Abstract
A complex phenotype such as seed germination is the result of several genetic and environmental cues and requires the concerted action of many genes. The use of well-structured recombinant inbred lines in combination with "omics" analysis can help to disentangle the genetic basis of such quantitative traits. This so-called genetical genomics approach can effectively capture both genetic and epistatic interactions. However, to understand how the environment interacts with genomic-encoded information, a better understanding of the perception and processing of environmental signals is needed. In a classical genetical genomics setup, this requires replication of the whole experiment in different environmental conditions. A novel generalized setup overcomes this limitation and includes environmental perturbation within a single experimental design. We developed a dedicated quantitative trait loci mapping procedure to implement this approach and used existing phenotypical data to demonstrate its power. In addition, we studied the genetic regulation of primary metabolism in dry and imbibed Arabidopsis (Arabidopsis thaliana) seeds. In the metabolome, many changes were observed that were under both environmental and genetic controls and their interaction. This concept offers unique reduction of experimental load with minimal compromise of statistical power and is of great potential in the field of systems genetics, which requires a broad understanding of both plasticity and dynamic regulation.
Highlights
A complex phenotype such as seed germination is the result of several genetic and environmental cues and requires the concerted action of many genes
G:E interactions have been detected previously in genetical genomics studies for expression (Li et al, 2006; Smith and Kruglyak, 2008; Gerrits et al, 2009; Yeung et al, 2011) and metabolite content (Zhu et al, 2012) by analyzing all lines in a population under different environments, the generalized genetical genomics (GGG) concept offers an effective way of studying a combination of G and E perturbations and is of great potential in the field of systems genetics, in which a broad understanding of both plasticity and dynamics is required (Li et al, 2008)
Previous studies that focused on the comparative analysis of developmental and metabolic variation suggest a link between central metabolism and plant physiology, but G coregulation is not frequently observed (Keurentjes et al, 2006; Meyer et al, 2007)
Summary
A complex phenotype such as seed germination is the result of several genetic and environmental cues and requires the concerted action of many genes. Arabidopsis mutants affected in their oil reserve content or its mobilization show delayed but not full inhibition of germination (Kinnersley and Turano, 2000; Bouché and Fromm, 2004; Shu et al, 2008; Kelly et al, 2011) This suggests an additional metabolic switch that occurs during seed desiccation after seed maturation involving a change from accumulation of oil and storage proteins to the synthesis of free amino acids, sugars, fatty acids, and their degradation products functioning to prepare for rapid metabolic recovery during imbibition (Fait et al, 2006; Angelovici et al, 2010). We will demonstrate here that much of the observed variation in biochemical profiles can be attributed to genotype-by-environment interactions, which can be effectively identified in a GGG approach
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