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  A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula

Kakar, K., Wandrey, M., Czechowski, T., Gaertner, T., Scheible, W.-R., Stitt, M., et al. (2008). A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula. Plant Methods, 4, 18. doi:10.1186/1746-4811-4-18.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-2761-C Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0017-DFA7-0
Genre: Journal Article

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 Creators:
Kakar, K.1, Author              
Wandrey, M.1, Author              
Czechowski, T.2, Author              
Gaertner, T.3, Author
Scheible, W.-R.2, Author              
Stitt, M.4, Author              
Torres-Jerez, I.3, Author
Xiao, Y.3, Author
Redman, J. C.3, Author
Wu, H. C.3, Author
Cheung, F.3, Author
Town, C. D.3, Author
Udvardi, M. K.1, Author              
Affiliations:
1Molecular Plant Nutrition, Max Planck Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753321              
2Molecular Genomics, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753328              
3External Organizations, ou_persistent22              
4System Regulation, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753327              

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 Abstract: ABSTRACT: BACKGROUND: Medicago truncatula is a model legume species that is currently the focus of an international genome sequencing effort. Although several different oligonucleotide and cDNA arrays have been produced for genome-wide transcript analysis of this species, intrinsic limitations in the sensitivity of hybridization-based technologies mean that transcripts of genes expressed at low-levels cannot be measured accurately with these tools. Amongst such genes are many encoding transcription factors (TFs), which are arguably the most important class of regulatory proteins. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is the most sensitive method currently available for transcript quantification, and one that can be scaled up to analyze transcripts of thousands of genes in parallel. Thus, qRT-PCR is an ideal method to tackle the problem of TF transcript quantification in Medicago and other plants. RESULTS: We established a bioinformatics pipeline to identify putative TF genes in Medicago truncatula and to design gene-specific oligonucleotide primers for qRT-PCR analysis of TF transcripts. We validated the efficacy and gene-specificity of over 1000 TF primer pairs and utilized these to identify sets of organ-enhanced TF genes that may play important roles in organ development or differentiation in this species. This community resource will be developed further as more genome sequence becomes available, with the ultimate goal of producing validated, gene-specific primers for all Medicago TF genes. CONCLUSION: High-throughput qRT-PCR using a 384-well plate format enables rapid, flexible, and sensitive quantification of all predicted Medicago transcription factor mRNAs. This resource has been utilized recently by several groups in Europe, Australia, and the USA, and we expect that it will become the 'gold-standard' for TF transcript profiling in Medicago truncatula.

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Language(s): eng - English
 Dates: 2008-07-082008
 Publication Status: Published in print
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Title: Plant Methods
Source Genre: Journal
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Pages: - Volume / Issue: 4 Sequence Number: - Start / End Page: 18 Identifier: -