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  EST sequencing, annotation and macroarray transcriptome analysis identify preferentially root-expressed genes in sugar beet

Bellin, D., Werber, M., Theis, T., Schulz, B., Weisshaar, B., & Schneider, K. (2002). EST sequencing, annotation and macroarray transcriptome analysis identify preferentially root-expressed genes in sugar beet. Plant Biology, 4(6), 700-710.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0012-3D4E-9 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0012-3D4F-7
Genre: Journal Article

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 Creators:
Bellin, D.1, Author              
Werber, M.2, Author              
Theis, T., Author
Schulz, B., Author
Weisshaar, B.2, 3, Author              
Schneider, K.4, Author              
Affiliations:
1Dept. of Plant Breeding and Genetics (Maarten Koornneef), MPI for Plant Breeding Research, Max Planck Society, ou_1113569              
2ADIS, MPI for Plant Breeding Research, Max Planck Society, ou_1113564              
3Dept. of Biochemistry (Klaus Hahlbrock), MPI for Plant Breeding Research, Max Planck Society, ou_1113566              
4Dept. of Plant Breeding and Yield Physiology (Francesco Salamini), MPI for Plant Breeding Research, Max Planck Society, ou_1113570              

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Free keywords: EST; cluster analysis; macroarray; expression profiling; sugar beet; root-expressed genes
 Abstract: An integrated approach involving EST sequencing, data mining and multiparallel expression profiling by macroarray analysis was established to classify sugar beet gene products with respect to their expression in three different organs. The DNA sequences of 2996 ESTs derived from young sugar beet plants specified 2048 unique gene products with putative functions in primary and secondary metabolism (651), transport processes (136), signal transduction (78) and cellular organization (39). The cDNA clone collection was the basis for the generation of a macroarray. Sensitivity and reproducibility of our macroarray hybridization procedure were estimated first. The detection limit was found to correspond to 10-50 copies of single transcripts per cell. Within an interval of two-fold variation in signal intensities, reproducibility between spots on the same filter was determined to be 98.9%, between spots on different filters 89.8%, and reproducibility after hybridization with two probes synthesized from the same poly(A)(+)RNA sample was 97.6%. Expression profiles from roots, leaves and inflorescences of field-grown plant material were generated. Two different samples of each organ were analysed to reduce sampling effects, which accounted on average for 30.3% of spots with at least two-fold deviation. Expression values for each organ were determined by a stringent statistical evaluation of eight hybridizations for each clone. Macroarray expression data were confirmed by Northern blot analysis and quantitative RT-PCR experiments concerning eleven cDNAs. The analysis was then focused on 76 unique cDNAs, for which the amount of detected transcript in roots was at least twice as high as in the other organs tested. Functions of preferentially root-expressed candidate genes in taproot morphology and physiology are discussed.

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Language(s): eng - English
 Dates: 2002-11
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: eDoc: 28749
ISI: 000181591700008
 Degree: -

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Title: Plant Biology
  Alternative Title : Plant Biol.
Source Genre: Journal
 Creator(s):
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Publ. Info: -
Pages: - Volume / Issue: 4 (6) Sequence Number: - Start / End Page: 700 - 710 Identifier: ISSN: 1435-8603