Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

SuperSAGE: Exploring The Stress Transcriptomes In Chickpea

Guenter Kahl¹ , Carlos Molina¹ , Sripada M Udupa² , Bjoern Rotter³ , Ralf Horres³ , Ruth Jungmann¹ , Luis C Belarmino⁴ , Boulbaba L'Taief¹ , Jean-Jaques Drevon⁵ , Michael Baum² , Peter Winter³

¹  Plant Molecular Biology, University of Frankfurt, Biocentre, Marie-Curie-Str 9, D-60439, Germany

²  International Centre for Agricultural Research in the Dry Areas, ICARDA, Aleppo, Syria

³  GenXPro GmbH, Altenhöferallee 3, Frankfurt am Main, D-60438, Germany

⁴  Universidade Federal de Pernambuco, Recife, Brasil

⁵  ENSAM-INRA, Montpellier, France

SuperSAGE (1) is the most versatile whole genome open-architecture transcription profiling tool available to data. We developed and used this technology to investigate the salt- and drought-stress transcriptomes of chickpea roots and nodules and cold-stressed leaves from chickpea and lentil by analysing 360.000 transcripts representing 40.000 unique mRNAs. Within these we identified 3000 genes responding to these stresses, many of them in a tissue and organ-specific manner.
We observe differential expression of members of large gene families (as e.g. transcription factors), stress-and organ-specific regulation of sense and antisense transcripts and possible molecular explanations for physiological reactions to stress environments. Comparative profiling of cold-stress transcriptomes of chickpea and lentil revealed 30 % of SuperTags common to the crops, many of which are regulated the same way.
We demonstrate that the 26 bp long SuperTags are readily annotated to the data base, serve as specific primers for development of complete cDNA sequences by 3’- and 5’-RACE, and can be used for the design of focussed chips for broader studies (2). Thus, our results demonstrate the unmet power of SuperSAGE as a superior alternative to EST-sequencing and to unfocussed chips for genome-wide transcription profiling in legume and other crops.
Here, we will focus on stress-induced differential expression of genes coding for proteins from the signal transduction cascade, and sequence features of antisense transcripts in relation to their coding counterparts.
References (1) Matsumura et al. 2003, Proc Natl Acad Sci U S A. 100:15718-15723, (2) Matsumura et al. 2006, Nature Methods 3: 469-474.