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Review article2024Peer reviewedOpen access

Unlocking allelic variation in circadian clock genes to develop environmentally robust and productive crops

Dwivedi, Sangam Lal; Quiroz, Luis Felipe; Spillane, Charles; Wu, Rongling; Mattoo, Autar K.; Ortiz, Rodomiro


Main conclusionMolecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks to develop more climate-resilient and productive germplasm.AbstractThe circadian clock senses light and temperature in day-night cycles to drive biological rhythms. The clock integrates endogenous signals and exogenous stimuli to coordinate diverse physiological processes. Advances in high-throughput non-invasive assays, use of forward- and inverse-genetic approaches, and powerful algorithms are allowing quantitation of variation and detection of genes associated with circadian dynamics. Circadian rhythms and phytohormone pathways in response to endogenous and exogenous cues have been well documented the model plant Arabidopsis. Novel allelic variation associated with circadian rhythms facilitates adaptation and range expansion, and may provide additional opportunity to tailor climate-resilient crops. The circadian phase and period can determine adaptation to environments, while the robustness in the circadian amplitude can enhance resilience to environmental changes. Circadian rhythms in plants are tightly controlled by multiple and interlocked transcriptional-translational feedback loops involving morning (CCA1, LHY), mid-day (PRR9, PRR7, PRR5), and evening (TOC1, ELF3, ELF4, LUX) genes that maintain the plant circadian clock ticking. Significant progress has been made to unravel the functions of circadian rhythms and clock genes that regulate traits, via interaction with phytohormones and trait-responsive genes, in diverse crops. Altered circadian rhythms and clock genes may contribute to hybrid vigor as shown in Arabidopsis, maize, and rice. Modifying circadian rhythms via transgenesis or genome-editing may provide additional opportunities to develop crops with better buffering capacity to environmental stresses. Models that involve clock gene-phytohormone-trait interactions can provide novel insights to orchestrate circadian rhythms and modulate clock genes to facilitate breeding of all season crops.


Adaptation; Allelic variation; Biological rhythms; Breeding all season crops; Clock genes and signaling; Heterosis; Non-invasive assays; Stress tolerance

Published in

2024, Volume: 259, number: 4, article number: 72

    Sustainable Development Goals

    SDG2 Zero hunger

    UKÄ Subject classification

    Agricultural Science
    Genetics and Breeding

    Publication identifier


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