Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway

Kleindt CK, Stracke R, Mehrtens F, Weisshaar B (2010)
BMC Research Notes 3(1): 255.

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Abstract
Background: The coordinated activity of different flavonoid biosynthesis genes in Arabidopsis thaliana results in tissue-specific accumulation of flavonols, anthocyanins and proanthocyanidins (PAs). These compounds possess diverse functions in plants including light-attenuation and oxidative stress protection. Flavonoids accumulate in a stimulus- and/or development-dependent manner in specific parts of the plant. PAs accumulate in the seed coat (testa). Findings: We describe the biological material and the preparation of total RNA for the AtGenExpress developmental silique and seed series. AtGenExpress ATH1 GeneChip expression data from the different stages were reanalyzed and verified using quantitative real time PCR (qPCR). We observed organ-specific transcript accumulation of specific flavonoid biosynthetic genes consistent with previously published data and our PA compound accumulation data. In addition, we investigated the regulation of PA accumulation in developing A. thaliana seeds by correlating gene expression patterns of specific flavonoid biosynthesis genes with different seed embryonic developmental stages and organs and present two useful marker genes for isolated valve and replum organs, as well as one seed-specific marker. Conclusions: Potential caveats of array-based expression data are discussed based on comparisons with qPCR data. Results from ATH1 microarray and qPCR experiments revealed a shift in gene activity from general flavonoid biosynthesis at early stages of seed development to PA synthesis at late (mature) stages of embryogenesis. The examined PA accumulation-associated genes, including biosynthetic and regulatory genes, were found to be exclusively expressed in immature seeds. Accumulation of PAs initiates at the early heart stage of silique and seed development. Our findings provide new insights for further studies targeting the PA pathway in seeds.
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Kleindt CK, Stracke R, Mehrtens F, Weisshaar B. Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway. BMC Research Notes. 2010;3(1): 255.
Kleindt, C. K., Stracke, R., Mehrtens, F., & Weisshaar, B. (2010). Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway. BMC Research Notes, 3(1): 255.
Kleindt, C. K., Stracke, R., Mehrtens, F., and Weisshaar, B. (2010). Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway. BMC Research Notes 3:255.
Kleindt, C.K., et al., 2010. Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway. BMC Research Notes, 3(1): 255.
C.K. Kleindt, et al., “Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway”, BMC Research Notes, vol. 3, 2010, : 255.
Kleindt, C.K., Stracke, R., Mehrtens, F., Weisshaar, B.: Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway. BMC Research Notes. 3, : 255 (2010).
Kleindt, Christiane Katja, Stracke, Ralf, Mehrtens, Frank, and Weisshaar, Bernd. “Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway”. BMC Research Notes 3.1 (2010): 255.
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PMID: 24009336
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PMID: 22730287

69 References

Data provided by Europe PubMed Central.

EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
Dondrup M, Albaum SP, Griebel T, Henckel K, Junemann S, Kahlke T, Kleindt CK, Kuster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Puhler A, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19200358
Bioconductor: open software development for computational biology and bioinformatics.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J., Genome Biol. 5(10), 2004
PMID: 15461798
Summaries of Affymetrix GeneChip probe level data.
Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP., Nucleic Acids Res. 31(4), 2003
PMID: 12582260
Exploration, normalization, and summaries of high density oligonucleotide array probe level data.
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP., Biostatistics 4(2), 2003
PMID: 12925520
affy--analysis of Affymetrix GeneChip data at the probe level.
Gautier L, Cope L, Bolstad BM, Irizarry RA., Bioinformatics 20(3), 2004
PMID: 14960456
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.
Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P., Nucleic Acids Res. 31(1), 2003
PMID: 12519987
The Arabidopsis transcription factor MYB12 is a flavonol-specific regulator of phenylpropanoid biosynthesis.
Mehrtens F, Kranz H, Bednarek P, Weisshaar B., Plant Physiol. 138(2), 2005
PMID: 15923334
Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes.
Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P., Adv Bioinformatics 2008(), 2008
PMID: 19956698
A transcriptomic and proteomic characterization of the Arabidopsis mitochondrial protein import apparatus and its response to mitochondrial dysfunction.
Lister R, Chew O, Lee MN, Heazlewood JL, Clifton R, Parker KL, Millar AH, Whelan J., Plant Physiol. 134(2), 2004
PMID: 14730085
The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments.
Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT., Clin. Chem. 55(4), 2009
PMID: 19246619

AUTHOR UNKNOWN, 0
Standardized determination of real-time PCR efficiency from a single reaction set-up.
Tichopad A, Dilger M, Schwarz G, Pfaffl MW., Nucleic Acids Res. 31(20), 2003
PMID: 14530455
Thirteen Ways to Look at the Correlation Coefficient
AUTHOR UNKNOWN, 1988
Tannin analysis of food products.
Deshpande SS, Cheryan M, Salunkhe DK., Crit Rev Food Sci Nutr 24(4), 1986
PMID: 3536314
The flavonoid biosynthetic pathway in plants: function and evolution
AUTHOR UNKNOWN, 1994
Flavonoid diversity and biosynthesis in seed of Arabidopsis thaliana.
Routaboul JM, Kerhoas L, Debeaujon I, Pourcel L, Caboche M, Einhorn J, Lepiniec L., Planta 224(1), 2006
PMID: 16395586

AUTHOR UNKNOWN, 0

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