Submitted to: Functional and Integrative Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/9/2008
Publication Date: 4/15/2008
Citation: Choi, J.J., Alkharouf, N.W., Schneider, K., Matthews, B.F., Frederick, R.D. 2008. Expression patterns in soybean resistant to Phakopsora pachyrhizi reveal the importance of peroxidases and lipoxygenases. Functional and Integrative Genomics. 8:341-359 Interpretive Summary: Soybeans are the most important legume grown in the United States, used for food, feed, and fuel. Asian soybean rust (ASR), caused by the fungal pathogen Phakopsora pachyrhizi, is a devastating disease in most soybean growing regions throughout the world. In 2004, ASR was discovered for the first time in the United States. While four single rust resistance genes have been described in soybean (Rpp1-Rpp4), no cultivars have been found that are resistant to all rust isolates. In order to develop novel methods for controlling this disease, it is important to develop an understanding of the molecular and biochemical processes that occur throughout the infection process. In this study, we developed a library of DNA sequences enriched for genes in involved in resistance from resistant and susceptible soybeans following inoculation with ASR. Expression profiles of the sequences were examined at 6, 12, 24, and 48 after inoculation using cDNA microarrays. The majority of the upregulated sequences fall into the functional category of defense. The sequences identified in this study will facilitate our understanding of single gene resistance to this obligate fungal pathogen and will also advance our efforts to develop effective means for soybean rust control.
Technical 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 United States. While no soybean cultivars have been found that are resistant to all isolates of P. pachyrhizi, four independent rust resistance genes, Rpp1-Rpp4, have been identified that recognize specific P. pachyrhizi isolates. A suppressive subtraction hybridization (SSH) cDNA library was constructed from the soybean accession PI200492, which contains Rpp1, following inoculation with isolates of P. pachyrhizi that result in susceptible and immune reactions. Both forward and reverse SSH was performed using cDNA from mRNA pooled from 1, 6, 12, 24 and 48h post inoculation (hpi). A total of 1728 SSH clones were sequenced and compared to sequences in GenBank for similarity. Microarray analyses were conducted on a 7883 soybean-cDNA clone array encompassing the soybean-rust SSH clones and other cDNA libraries at 6, 12, 24 and hpi. Results of the microarray revealed 558 cDNA clones differentially expressed in the immune reaction. The majority of the up-regulated cDNA clones fall 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.