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Comparative transcriptome profiling of a rice line carrying Xa39 and its parents triggered by Xanthomonas oryzae pv. oryzae provides novel insights into the broad-spectrum hypersensitive response.
BMC Genomics. 2015 Feb 21; 16:111.BG

Abstract

BACKGROUND

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating rice disease worldwide. Xa39 is a resistance (R) gene with a broad-spectrum hypersensitive response (BSHR) to Xoo. Nevertheless, the molecular mechanisms of resistance mediated by Xa39 remain unclear. In this study, the transcriptome profiling of a rice line carrying Xa39 and its parents at the early stage of Xoo infection were investigated.

RESULTS

A rice introgression line H471 carrying Xa39 exhibited a typical local hypersensitive response phenotype, accompanied by programmed cell death after inoculation with the Xoo Philippines' race 9b. Transcriptome profiling of H471 and its parents at 1 and 2 days post-inoculation was performed using RNA sequencing. In total, 306 differentially expressed genes (DEGs) were identified in H471 compared with its recurrent parent Huang-Hua-Zhan after inoculation with Xoo. Among them, 121 (39.5%) genes, with functional enrichments that were related to defense response, protein amino acid phosphorylation, and apoptosis, were found to be constitutively expressed. The other 185 (60.5%) genes, with GO terms that belonged to defense response, were significantly responsive to Xoo infection in H471. Ten up-regulated and 12 down-regulated genes encoding intracellular immune receptors were identified in H471 compared with Huang-Hua-Zhan. LOC_Os11g37759, which was located in the fine-mapping region harboring Xa39, is a Xa39 candidate gene. The putative BSHR-related co-regulatory networks were constructed using 33 DEGs from four functional groups, including gibberellic acid receptors and brassinosteroid regulators, which were differentially co-expressed with LOC_Os11g37759 in infected H471. Our results indicated that there might be cross-talk between the Xa39-mediated signal transduction cascades and the GA/BR signaling pathway, and that the defense mechanism was related to diverse kinases, transcription factors, post-translational regulation, and R genes.

CONCLUSIONS

The present study provides the comprehensive transcriptome profile of a rice introgression line carrying Xa39 and its parents, and identifies a set of DEGs involved in BSHR mediated by Xa39. These data provide novel insights into the regulatory networks of plant disease resistance mediated by R genes, and the identified DEGs will serve as candidates for Xa39 cloning and for further understanding the molecular mechanism of BSHR.

Authors+Show Affiliations

Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing, 100081, China. zhangfan03@caas.cn.Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing, 100081, China. lyhuang2007@163.com. Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Longtou Street, North suburbs, Kunming, Yunnan, 650250, China. lyhuang2007@163.com.Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing, 100081, China. zhangfan881029@126.com.International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines. j.ali@irri.org.International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines. c.veracruz@irri.org.Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing, 100081, China. dalong9300@163.com.Beijing Institute of Genomics, Chinese Academy of Sciences, No. 7 Beichen West Road, Chaoyang District, Beijing, 100029, China. duzhl@big.ac.cn.Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing, 100081, China. lizhikang@caas.cn.Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing, 100081, China. zhouylcaas@126.com.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

