Maize global transcriptomics reveals pervasive leaf diurnal rhythms but rhythms in developing ears are largely limited to the core oscillator

Abstract

Background: Plant diurnal rhythms are vital environmental adaptations to coordinate internal physiological responses to alternating day-night cycles. A comprehensive view of diurnal biology has been lacking for maize (Zea mays), a major world crop.

Methodology: A photosynthetic tissue, the leaf, and a non-photosynthetic tissue, the developing ear, were sampled under natural field conditions. Genome-wide transcript profiling was conducted on a high-density 105 K Agilent microarray to investigate diurnal rhythms.

Conclusions: In both leaves and ears, the core oscillators were intact and diurnally cycling. Maize core oscillator genes are found to be largely conserved with their Arabidopsis counterparts. Diurnal gene regulation occurs in leaves, with some 23% of expressed transcripts exhibiting a diurnal cycling pattern. These transcripts can be assigned to over 1700 gene ontology functional terms, underscoring the pervasive impact of diurnal rhythms on plant biology. Considering the peak expression time for each diurnally regulated gene, and its corresponding functional assignment, most gene functions display temporal enrichment in the day, often with distinct patterns, such as dawn or midday preferred, indicating that there is a staged procession of biological events undulating with the diurnal cycle. Notably, many gene functions display a bimodal enrichment flanking the midday photosynthetic maximum, with an initial peak in mid-morning followed by another peak during the afternoon/evening. In contrast to leaves, in developing ears as few as 47 gene transcripts are diurnally regulated, and this set of transcripts includes primarily the core oscillators. In developing ears, which are largely shielded from light, the core oscillator therefore is intact with little outward effect on transcription.

Figure 1. Gene expression in maize leaf.

As assayed by Agilent microarray analysis, 10,037 transcripts were identified as diurnally cycling with a period near 24 hours via the GeneTS method. A) A heat map showing normalized gene expression patterns of significant transcripts. Each transcript is normalized to the median of that transcript's signal intensity. Color scale runs from 0.25 (blue) to 4 (yellow). B) Phase diagram of significant cycling transcripts, as determined by greatest mean expression. Time points immediately following light/dark transitions are enriched for peak expression.

Figure 2. Gene expression in maize developing ears.

As assayed by Agilent microarray analysis, 149 transcripts were identified as cycling with a period near 24 hours via the GeneTS method. A) A heat map showing normalized gene expression patterns of significant transcripts. Each transcript is normalized to the median of that transcript's signal intensity. Color scale runs from 0.25 (blue) to 4 (yellow). B) Phase diagram of significant cycling transcripts, as determined by greatest mean expression. Despite low numbers of cycling transcripts, there appears to be enrichment for early evening peak expression.

Figure 3. Diurnal oscillation of the core clock components.

Leaf transcripts are plotted in blue, and ear data are plotted in red, overlaid with light/dark cycles for: ZmCCA1, ZmLHY, ZmTOC1a, ZmTOC1b, ZmPRR73, ZmPRR59, ZmGI1A (gigz1A), ZmGI1B (gigz1B), ZmFKF1a and ZmFKF1b.

Figure 4. Diurnal Representation Patterns of 1737 Gene Functional Terms.

1737 Gene Functional Terms were horizontally categorized by the time point at which their representation peaks, and vertically into descriptive diurnal patterns, such as ‘Dawn’ or ‘Bimodal’. The gray-scale plot is the percent of maximum FEI for the six time points. FEI stands for Functional Enrichment Index, which is the absolute Log of the binomial probability (see Material and Methods). The table at the top shows the number of transcripts and functional terms peaking at the six time points, and also the number of functional terms that peaked at those time points following filtering at a 10% and 1% FDR (false discovery rate).

Figure 5. Diurnal Patterns for Temporally Enriched Gene Functional Terms.

A selection of 77 of 168 functional terms that had a false discovery rate of 1% for temporal functional enrichment at particular time points in the day is presented. The gray-scale plot is the percent of maximum FEI (for the six time points). FEI stands for Functional Enrichment Index, which is the absolute Log of the binomial probability (see Materials and Methods).