Abstract
In this study, we used a five-step process to identify those genes most likely involved in flowering repression in the Chinese cabbage (Brassica rapa). We tested 6,275 candidate genes with 300K microarrays, which included specific gene expression profiles of FLOWERING LOCUS C (FLC) mutants and normal cultivars during five cold vernalization stages. From that, we identified 289 transcription factor genes and 59 pathway network genes associated with floweringrelated metabolism. Then we compared the 348 genes to 1,287 genes from Gene Ontology and Clusters of Orthologous Groups analyses, which use similar orthologs to categorize conserved genes. Those analyses revealed 10 hypothetical genes for B. rapa, which we verified by reverse transcription-polymerase chain reaction. The final selected genes most likely play regulatory roles in either B. rapa flowering time control or flowering repression during vernalization. While these final genes require further characterization and validation, our study illustrates the usefulness of a multi-layered screening method after initially identifying genes from microarrays.
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Sanda, S.L. & Amasino, R.M. Ecotype-specific expression of a flowering mutant phenotype in Arabidopsis thaliana. Plant Physiol. 111, 641–645 (1996).
Koornneef, M., Blankestijn-de Vries, H., Hanhart, C., Soppe, W. & Peeters, T. The phenotype of some lateflowering mutants is enhanced by a locus on chromosome 5 that is not effective in the Landsberg erecta wild-type. Plant J. 6, 911–919 (1994).
Lee, I. & Amasino, R.M. Effect of vernalization, photoperiod, and light quality on the flowering phenotype of Arabidopsis plants containing the FRIGIDA gene. Plant Physiol. 108, 157–162 (1995).
Michaels, S.D. & Amasino, R.M. FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11, 949–956 (1999).
Sheldon, C.C. et al. The FLF MADS box gene: A repressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant Cell 11, 445–458 (1999).
He, Y. & Amasino, R.M. Role of chromatin modification in flowering time control. Trends Plant Sci. 10, 30–35 (2005).
Osborn, T.C. et al. Comparison of flowering time genes in Brassica rapa, B. napus and Arabidopsis thaliana. Genetics 146, 1123–1129 (1997).
Kim, S.Y. et al. Delayed flowering time in Arabidopsis and Brassica rapa by the over expression of FLOWERING LOCUS C (FLC) homologs isolated from Chinese cabbage (Brassica rapa L.: ssp. pekinensis). Plant Cell Rep. 26, 327–336 (2007).
Sheldon, C.C., Rouse, D.T., Finnegan, E.J., Peacock, W.J. & Dennis, E.S. The molecular basis of vernalization: the control role of FLOWERING LOCUS C (FLC). Proc. Natl. Acad. Sci. 97, 3753–3758 (2000).
Deng, W. et al. FLOWERING LOCUS C (FLC) regulates development pathways throughout the life cycle of Arabidopsis. Proc. Natl. Acad. Sci. 108, 6680–6685 (2011).
Kim, C.K. et al. Identification and characterization of seed-specific transcription factors regulating anthocyanin biosynthesis in black rice. J. Appl. Genetics 52, 161–169 (2011).
Kim, C.K. et al. Computational identification of anthocyanin-specific transcription factors using a rice microarray and maximum boundary range algorithm. Evol. Bioinform. 20, 133–141 (2010).
Parenicova, L. et al. Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world. Plant Cell 15, 1538–1551 (2003).
Folter, S. et al. Comprehensive interaction map of the Arabidopsis MADS box transcription factors. Plant Cell 17, 1424–1433 (2005).
Riechmann, J.L. & Meyerowitz, E.M. The AP2/EREBP family of plant transcription factors. Biol. Chem. 379, 633–646 (1998).
Magome, H., Yamaguchi, S., Hanada, A., Kamiya, Y. & Oda, K. Dwarf and delayed-flowering 1, a novel Arabidopsis mutant deficient ingibberellin biosynthesis because of overexpression of a putative AP2transcription factor. Plant J. 37, 720–729 (2004).
Ruth, R.F. & Tim, J.L. The Arabidopsis Abscisic acid response gene ABI5 encodes a basic leucine zipper transcription factor. Plant Cell 12, 599–610 (2000).
Stracke, R., Werber, M. & Weisshaar, B. Related articles, links the R2R3-MYB gene family in arabidopsis thaliana. Curr. Opin. Plant Biol. 4, 447–56 (2001).
Ayadi, M., Delaporte, V., Li, Y.F. & Zhou, D.X. Analysis of GT-3a identifies a distinct subgroup of trihelix DNA-binding transcription factors in Arabidopsis. FEBS Lett. 562, 147–154 (2004).
Kim, S.Y. et al. Induction of Brassica rapa transgenic plant line showing delayed bolting time using over expression of BrFLC genes. Korean J. Intl. Agri. 23, 218–225 (2011).
Kim, C.K. et al. Computational identification of Chinese cabbage anthocyanin-specific genes. BioChip J. 5, 184–192 (2011).
Irizarry, R.A. et al. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 15, e15 (2003).
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. 57, 289–300 (1995).
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Kim, C., Lee, YH., Hong, JK. et al. Identification and characterization of flowering repressor-related genes in Chinese cabbage. BioChip J 6, 120–127 (2012). https://doi.org/10.1007/s13206-012-6203-7
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DOI: https://doi.org/10.1007/s13206-012-6203-7