title: 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.
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.affiliation: 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.
authors.forename: Fan
authors.initials: F
authors.lastname: Zhang
authors.affiliation: 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.
authors.forename: Li-Yu
authors.initials: LY
authors.lastname: Huang
authors.affiliation: 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.
authors.forename: Fan
authors.initials: F
authors.lastname: Zhang
authors.affiliation: International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines. j.ali@irri.org.
authors.forename: Jauhar
authors.initials: J
authors.lastname: Ali
authors.affiliation: International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines. c.veracruz@irri.org.
authors.forename: Casiana Vera
authors.initials: CV
authors.lastname: Cruz
authors.affiliation: 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.
authors.forename: Da-Long
authors.initials: DL
authors.lastname: Zhuo
authors.affiliation: Beijing Institute of Genomics, Chinese Academy of Sciences, No. 7 Beichen West Road, Chaoyang District, Beijing, 100029, China. duzhl@big.ac.cn.
authors.forename: Zheng-Lin
authors.initials: ZL
authors.lastname: Du
authors.affiliation: 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.
authors.forename: Zhi-Kang
authors.initials: ZK
authors.lastname: Li
authors.affiliation: 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.
authors.forename: Yong-Li
authors.initials: YL
authors.lastname: Zhou
mesh_terms: D060467:Disease Resistance / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics / Q000382:microbiology*; D010935:Plant Diseases / Q000382:microbiology; D010940:Plant Proteins / Q000096:biosynthesis / Q000235:genetics; D015398:Signal Transduction; D059467:Transcriptome / Q000235:genetics*; D014974:Xanthomonas / Q000235:genetics* / Q000472:pathogenicity
chemical_list: D010940:Plant Proteins