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Title: cDNA-AFLP analysis reveals differential gene expression in compatible reaction of wheat challenged with Puccinia striiformis f. sp. tritici

Author
item WANG, XIAOJIE - Northwest Agricultural & Forestry University
item TANG, CHUNLEI - Northwest Agricultural & Forestry University
item ZHANG, GAN - Northwest Agricultural & Forestry University
item LI, YINGCHUN - Northwest Agricultural & Forestry University
item WANG, CHENFANG - Northwest Agricultural & Forestry University
item LIU, BO - Northwest Agricultural & Forestry University
item QU, ZHIPENG - Northwest Agricultural & Forestry University
item ZHAO, JIE - Northwest Agricultural & Forestry University
item HAN, QINGMEI - Northwest Agricultural & Forestry University
item HUANG, LILI - Northwest Agricultural & Forestry University
item Chen, Xianming
item KANG, ZHENSHENG - Northwest Agricultural & Forestry University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/30/2009
Publication Date: 6/30/2009
Citation: Wang, X., Tang, C., Zhang, G., Li, Y., Wang, C., Liu, B., Qu, Z., Zhao, J., Han, Q., Huang, L., Chen, X., Kang, Z. 2009. cDNA-AFLP analysis reveals differential gene expression in compatible reaction of wheat challenged with Puccinia striiformis f. sp. tritici. BMC Genomics 10:289.

Interpretive Summary: The stripe rust fungus causes one of the most important wheat diseases worldwide. In this study, we identified wheat and the pathogen genes associated with the infection process by conducting a large-scale transcriptomic analysis using cDNA-amplified fragment length polymorphism (cDNA-AFLP). Of a total of 54,912 expressed genes obtained, 2,306 (4.2%) displayed altered expression patterns after inoculation with 966 up-regulated and 1,340 down-regulated. Sequence analysis of selected 186 genes with altered expressions identified 74 (40%) with known functions. The majority of the 74 genes had predicted gene products involved in energy (13%), signal transduction (5.4%), disease/defense (5.9%), and metabolism (5%). Nine of the genes were identified as the pathogen genes, which were the first group of genes identified from infected wheat leaves. Quantitative real-time PCR analysis confirmed the cDNA-AFLP expression patterns for 28 of the 29 selected genes with putative functions in disease/defense, signal transduction or uncharacterized genes. The results show that cDNA-AFLP is a reliable technique for studying expression patterns of genes involved in the wheat-stripe rust interactions. This study should be helpful in elucidating the molecular basis of the infection process and identifying genes that can be targeted for inhibiting the growth and reproduction of the pathogen.

Technical Abstract: BACKGROUND: Puccinia striiformis f. sp. tritici is a fungal pathogen causing stripe rust, one of the most important wheat diseases worldwide. The fungus is strictly biotrophic and thus, completely dependent on living host cells for its reproduction, which makes it difficult to study genes of the pathogen. In spite of its economic importance, little is known about the molecular basis of compatible interaction between the pathogen and wheat host. In this study, we identified wheat and P. striiformis f. sp. tritici genes associated with the infection process by conducting a large-scale transcriptomic analysis using cDNA-amplified fragment length polymorphism (cDNA-AFLP). RESULTS: cDNA from total mRNA isolated from leaves of susceptible wheat genotype Suwon 11 at 0, 6, 12, 18, 24, 36, 48, 72, 96, 120, 144 and 168 h post-inoculation with virulent pathotype CY31 of P. striiformis f. sp. tritici was used in AFLP analysis. Of a total of 54,912 transcript derived fragments (TDFs) obtained with 64 primer pairs, 2,306 (4.2%) displayed altered expression patterns after inoculation with 966 up-regulated and 1,340 down-regulated. A total of 208 TDFs with altered expressions were selected for sequencing and 186 of them produced reliable sequences (>100 bp), of which 74 (40%) had known functions through BLAST searching the GenBank database. The majority of the latter group had predicted gene products involved in energy (13%), signal transduction (5.4%), disease/defense (5.9%) and metabolism (5% of the sequenced TDFs). BLAST search of the P. graminis f. sp. tritici (the wheat stem rust pathogen) identified 18 TDFs possibly from the stripe rust pathogen, of which 9 were confirmed of the pathogen origin by PCR assay and sequencing. Of the 186 TDFs with reliable sequences, 29 homologous to genes known to play a role in disease/defense, signal transduction or uncharacterized genes were further selected for validation of cDNA-AFLP expression patterns using qRT-PCR. The results confirmed the altered expression patterns of 28 (96.5%) genes revealed by the cDNA-AFLP technique. CONCLUSION: The results show that cDNA-AFLP is a reliable technique for studying expression patterns of genes involved in the wheat-stripe rust interactions. Genes involved in compatible interactions between wheat and the stripe rust pathogens were identified and their expression patterns were determined. This study should be helpful in elucidating the molecular basis of the infection process and identifying genes that can be targeted for inhibiting the growth and reproduction of the pathogen.