Every organism under the sun lives by day and night with a constant cycle of ∼24 hours. Plants, in particular, during the day, convert sunlight, water, and carbon dioxide into carbohydrates and eventually biomass, and emit oxygen as a byproduct of photosynthesis. At night, plants store, transport, and use the carbohydrates, and release energy, carbon dioxide, and water as a byproduct of respiration. Moreover, the temperature and growth conditions change during day and night. These rhythmic cycles are known as the circadian clock, which is derived from the Latin words “circa” (about) and “dies” (day) [136]. The scientific literature on circadian rhythms began with the daily leaf movements of heliotrope plants even in continuous darkness [137], suggesting an internal circadian rhythm. Figure I (a) Internal time keepers or circadian clock regulators include CCA1, LHY and TOC1 in a major negative feedback loop (Loop I) of the circadian oscillator in Arabidopsis, which produces a self-sustaining and constant periodicity of 24 hours, even when plants are grown under constant light and temperature. CCA1 Hiking Expedition (CHE) has recently been shown to be a negative regulator of CCA1 [90]. In addition to CCA1, LHY, and TOC1, other regulatory loops include one (Loop III) consisting of PSEUDO-RESPONSE REGULATOR (PRR) 7 and 9, another (Loop II) of GI and unknown protein, and another (Loop IV) of ZEITLUPE (ZTL), GI, and PRR3. Figure I (b) Diagram of CCA1 and LHY (red line) and TOC1 (green line) expression rhythms in a 24-hour clock with 16 hours of light (open bar) and 8 hours of darkness (filled bar). Zeitgeber (ZT) is German for time giver, and dawn is defined as ZT0. Period is the time for completing one cycle of rhythms and is shown from one peak to another (or form one trough to another). The expression amplitude of rhythm is defined as one-half the distance between the peak and trough. Many aspects of plant physiology, metabolism and development are under circadian control, and a large proportion of transcriptome (from 15% up to ∼90%) shows circadian regulation [96, 98]. For further information, see the many excellent reviews in the field, including historical perspectives of circadian rhythms [94], how plants tell time [138], regulation of output from the circadian clock [139], and the most recent reviews of circadian systems in higher plants [95, 140].

Arabidopsis hybrids and allotetraploids. (a) Seedlings of the F₁ hybrid produced by crossing Arabidopsis thaliana Columbia × A. thaliana C24. (b) A stable allotetraploid (in F₈ generation) was maintained by self-pollination. (a) and (b) were reproduced from [101] with permission. The F₁ interspecific hybrid or allotetraploid was produced by pollinating A. thaliana Ler autotetraploid with pollen from the outcrossing A. arenosa tetraploid [48, 132]. (c) Typical flowers of the allotetraploid and its progenitors, A. thaliana tetraploid (inset, diploid) and A. aresona. (d) Seeds of the allotetraploid and its progenitors, A. thaliana Ler tetraploid and Arabidopsis arenosa. Seeds of A. thaliana Ler diploid are also shown.

Genetic models and nonadditive gene expression for heterosis. (a) The dominance model. The F₁ with both dominant alleles (AaBb) of two loci is superior to the parents that contain only one pair of dominant alleles (aaBB and AAbb) because the superior or dominant allele complements the inferior or recessive allele. (b) The overdominance model. The interactions between heterozygous alleles in F₁ (AA′BB′) causes superior phenotypes compared with the combinations of homozygous alleles in the parents (A′A′BB and AAB′B′). (c) The pseudo-overdominance model. The combination of dominant alleles (AaBb) in repulsion (AbC/aBC) in the F₁ acts as overdominance compared with homozygous parents (AAbbCC and aaBBCC). The presence of dominant alleles in F₁ complements the recessive alleles, leading to a better phenotype. (d) Additive expression. The expression level of a gene, genotype or phenotype is additive. Abbreviations: MPV, mid-parent value (1/2P1 + 1/2P2); P1, parent 1; P2, parent 2. P1, P2, MPV, and F₁ represent the values of gene expression, genotype or phenotype. (e, f) Nonadditive expression. (e) Gene repression. The expression of a gene, genotype or phenotype is lower than the MPV. (f) Gene activation. The expression of a gene, genotype or phenotype is higher than the MPV, which includes dominance, overdominance, and pseudo-overdominance models. Gene repression and activation also explain epistatic interactions. Relative expression levels (1, 2 and 3) are shown on y-axis.

Growing around the clock: a molecular mechanism for hybrid vigor. A molecular clock model explains the basis of heterosis. The internal clocks of plants are controlled by multiple feedback loops, including a major loop that consists of two transcription repressors CCA1 and LHY with redundant but incompletely overlapping functions and feedback regulators TOC1 and CHE (see Box 1). The clock receives input signals such as lights and temperature and controls output traits and pathways, including photosynthesis and light signaling, flowering, starch biosynthesis and metabolism, responses to stresses and hormones, and carbon allocation and nitrogen assimilation, through the expression of evening element (EE) or CCA1 binding site (CBS)-associated genes. The expression amplitude and periodicity of circadian clock regulators can be changed or fine-tuned in response to input (external) signals such as light and temperature, as well as internal mechanisms such as allelic expression variation. L and D indicate the length of light (L) and darkness (D) in a circadian cycle. In the hybrids, the allelic interactions between parent 1 (P1) and parent 2 (P2) induce epigenetic repression of CCA1 and LHY expression amplitudes (red dashed line) and upregulation of TOC1 expression amplitudes (green dashed line) relative to the expression values in the parents (solid red and green lines, respectively), whereas the periodicity of the clock remains the same [101] because maintaining clock periodicity and rhythm is important for plant growth and fitness [84]. The reduced amount of CCA1 repressors in the hybrids during the day induces the expression of circadian-clock-associated genes (CCGs) in various output pathways, including chlorophyll biosynthesis and starch metabolism and degradation. As a result, the hybrids produce more chlorophyll and starch than the parents, which promotes vegetative growth and morphological vigor. The CCA1 expression amplitude is regulated by chromatin modifications, where the levels of active histone marks are reduced during the day and increased at night. The hybrid-induced changes in the CCA1 expression amplitude are reminiscent of expression alterations in response to changes in input signals such as light (intensities) and temperature. The clock modulates auxin signaling and responses [141]. In addition, the output pathways also produce feedback regulation for the internal clocks. For example, circadian oscillator regulation requires organic nitrogen signals [142] and free cytosolic Ca²⁺ [143]. Allelic interactions in the hybrids induce superior performance of physiological pathways for chlorophyll biosynthesis and starch metabolism. The overdominant performance is caused by epigenetic repression (nonadditive expression) of a key regulator in the feedback loop of the clock oscillator, which mediates the downstream genes in chlorophyll biosynthesis and starch metabolism. Clock-mediated heterosis is probably universal because internal clocks mediate physiological and metabolic pathways in plants and animals. Moreover, this model can be extrapolated to explain superior traits of many other biological pathways.