International Journal of Genomics
Volume 2017 (2017), Article ID 7305684, 16 pages
https://doi.org/10.1155/2017/7305684
Research Article
Comparative Transcriptome Analyses of Resistant and Susceptible Near-Isogenic Wheat Lines following Inoculation with Blumeria graminis f. sp. tritici
1State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, China
2Agronomy College, Shandong Agricultural University, Taian, Shandong, China
3College of Life Science, Zaozhuang University, Zaozhuang, Shandong, China
Correspondence should be addressed to Xingfeng Li; nc.ude.uads@fxil
Received 12 December 2016; Revised 8 February 2017; Accepted 6 March 2017; Published 2 May 2017
Academic Editor: Marco Gerdol
Copyright © 2017 Piyi Xing et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Linked References
- Z. Yang and Z. Ren, “Expression of gene Pm8 for resistance to powdery mildew in wheat from Sichuan,” Journal of Sichuan Agricultural University, vol. 15, no. 4, pp. 452–456, 1997. View at Publisher · View at Google Scholar
- R. A. McIntosh, P. Zhang, C. Cowger, R. Parks, E. S. Lagudah, and S. Hoxha, “Rye-derived powdery mildew resistance gene Pm8 in wheat is suppressed by the Pm3 locus,” Theoretical and Applied Genetics, vol. 123, no. 3, pp. 359–367, 2011. View at Publisher · View at Google Scholar · View at Scopus
- V. Mohler, C. Bauer, G. Schweizer, H. Kempf, and L. Hartl, “Pm50: a new powdery mildew resistance gene in common wheat derived from cultivated emmer,” Journal of Applied Genetics, vol. 54, no. 3, pp. 259–263, 2013. View at Publisher · View at Google Scholar · View at Scopus
- S. Hsam, F. Zeller, R. Bélanger, W. Bushnell, A. Dik, and T. Carver, “Breeding for powdery-mildew-resistance in common wheat (Triticum aestivum L.),” The Powdery Mildews: a Comprehensive Treatise, vol. 114, no. 2, pp. 219–238, 2002. View at Publisher · View at Google Scholar · View at Scopus
- N. Yahiaoui, P. Srichumpa, R. Dudler, and B. Keller, “Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene Pm3b from hexaploid wheat,” The Plant Journal, vol. 37, no. 4, pp. 528–538, 2004. View at Publisher · View at Google Scholar · View at Scopus
- N. Yahiaoui, S. Brunner, and B. Keller, “Rapid generation of new powdery mildew resistance genes after wheat domestication,” The Plant Journal, vol. 47, no. 1, pp. 85–98, 2006. View at Publisher · View at Google Scholar · View at Scopus
- N. Yahiaoui, N. Kaur, and B. Keller, “Independent evolution of functional Pm3 resistance genes in wild tetraploid wheat and domesticated bread wheat,” The Plant Journal, vol. 57, no. 5, pp. 846–856, 2009. View at Publisher · View at Google Scholar · View at Scopus
- P. Srichumpa, S. Brunner, B. Keller, and N. Yahiaoui, “Allelic series of four powdery mildew resistance genes at the Pm3 locus in hexaploid bread wheat,” Plant Physiology, vol. 139, no. 2, pp. 885–895, 2005. View at Publisher · View at Google Scholar · View at Scopus
- N. K. Bhullar, K. Street, M. Mackay, N. Yahiaoui, and B. Keller, “Unlocking wheat genetic resources for the molecular identification of previously undescribed functional alleles at the Pm3 resistance locus,” Proceedings of the National Academy of Sciences, vol. 106, no. 23, pp. 9519–9524, 2009. View at Publisher · View at Google Scholar · View at Scopus
- N. K. Bhullar, Z. Zhang, T. Wicker, and B. Keller, “Wheat gene bank accessions as a source of new alleles of the powdery mildew resistance gene Pm3: a large scale allele mining project,” BMC Plant Biology, vol. 10, no. 1, p. 1, 2010. View at Publisher · View at Google Scholar
