The ability of an organism to measure time is the product of a cellular biological clock. Many phenomena controlled by the biological clock cycle on a daily basis and are called circadian rhythms. My goal is to understand the genetic and biochemical mechanisms by which an organism measures time and uses that temporal information to regulate gene expression, metabolism, and physiology. The circadian clock is an endogenous oscillator that drives rhythms with periods of ~24 hours. By definition, these circadian (from the Latin, circa, approximately; dies, day) rhythms persist in constant conditions and reflect the activity of an endogenous biological clock. Plants are richly rhythmic and the circadian clock regulates a number of key metabolic pathways and stress responses. In addition, the circadian clock plays a critical role in the photoperiodic regulation of the transition to flowering in many species. Circadian rhythms in plants have been the subject of a number of recent reviews (McClung and Gutiérrez, 2010; McClung, 2011; McClung, 2013; McClung, 2014).

POTENTIAL THESIS PROJECTS

 1. Mutational Analysis of the Arabidopsis Circadian Clock. We have identified a number of loci which, when mutated, alter circadian rhythmicity (period or phase is altered, or the plants are arrhythmic). The genetic and molecular biological analysis of these mutations offers a number of thesis projects. We have recently identified a novel period mutants defective in Protein Arginine Methyltransferase 5 (Hong et al., 2010) and SKIP (Wang et al., 2012), which link clock function to alternative splicing of clock gene transcripts. We also have identified genes critical for the clock response to temperature (Salomé and McClung, 2005; Salomé et al., 2010), although the identity of the temperature sensor(s) remain a mystery (McClung and Davis, 2010).  Most recently, we have defined reciprocal relationships between the circadian clock as the responses to two stresses, the abiotic stress of iron deficiency (Hong et al., 2013) and the biotic stress, pathogen challenge (Zhang et al., 2013).

2. Natural Variation to Identify Novel Components of the Arabidopsis Circadian Clock. Quantitative Trait Locus (QTL) analysis can identify genes important for clock function (Michael et al., 2003). However, standard QTL analysis is limited by the amount of genetic variation present in the parents of a single cross, basically two alleles per locus. The “next generation” of such analyses considers nested association mapping (NAM) populations among multiple parents, thus greatly increasing the diversity tested. We wish to assess circadian function in a population derived from eight parents, which promises to expand the collection of QTL known to affect circadian clock function.

3. Evolutionary and Quantitative Analysis of the Brassica rapa Circadian Clock. It is important to determine whether the model of the circadian clock developed in Arabidopsis can be applied to crop species. We are addressing this using Brassica rapa (Chinese cabbage, turnip), a clock relative of Arabidopsis and also of canola. We are measuring clock parameters (by leaf movement) and have identified QTLs that contribute to period, phase and amplitude (Lou et al., 2011). We have developed a tractable tissue culture system in which we can measure clock function in transgenically-manipulated genotypes (Xu et al., 2010). One exciting observation has been that QTL for circadian period length often co-localize with QTL for water-use efficiency (WUE)(Edwards et al., 2011; Edwards et al., 2012). There are a number of mechanisms by which the clock could contribute to WUE, including regulation of stomatal aperture, photosynthetic performance, and hydraulic conductivity (many aquaporins are clock-regulated). To study clock modulation of the drought response in B. rapa we are using next generation sequencing (RNAseq) to probe the transcriptomic response to drought. Because water availability frequently limits crop yield, it is possible that manipulation of clock performance can enhance productivity. The recent availability of a B. rapa genome also has allowed the identification of B. rapa orthologs of Arabidopsis clock genes (Lou et al., 2012). We will test whether they play similar roles in the B. rapa clock. Since Arabidopsis and B. rapa separated, the latter has tripled its genome, so it will be very interesting to probe the evolutionary consequences of this genome expansion. Indeed, our analysis shows that clock genes have been preferentially retained in B. rapa, offering a explanation for increased clock complexity during the evolution of higher plants (Lou et al., 2012; McClung, 2013).

Brassica field in Poitou-Charentes, France