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Expression patterns in soybean resistant to Phakopsora pachyrhizi reveal the importance of peroxidases and lipoxygenases

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Abstract

Soybean rust caused by Phakopsora pachyrhizi Sydow is a devastating foliar disease that has spread to most soybean growing regions throughout the world, including the USA. Four independent rust resistance genes, Rpp1–Rpp4, have been identified in soybean that recognize specific isolates of P. pachyrhizi. A suppressive subtraction hybridization (SSH) complementary DNA (cDNA) library was constructed from the soybean accession PI200492, which contains Rpp1, after inoculation with two different isolates of P. pachyrhizi that result in susceptible or immune reactions. Both forward and reverse SSH were performed using cDNA from messenger RNA pooled from 1, 6, 12, 24, and 48 h post-inoculation. A total of 1,728 SSH clones were sequenced and compared to sequences in GenBank for similarity. Microarray analyses were conducted on a custom 7883 soybean-cDNA clone array encompassing all of the soybean-rust SSH clones and expressed sequence tags from four other soybean cDNA libraries. Results of the microarray revealed 558 cDNA clones differentially expressed in the immune reaction. The majority of the upregulated cDNA clones fell into the functional category of defense. In particular, cDNA clones with similarity to peroxidases and lipoxygenases were prevalent. Downregulated cDNA clones included those with similarity to cell-wall-associated protein, such as extensins, proline-rich proteins, and xyloglucan endotransglycosylases.

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Acknowledgments

We gratefully acknowledge Christine Stone and Craig Austin for maintenance and propagation of P. Pachyrhizi isolates and with the inoculations. We also would like to thank Hunter Beard for microarray slide spotting and technical expertise. This project was funded in part by the United Soybean Board as Projects 2229, 3217, and 4217 and supports the goals of the USDA National Strategic Plan for the Coordination and Integration of Soybean Rust Research. The use of trade, firm, or corporation names in this publication is for the information and convenience of the reader. Such use does not constitute an official endorsement or approval by the US Department of Agriculture or the Agricultural Research Service of any product or service to exclusion of others that may be suitable.

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  1. Foreign Disease-Weed Science Research Unit, USDA-Agricultural Research Service, 1301 Ditto Avenue, Fort Detrick, MD, 21702, USA

    J. J. Choi, K. T. Schneider & R. D. Frederick

  2. Department of Computer and Information Sciences, Towson University, 8000 York Road, Towson, MD, 21252, USA

    N. W. Alkharouf

  3. Soybean Genomics and Improvement Laboratory, USDA-Agricultural Research Service, Bldg. 006, Room 118, 10300 Baltimore Ave, Beltsville, MD, 20705, USA

    B. F. Matthews

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  1. J. J. Choi
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Supplementary Table 1

Transcripts found to be differentially expressed by custom microarray analysis of immune vs. susceptible soybean leaves inoculated with P. pachryhizi and sampled at four times after inoculationa (DOC 1.05 mb)

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Choi, J.J., Alkharouf, N.W., Schneider, K.T. et al. Expression patterns in soybean resistant to Phakopsora pachyrhizi reveal the importance of peroxidases and lipoxygenases. Funct Integr Genomics 8, 341–359 (2008). https://doi.org/10.1007/s10142-008-0080-0

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