Identification and analysis of safener-inducible expressed sequence tags in Populus using a cDNA microarray

A. S. Rishi, Shirin Munir, Vivek Kapur, Neil D Nelson, Arun Goyal

Research output: Contribution to journalArticlepeer-review

27 Scopus citations


Safeners are the chemicals used to protect plants from detrimental effects of herbicides, but their mode of action at the molecular level is not well understood. As an initial step towards understanding the molecular mechanism of safener action in trees, homologous genes in hybrid poplar (Populus nigra x Populus maximowiczii) that were induced by a safener were identified. We here describe the identification of differentially expressed genes in Populus that are induced by Concep-III, a herbicide safener. Expressed sequence tags (ESTs) enriched for transcriptionally induced genes were isolated by suppressive subtractive hybridization (SSH). The SSH library cDNA inserts were used to construct a cDNA microarray for high-throughput validation of the up-regulated expression of safener-induced genes. Single-pass and partial sequences of 1,344 safener-induced ESTs were assembled into 418 single-tons and 328 clusters, but the putative functions of almost 53% of the ESTs are not known. Genes encoding proteins involved in all three different phases of safener action, viz., oxidation, conjugation, and sequestration, were found in the SSH library. Almost 75% of genes that showed greater than 2-fold expression upon safener treatment were redundant in the SSH library. The expression pattern for selected genes was validated by reverse transcription-polymerase chain reaction. A few safener-induced genes that were not previously reported to be induced by safeners, but which may have a role in herbicide metabolism, were identified. The newly identified genes could have potential for application in genetic engineering of plants for herbicide detoxification and tolerance.

Original languageEnglish (US)
Pages (from-to)296-306
Number of pages11
Issue number2
StatePublished - Dec 2004

Bibliographical note

Funding Information:
Acknowledgements This project was funded by the Sota Tec Fund (Grant No: S2001-0003), USDA–CSREES (Grant No. 2001-34158-11118), and the Minnesota State Special appropriations to UMD–NRRI. The authors thank Todd Markowski, Q. Zhang, V. Thompson and T. Levar for printing microarray slides, Blast search, graphic design and plant material, respectively.


  • Concep-III
  • Expressed sequence tag
  • Populus
  • Safener
  • Suppressive subtractive hybridization
  • cDNA microarray


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