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Abstract The transcriptomes of many eukaryotic genomes exhibit rhythmic gene expression, resulting in genes that show peak expression at specific times of the day. In plants, genes that are considered to be oscillator components alter the circadian period and/or phase (time of peak expression) when misexpressed. The first plant circadian clock gene was identified almost 30 years ago, and since then additional components have been identified through forward and reverse genetic mutant screens. Over the years, mathematical modeling has helped to refine our understanding of oscillator interactions within the network and in the context of environmental cues. The complexity of the clock network suggests that additional components are yet to be discovered. In the era of genomics and genome-scale analysis, circadian research has focused on understanding the mechanisms of clock gene control of cellular and physiological output processes, often in the context of environmental stimuli. Transcriptome studies with temporal and/or spatial resolution are increasingly being carried out and the resulting comprehensive datasets can be mined to predict new oscillator components. Most clock genes show stronger oscillatory expression patterns compared to other genes in the genome. By selecting from transcriptome data genes that are significantly and robustly rhythmic, putative clock genes can be identified and characterized. 

Abstract Seed storage proteins (SSPs) are of great importance in plant science and agriculture, particularly in cereal crops, due to their nutritional value and their impact on food properties. During seed maturation, massive amounts of SSPs are synthesized and deposited either within protein bodies derived from the endoplasmic reticulum, or into specialized protein storage vacuoles (PSVs). The processing and trafficking of SSPs vary among plant species, tissues, and even developmental stages, as well as being influenced by SSP composition. The different trafficking routes, which affect the amount of SSPs that seeds accumulate and their composition and modifications, rely on a highly dynamic and functionally specialized endomembrane system. Although the general steps in SSP trafficking have been studied in various plants, including cereals, the detailed underlying molecular and regulatory mechanisms are still elusive. In this review, we discuss the main endomembrane routes involved in SSP trafficking to the PSV in Arabidopsis and other eudicots, and compare and contrast the SSP trafficking pathways in major cereal crops, particularly in rice and maize. In addition, we explore the challenges and strategies for analyzing the endomembrane system in cereal crops.