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Analysis of T-DNA alleles of flavonoid biosynthesis genes in Arabidopsis ecotype Columbia

Peter A Bowerman13, Melissa V Ramirez14, Michelle B Price15, Richard F Helm2 and Brenda SJ Winkel1*

Author affiliations

1 Department of Biological Sciences, Blacksburg, VA, 24061, USA

2 Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24061, USA

3 Current address: Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA

4 Current address: Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO, 80523, USA

5 Current address: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA

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Citation and License

BMC Research Notes 2012, 5:485  doi:10.1186/1756-0500-5-485

Published: 4 September 2012



The flavonoid pathway is a long-standing and important tool for plant genetics, biochemistry, and molecular biology. Numerous flavonoid mutants have been identified in Arabidopsis over the past several decades in a variety of ecotypes. Here we present an analysis of Arabidopsis lines of ecotype Columbia carrying T-DNA insertions in genes encoding enzymes of the central flavonoid pathway. We also provide a comprehensive summary of various mutant alleles for these structural genes that have been described in the literature to date in a wide variety of ecotypes.


The confirmed knockout lines present easily-scorable phenotypes due to altered pigmentation of the seed coat (or testa). Knockouts for seven alleles for six flavonoid biosynthetic genes were confirmed by PCR and characterized by UPLC for altered flavonol content.


Seven mutant lines for six genes of the central flavonoid pathway were characterized in ecotype, Columbia. These lines represent a useful resource for integrating biochemical and physiological studies with genomic, transcriptomic, and proteomic data, much of which has been, and continues to be, generated in the Columbia background.

Arabidopsis; Ecotype; Insertional inactivation lines; Flavonoid; Transparent testa