25765449

Citation

Zhang, Fan, et al. "Comparative Transcriptome Profiling of a Rice Line Carrying Xa39 and Its Parents Triggered By Xanthomonas Oryzae Pv. Oryzae Provides Novel Insights Into the Broad-spectrum Hypersensitive Response." BMC Genomics, vol. 16, 2015, p. 111.
Zhang F, Huang LY, Zhang F, et al. Comparative transcriptome profiling of a rice line carrying Xa39 and its parents triggered by Xanthomonas oryzae pv. oryzae provides novel insights into the broad-spectrum hypersensitive response. BMC Genomics. 2015;16:111.
Zhang, F., Huang, L. Y., Zhang, F., Ali, J., Cruz, C. V., Zhuo, D. L., Du, Z. L., Li, Z. K., & Zhou, Y. L. (2015). Comparative transcriptome profiling of a rice line carrying Xa39 and its parents triggered by Xanthomonas oryzae pv. oryzae provides novel insights into the broad-spectrum hypersensitive response. BMC Genomics, 16, 111. https://doi.org/10.1186/s12864-015-1329-3
Zhang F, et al. Comparative Transcriptome Profiling of a Rice Line Carrying Xa39 and Its Parents Triggered By Xanthomonas Oryzae Pv. Oryzae Provides Novel Insights Into the Broad-spectrum Hypersensitive Response. BMC Genomics. 2015 Feb 21;16:111. PubMed PMID: 25765449.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comparative transcriptome profiling of a rice line carrying Xa39 and its parents triggered by Xanthomonas oryzae pv. oryzae provides novel insights into the broad-spectrum hypersensitive response. AU - Zhang,Fan, AU - Huang,Li-Yu, AU - Zhang,Fan, AU - Ali,Jauhar, AU - Cruz,Casiana Vera, AU - Zhuo,Da-Long, AU - Du,Zheng-Lin, AU - Li,Zhi-Kang, AU - Zhou,Yong-Li, Y1 - 2015/02/21/ PY - 2014/09/25/received PY - 2015/02/06/accepted PY - 2015/3/14/entrez PY - 2015/3/15/pubmed PY - 2015/12/15/medline SP - 111 EP - 111 JF - BMC genomics JO - BMC Genomics VL - 16 N2 - BACKGROUND: Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating rice disease worldwide. Xa39 is a resistance (R) gene with a broad-spectrum hypersensitive response (BSHR) to Xoo. Nevertheless, the molecular mechanisms of resistance mediated by Xa39 remain unclear. In this study, the transcriptome profiling of a rice line carrying Xa39 and its parents at the early stage of Xoo infection were investigated. RESULTS: A rice introgression line H471 carrying Xa39 exhibited a typical local hypersensitive response phenotype, accompanied by programmed cell death after inoculation with the Xoo Philippines' race 9b. Transcriptome profiling of H471 and its parents at 1 and 2 days post-inoculation was performed using RNA sequencing. In total, 306 differentially expressed genes (DEGs) were identified in H471 compared with its recurrent parent Huang-Hua-Zhan after inoculation with Xoo. Among them, 121 (39.5%) genes, with functional enrichments that were related to defense response, protein amino acid phosphorylation, and apoptosis, were found to be constitutively expressed. The other 185 (60.5%) genes, with GO terms that belonged to defense response, were significantly responsive to Xoo infection in H471. Ten up-regulated and 12 down-regulated genes encoding intracellular immune receptors were identified in H471 compared with Huang-Hua-Zhan. LOC_Os11g37759, which was located in the fine-mapping region harboring Xa39, is a Xa39 candidate gene. The putative BSHR-related co-regulatory networks were constructed using 33 DEGs from four functional groups, including gibberellic acid receptors and brassinosteroid regulators, which were differentially co-expressed with LOC_Os11g37759 in infected H471. Our results indicated that there might be cross-talk between the Xa39-mediated signal transduction cascades and the GA/BR signaling pathway, and that the defense mechanism was related to diverse kinases, transcription factors, post-translational regulation, and R genes. CONCLUSIONS: The present study provides the comprehensive transcriptome profile of a rice introgression line carrying Xa39 and its parents, and identifies a set of DEGs involved in BSHR mediated by Xa39. These data provide novel insights into the regulatory networks of plant disease resistance mediated by R genes, and the identified DEGs will serve as candidates for Xa39 cloning and for further understanding the molecular mechanism of BSHR. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/25765449/Comparative_transcriptome_profiling_of_a_rice_line_carrying_Xa39_and_its_parents_triggered_by_Xanthomonas_oryzae_pv__oryzae_provides_novel_insights_into_the_broad_spectrum_hypersensitive_response_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1329-3 DB - PRIME DP - Unbound Medicine ER -