their tolerance to inbreeding, short generation time and ease to generate large families, plants are ideal subjects to test new concepts in genetics. The comprehensive resources which are available for Arabidopsis make it a favorite model plant but genetical genomics also found its way to important crop species like rice, barley and wheat. We discuss eQTL profiling with respect to cis and trans regulation and show how combined studies with other ‘omics’ technologies, such as metabolomics and proteomics may further augment current information on transcriptional, translational and metabolomic signaling pathways and enable reconstruction of detailed regulatory networks. The fast developments in the ‘omics’ area will offer great potential for genetical genomics to elucidate the genotype-phenotype relationships for both fundamental and applied research.
Highlights
Ever since the current paradigm of gene transcription preceding biological function, research on gene function has focused on expression studies
Can be caused by strong polymorphisms in promoter regions, premature stop mutations and even the complete absence of genes in one of the parental lines [39]. Both hybridization and true transcription variation will lead to strong cis-expression QTLs (eQTLs) which can subsequently be used as molecular markers, allowing the construction of high-resolution maps [40, 41]
These findings suggest that the effects of key-regulators in gene expression are progressed to the phenotypic level
Summary
Ever since the current paradigm of gene transcription preceding biological function, research on gene function has focused on expression studies. In a relatively small population of 40 haploid segregants from a cross between a laboratory and a wild type strain, it was shown that parental differences in gene expression were highly heritable and amenable to genetic mapping This first report was quickly followed by more comprehensive eQTL studies in higher eukaryotes [14] and has been applied in a broad range of taxonomic kingdoms including yeast [13, 15,16,17], nematodes [18], insects [19, 20], plants [21,22,23,24], rodents [25,26,27] and humans [28,29,30,31,32,33]. We will discuss future prospects and speculate on the utilization of advancing technological developments for genetic studies
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