Abstract
WRKY transcription factors are key regulators of numerous biological processes in plant growth and development, as well as plant responses to abiotic and biotic stresses. Research on biological functions of plant WRKY genes has focused in the past on model plant species or species with largely characterized transcriptomes. However, a variety of non-model plants, such as forest conifers, are essential as feed, biofuel, and wood or for sustainable ecosystems. Identification of WRKY genes in these non-model plants is equally important for understanding the evolutionary and function-adaptive processes of this transcription factor family. Because of limited genomic information, the rarity of regulatory gene mRNAs in transcriptomes, and the sequence divergence to model organism genes, identification of transcription factors in non-model plants using methods similar to those generally used for model plants is difficult. This chapter describes a gene family discovery strategy for identification of WRKY transcription factors in conifers by a combination of in silico-based prediction and PCR-based experimental approaches. Compared to traditional cDNA library screening or EST sequencing at transcriptome scales, this integrated gene discovery strategy provides fast, simple, reliable, and specific methods to unveil the WRKY gene family at both genome and transcriptome levels in non-model plants.
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Acknowledgments
The authors would like to thank Steve Glover for his critical review on the manuscript. This work was supported in part by Natural Resources Canada, the Canadian Forest Service, and Agriculture and Agri-Food Canada, the Pacific Agri-Food Research Centre.
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Liu, JJ., **ang, Y. (2011). In Silico Mining and PCR-Based Approaches to Transcription Factor Discovery in Non-model Plants: Gene Discovery of the WRKY Transcription Factors in Conifers. In: Yuan, L., Perry, S. (eds) Plant Transcription Factors. Methods in Molecular Biology, vol 754. Humana Press. https://doi.org/10.1007/978-1-61779-154-3_2
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DOI: https://doi.org/10.1007/978-1-61779-154-3_2
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