- S. Hurni, S. Brunner, G. Buchmann et al., “Rye Pm8 and wheat Pm3 are orthologous genes and show evolutionary conservation of resistance function against powdery mildew,” The Plant Journal, vol. 76, no. 6, pp. 957–969, 2013. View at Publisher · View at Google Scholar · View at Scopus
- J. Xiao, X. Jin, X. Jia et al., “Transcriptome-based discovery of pathways and genes related to resistance against Fusarium head blight in wheat landrace Wangshuibai,” BMC Genomics, vol. 14, no. 1, p. 197, 2013. View at Publisher · View at Google Scholar
- K. G. Kugler, G. Siegwart, T. Nussbaumer et al., “Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivum L.),” BMC Genomics, vol. 14, no. 1, p. 728, 2013. View at Publisher · View at Google Scholar
- Q.-H. Zhu, S. Stephen, K. Kazan et al., “Characterization of the defense transcriptome responsive to Fusarium oxysporum-infection in Arabidopsis using RNA-seq,” Gene, vol. 512, no. 2, pp. 259–266, 2013. View at Publisher · View at Google Scholar · View at Scopus
- C. Li, J. Shao, Y. Wang et al., “Analysis of banana transcriptome and global gene expression profiles in banana roots in response to infection by race 1 and tropical race 4 of Fusarium oxysporum f. sp. cubense,” BMC Genomics, vol. 14, no. 1, p. 851, 2013. View at Publisher · View at Google Scholar · View at Scopus
- J.-J. Liu, R. N. Sturrock, and R. Benton, “Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola,” BMC Genomics, vol. 14, no. 1, p. 1, 2013. View at Publisher · View at Google Scholar
- L. M. Wang, Y. L. Zhu, X. F. Li, and H. G. Wang, “Screening for SSR markers linked to wheat powdery mildew resistance gene Pm2,” Acta Phytophylactica Sinica, vol. 38, no. 3, pp. 216–220, 2011. View at Publisher · View at Google Scholar
- A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer, and B. Wold, “Mapping and quantifying mammalian transcriptomes by RNA-Seq,” Nature Methods, vol. 5, no. 7, pp. 621–628, 2008. View at Publisher · View at Google Scholar · View at Scopus
- S. Anders and W. Huber, “Differential expression analysis for sequence count data,” Genome Biology, vol. 11, no. 10, p. 1, 2010. View at Publisher · View at Google Scholar · View at Scopus
- H. Zhang, Y. Yang, C. Wang et al., “Large-scale transcriptome comparison reveals distinct gene activations in wheat responding to stripe rust and powdery mildew,” BMC Genomics, vol. 15, no. 1, p. 898, 2014. View at Publisher · View at Google Scholar
- A. Chini, S. Fonseca, G. Fernandez et al., “The JAZ family of repressors is the missing link in jasmonate signalling,” Nature, vol. 448, no. 7154, pp. 666–671, 2007. View at Publisher · View at Google Scholar · View at Scopus
- L. Gómez-Gómez and T. Boller, “FLS2: an LRR receptor–like kinase involved in the perception of the bacterial elicitor flagellin in Arabidopsis,” Molecular Cell, vol. 5, no. 6, pp. 1003–1011, 2000. View at Publisher · View at Google Scholar
- D. S. Kim and B. K. Hwang, “An important role of the pepper phenylalanine ammonia-lyase gene (PAL1) in salicylic acid-dependent signalling of the defence response to microbial pathogens,” Journal of Experimental Botany, vol. 65, no. 9, pp. 2295–2306, 2014. View at Publisher · View at Google Scholar · View at Scopus
- Z. Wang, M. Gerstein, and M. Snyder, “RNA-Seq: a revolutionary tool for transcriptomics,” Nature Reviews. Genetics, vol. 10, no. 1, pp. 57–63, 2009. View at Publisher · View at Google Scholar · View at Scopus
- A. Kratz and P. Carninci, “The devil in the details of RNA-seq,” Nature Biotechnology, vol. 32, no. 9, pp. 882–884, 2014. View at Publisher · View at Google Scholar · View at Scopus
