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Open Access Research article

Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids

Hyun Jo Koo16, Eric T McDowell1, Xiaoqiang Ma17, Kevin A Greer28, Jeremy Kapteyn1, Zhengzhi Xie139, Anne Descour2, HyeRan Kim1104, Yeisoo Yu14, David Kudrna14, Rod A Wing14, Carol A Soderlund2 and David R Gang1115*

  • * Corresponding author: David R Gang gangd@wsu.edu

  • † Equal contributors

Author affiliations

1 School of Plant Sciences and BIO5 Institute, The University of Arizona, Tucson, AZ, 85721, USA

2 Arizona Genomics Computational Laboratory and BIO5 Institute, The University of Arizona, Tucson, AZ, 85721, USA

3 Department of Pharmaceutical Sciences, The University of Arizona, Tucson, AZ, 85721, USA

4 Arizona Genomics Institute, The University of Arizona, Tucson, AZ, 85721, USA

5 Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA

6 Present address: Salk Institute for Biological Studies, PO Box 85800, San Diego, CA, 92186, USA

7 Present address: XenoBiotic Laboratories, Inc., Morgan Ln 107, Plainsboro, NJ, 08536, USA

8 Present address: Department of Surgery, College of Medicine, The University of Arizona, Tucson, AZ, 85724, USA

9 Present address: Division of Cardiovascular Medicine, University of Louisville, Louisville, KY, 40202, USA

10 Present address: Plant Genome Research Center, KRIBB, Daejeon, 305-803, South Korea

11 Institute of Biological Chemistry, Washington State University, P.O. Box 646340, Pullman, WA, 99164-6340, USA

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Citation and License

BMC Plant Biology 2013, 13:27  doi:10.1186/1471-2229-13-27

Published: 15 February 2013

Abstract

Background

Ginger (Zingiber officinale) and turmeric (Curcuma longa) accumulate important pharmacologically active metabolites at high levels in their rhizomes. Despite their importance, relatively little is known regarding gene expression in the rhizomes of ginger and turmeric.

Results

In order to identify rhizome-enriched genes and genes encoding specialized metabolism enzymes and pathway regulators, we evaluated an assembled collection of expressed sequence tags (ESTs) from eight different ginger and turmeric tissues. Comparisons to publicly available sorghum rhizome ESTs revealed a total of 777 gene transcripts expressed in ginger/turmeric and sorghum rhizomes but apparently absent from other tissues. The list of rhizome-specific transcripts was enriched for genes associated with regulation of tissue growth, development, and transcription. In particular, transcripts for ethylene response factors and AUX/IAA proteins appeared to accumulate in patterns mirroring results from previous studies regarding rhizome growth responses to exogenous applications of auxin and ethylene. Thus, these genes may play important roles in defining rhizome growth and development. Additional associations were made for ginger and turmeric rhizome-enriched MADS box transcription factors, their putative rhizome-enriched homologs in sorghum, and rhizomatous QTLs in rice. Additionally, analysis of both primary and specialized metabolism genes indicates that ginger and turmeric rhizomes are primarily devoted to the utilization of leaf supplied sucrose for the production and/or storage of specialized metabolites associated with the phenylpropanoid pathway and putative type III polyketide synthase gene products. This finding reinforces earlier hypotheses predicting roles of this enzyme class in the production of curcuminoids and gingerols.

Conclusion

A significant set of genes were found to be exclusively or preferentially expressed in the rhizome of ginger and turmeric. Specific transcription factors and other regulatory genes were found that were common to the two species and that are excellent candidates for involvement in rhizome growth, differentiation and development. Large classes of enzymes involved in specialized metabolism were also found to have apparent tissue-specific expression, suggesting that gene expression itself may play an important role in regulating metabolite production in these plants.

Keywords:
Ginger; Turmeric; EST; Microarray; Metabolite; Rhizome development