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Genome-wide analysis of gene expression to distinguish photoperiod-dependent and -independent flowering in Brassicaceae

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Abstract

Photoperiod is the most important environmental cue for the regulation of flowering time, a highly important agronomic trait for crop productivity. To help elucidate the photoperiodic control of flowering in Brassicaceae, we performed microarray experiments using species-specific oligo-arrays with the long day (LD) plant Arabidopsis thaliana and the photoperiod-independent plant rapid cycling Brassica rapa (RCBr). Enrichment analysis of the gene ontologies of differentially expressed genes (DEGs) did not uncover clear differences in gene expression between photoperiod-dependent and -independent plants. Most genes that were up-regulated under LD conditions in Arabidopsis were also up-regulated in RCBr. In addition, most genes associated with light signaling and the circadian clock showed similar expression patterns between Arabidopsis and RCBr, implying that most components known to be key regulators in the photoperiodic flowering pathway are not responsible for the photoperiod independence of RCBr. Nonetheless, we identified one clock-associated gene, PSEUDO-RESPONSE REGULATOR9 (PRR9), as a candidate gene explaining the photoperiod independence of RCBr. The mechanism underlying the role of PRR9 in photoperiodic control and genomic polymorphisms should be further explored using different B. rapa species.

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Acknowledgements

This work was supported by Research Fund of Chungnam National University (CNU), Daejeon, Korea, to Yoonkang Hur (2015-1115-01) and by research grants from Golden Seed Project (Center for Horticultural Seed Development, 213003-04-4-SB230), Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), and Rural Development Administration (RDA).

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    Authors and Affiliations

    1. Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea

      Hayoung Song, Hankuil Yi & Yoonkang Hur

    2. Division of Animal and Dairy Science, Chungnam National University, Daejeon, 34134, Republic of Korea

      Changhee Do

    3. Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea

      Ching-Tack Han

    4. Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, 57922, Republic of Korea

      Ill-Sup Nou

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    Hayoung Song, Hankuil Yi, Ching-Tack Han, Ill-Sup Nou and Yoonkang Hur declares no conflict of interest.

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    Song, H., Yi, H., Do, C. et al. Genome-wide analysis of gene expression to distinguish photoperiod-dependent and -independent flowering in Brassicaceae. Genes Genom 39, 207–223 (2017). https://doi.org/10.1007/s13258-016-0487-2

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