- S. Li, S. W. Tighe, C. M. Nicolet et al., “Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study,” Nature Biotechnology, vol. 32, no. 9, pp. 915–925, 2014. View at Publisher · View at Google Scholar · View at Scopus
- SEQC/MAQC-III Consortium, “A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium,” Nature Biotechnology, vol. 32, no. 9, pp. 903–914, 2014. View at Publisher · View at Google Scholar · View at Scopus
- D. Risso, J. Ngai, T. P. Speed, and S. Dudoit, “Normalization of RNA-seq data using factor analysis of control genes or samples,” Nature Biotechnology, vol. 32, no. 9, pp. 896–902, 2014. View at Publisher · View at Google Scholar · View at Scopus
- M. Xin, X. Wang, H. Peng et al., “Transcriptome comparison of susceptible and resistant wheat in response to powdery mildew infection,” Genomics, Proteomics & Bioinformatics, vol. 10, no. 2, pp. 94–106, 2012. View at Publisher · View at Google Scholar · View at Scopus
- J. M. Elmore, Z. J. Lin, and G. Coaker, “Plant NB-LRR signaling: upstreams and downstreams,” Current Opinion in Plant Biology, vol. 14, no. 4, pp. 365–371, 2011. View at Publisher · View at Google Scholar · View at Scopus
- M. Bernoux, J. G. Ellis, and P. N. Dodds, “New insights in plant immunity signaling activation,” Current Opinion in Plant Biology, vol. 14, no. 5, pp. 512–518, 2011. View at Publisher · View at Google Scholar · View at Scopus
- T. K. Eitas and J. L. Dangl, “NB-LRR proteins: pairs, pieces, perception, partners, and pathways,” Current Opinion in Plant Biology, vol. 13, no. 4, pp. 472–477, 2010. View at Publisher · View at Google Scholar · View at Scopus
- P. Moffett, G. Farnham, J. Peart, and D. C. Baulcombe, “Interaction between domains of a plant NBS–LRR protein in disease resistance-related cell death,” The EMBO Journal, vol. 21, no. 17, pp. 4511–4519, 2002. View at Publisher · View at Google Scholar · View at Scopus
- J. Song, J. M. Bradeen, S. K. Naess et al., “Gene RB cloned from Solanum bulbocastanum confers broad spectrum resistance to potato late blight,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 16, pp. 9128–9133, 2003. View at Publisher · View at Google Scholar · View at Scopus
- E. Van Der Vossen, A. Sikkema, H. Bt et al., “An ancient R gene from the wild potato species Solanum bulbocastanum confers broad – spectrum resistance to Phytophthora infestans in cultivated potato and tomato,” The Plant Journal, vol. 36, no. 6, pp. 867–882, 2003. View at Publisher · View at Google Scholar · View at Scopus
- P. Tornero, R. A. Chao, W. N. Luthin, S. A. Goff, and J. L. Dangl, “Large-scale structure–function analysis of the Arabidopsis RPM1 disease resistance protein,” The Plant Cell, vol. 14, no. 2, pp. 435–450, 2002. View at Publisher · View at Google Scholar · View at Scopus
- D. Mackey, B. F. Holt, A. Wiig, and J. L. Dangl, “RIN4 interacts with Pseudomonas syringae type III effector molecules and is required for RPM1-mediated resistance in Arabidopsis,” Cell, vol. 108, no. 6, pp. 743–754, 2002. View at Publisher · View at Google Scholar · View at Scopus
- J. M. McDowell, M. Dhandaydham, T. A. Long et al., “Intragenic recombination and diversifying selection contribute to the evolution of downy mildew resistance at the RPP8 locus of Arabidopsis,” The Plant Cell, vol. 10, no. 11, pp. 1861–1874, 1998. View at Publisher · View at Google Scholar · View at Scopus
- H. S. Kim, M. S. Jung, S. M. Lee et al., “An S-locus receptor-like kinase plays a role as a negative regulator in plant defense responses,” Biochemical and Biophysical Research Communications, vol. 381, no. 3, pp. 424–428, 2009. View at Publisher · View at Google Scholar · View at Scopus