Using entrainment to discover clock genes: A QTL-Analysis in Neurospora crassa

One of the central aims of the field of chronobiology is to understand how organisms predict daily changes in the environment and adjust to them. How these environmental rhythms are perceived by the organism and how biological rhythms are generated on a cellular level has been studied extensively during the last decades. In all phyla investigated so far, distinct sets of clock genes have been found to generate circadian oscillations via a complex network of positive and negative feedback loops. Furthermore, the inheritance of circadian pheno-types does not simply follow the rules of Mendelian genetics, but is under control of multiple genes plus environment and is therefore an example of a complex genetic trait. Mapping quantitative trait loci in the context of circadian rhythmicity has been used in Arabidopsis, mice and other organisms and indicates that circadian behavior is influenced by many more clock genes than have been identified, yet. A QT (quantitative trait) is a pheno-type, that can be quantified (e.g. flowering time, growth rate, fertility, spore size, hyphal growth, tolerance to toxins etc.). Given the complexity of the circadian clock and the fact that in a previous study multiple genes could be attributed to circadian phenotypes like phase of entrainment and period, these traits seem to be optimal candidates for a QTL-analysis in Neurospora crassa. In addition to an obvious circadian rhythm (conidial band formation), N. crassa’s advan-tages include a relatively small, sequenced genome, high numbers of offspring from a single cross, and haploidy. To date, there has been only one published QTL-analysis in N. crassa. The aim of the underlying study is to find novel clock genes by associating circadian pheno-types with a linkage map for Neurospora crassa. Contrary to circadian theory and experi-mental evidence, but similar to findings in Arabidopsis, we found no straightforward correla-tions between phase and free running period (FRP). One QTL that we identified for the period trait was linked to the known clock gene frequency, demonstrating proof of principle