Genetic basis of the circadian clock

Natural variation in circadian clocks affects interactions between environmental factors and the timing of important physiological processes in plants. This could lead to complex genotype by environment interactions that in turn result in large changes in metabolite levels.

The 'Network QTL mapping of circadian clock' (NETWORK QTL MAPPING) project has cloned three metabolic loci controlling circadian output variation in Arabidopsis. They also looked for homologous genes in two of the Brassica family, Brassica oleracea (includes cabbage and broccoli) and Brassica rapa (turnip, rocket and mustard).

Team members studied phenotypes including bolting date, rosette diameter and flowering time that are influenced by daylight hour control. Secondary metabolites under investigation included glucosinolates and phenolic compounds, phytochemicals that may be linked to antioxidant activity.

Three loci controlling the Arabidopsis Bay x Sha circadian clock variation that controls time to flowering were cloned. High-resolution mapping and in silico candidate gene identification were used to multiply the three genes. Markers were developed to screen for recombination events and locate smaller regions of the tested locus, narrowing the regions down to about 30 genes.

In parallel, NETWORK QTL MAPPING constructed networks for all loci on those regions. As genes in the same pathway have similar expression patterns through diverse temporal and physiological conditions, the researchers connected each candidate gene to co-expressed genes across almost 1 400 microarray tests. Based on this, the researchers then looked for homologous genes in B. oleracea and B. rapa.

Three candidate genes for glucosinolate content and five candidate genes for flowering time emerged and all of them exhibit high circadian shift rhythms. Using mutant and transgenic lines, the project tested if the genes controlled variability in the phenotypes. All candidates for glucosinolate productivity and two genes for flowering time displayed the expected phenotype.

A clear view of the biochemistry molecules behind the accumulation of secondary metabolites in important salad and vegetable crops as a result of the circadian clock could be of great significance in breeding programmes. Brassicas also include varieties used for oil production, fodder and mustards, as well as being ecologically important for larvae of butterflies and moths.