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Transcriptome Analysis of Diurnal Gene Expression in Chinese Cabbage

Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 370, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si 560-500, Korea
Department of Forest Bio-resources, National Institute of Forest Science, Suwon 16631, Korea
Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-744, Korea
Division of Applied Life Science (BK21Plus), Institute of Agricultural and Life Science (IALS), Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea
Author to whom correspondence should be addressed.
These authors contribute equally to this work.
Genes 2019, 10(2), 130;
Received: 16 December 2018 / Revised: 31 January 2019 / Accepted: 4 February 2019 / Published: 11 February 2019
(This article belongs to the Special Issue Genetic Regulation of Circadian Rhythm in Plants)
PDF [2825 KB, uploaded 23 February 2019]


Plants have developed timing mechanisms that enable them to maintain synchrony with daily environmental events. These timing mechanisms, i.e., circadian clocks, include transcriptional/translational feedback loops that drive 24 h transcriptional rhythms, which underlie oscillations in protein abundance, thus mediating circadian rhythms of behavior, physiology, and metabolism. Circadian clock genes have been investigated in the diploid model plant Arabidopsis thaliana. Crop plants with polyploid genomes—such as Brassica species—have multiple copies of some clock-related genes. Over the last decade, numerous studies have been aimed at identifying and understanding the function of paralogous genes with conserved sequences, or those that diverged during evolution. Brassica rapa’s triplicate genomes retain sequence-level collinearity with Arabidopsis. In this study, we used RNA sequencing (RNAseq) to profile the diurnal transcriptome of Brassica rapa seedlings. We identified candidate paralogs of circadian clock-related genes and assessed their expression levels. These genes and their related traits that modulate the diurnal rhythm of gene expression contribute to the adaptation of crop cultivars. Our findings will contribute to the mechanistic study of circadian clock regulation inherent in polyploidy genome crops, which differ from those of model plants, and thus will be useful for future breeding studies using clock genes. View Full-Text
Keywords: Arabidopsis; Brassica rapa; circadian-related gene; polyploid genome; transcriptome Arabidopsis; Brassica rapa; circadian-related gene; polyploid genome; transcriptome

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Kim, J.A.; Shim, D.; Kumari, S.; Jung, H.-E.; Jung, K.-H.; Jeong, H.; Kim, W.-Y.; Lee, S.I.; Jeong, M.-J. Transcriptome Analysis of Diurnal Gene Expression in Chinese Cabbage. Genes 2019, 10, 130.

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