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Transcriptome analysis of a rice cultivar reveals the differentially expressed genes in response to wild and mutant strains of Xanthomonas oryzae pv. oryzae.
Sci Rep. 2019 03 06; 9(1):3757.SR

Abstract

Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating disease in most of the rice growing regions worldwide. Among the 42 BB resistance (R) genes, Xa23 is an executor R gene, conferring broad-spectrum disease resistance to all naturally occurring biotypes of Xoo. In this study, CBB23, a rice line carrying Xa23 gene, was inoculated with wild PXO99A and its mutant, P99M2, to retrieve the differentially expressed genes (DEGs). RNA-Seq analysis retrieved 1,235 DEGs (p-value ≤ 0.05) at 12, 24, 36, and 48 hours of post inoculation (hpi). Gene ontology (GO) analysis classified the DEGs functionally into biological process, cellular component and molecular function. KEGG pathway analysis categorized the DEGs into 11 different pathways, and the ribosome is a prominent pathway followed by biosynthesis of phenylpropanoids. Gene co-expression network analysis identified the clusters of transcription factors (TFs) which may be involved in PXO99A resistance. Additionally, we retrieved 67 differentially expressed TFs and 26 peroxidase responsive genes which may be involved in disease resistance mechanism. DEGs involved in the host-pathogen interaction, e.g., signaling mechanism, cell wall and plant hormones were identified. This data would be a valuable resource for researchers to identify the candidate genes associated with Xoo resistance.

Authors+Show Affiliations

National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081, China.National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081, China.National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081, China.National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081, China.National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081, China.National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081, China.National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081, China. zhaokaijun@caas.cn.

Pub Type(s)

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

Language

eng

PubMed ID

30842619

Citation

Wang, Chunlian, et al. "Transcriptome Analysis of a Rice Cultivar Reveals the Differentially Expressed Genes in Response to Wild and Mutant Strains of Xanthomonas Oryzae Pv. Oryzae." Scientific Reports, vol. 9, no. 1, 2019, p. 3757.
Wang C, Tariq R, Ji Z, et al. Transcriptome analysis of a rice cultivar reveals the differentially expressed genes in response to wild and mutant strains of Xanthomonas oryzae pv. oryzae. Sci Rep. 2019;9(1):3757.
Wang, C., Tariq, R., Ji, Z., Wei, Z., Zheng, K., Mishra, R., & Zhao, K. (2019). Transcriptome analysis of a rice cultivar reveals the differentially expressed genes in response to wild and mutant strains of Xanthomonas oryzae pv. oryzae. Scientific Reports, 9(1), 3757. https://doi.org/10.1038/s41598-019-39928-2
Wang C, et al. Transcriptome Analysis of a Rice Cultivar Reveals the Differentially Expressed Genes in Response to Wild and Mutant Strains of Xanthomonas Oryzae Pv. Oryzae. Sci Rep. 2019 03 6;9(1):3757. PubMed PMID: 30842619.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Transcriptome analysis of a rice cultivar reveals the differentially expressed genes in response to wild and mutant strains of Xanthomonas oryzae pv. oryzae. AU - Wang,Chunlian, AU - Tariq,Rezwan, AU - Ji,Zhiyuan, AU - Wei,Zheng, AU - Zheng,Kaili, AU - Mishra,Rukmini, AU - Zhao,Kaijun, Y1 - 2019/03/06/ PY - 2018/08/17/received PY - 2019/01/28/accepted PY - 2019/3/8/entrez PY - 2019/3/8/pubmed PY - 2020/10/2/medline SP - 3757 EP - 3757 JF - Scientific reports JO - Sci Rep VL - 9 IS - 1 N2 - Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating disease in most of the rice growing regions worldwide. Among the 42 BB resistance (R) genes, Xa23 is an executor R gene, conferring broad-spectrum disease resistance to all naturally occurring biotypes of Xoo. In this study, CBB23, a rice line carrying Xa23 gene, was inoculated with wild PXO99A and its mutant, P99M2, to retrieve the differentially expressed genes (DEGs). RNA-Seq analysis retrieved 1,235 DEGs (p-value ≤ 0.05) at 12, 24, 36, and 48 hours of post inoculation (hpi). Gene ontology (GO) analysis classified the DEGs functionally into biological process, cellular component and molecular function. KEGG pathway analysis categorized the DEGs into 11 different pathways, and the ribosome is a prominent pathway followed by biosynthesis of phenylpropanoids. Gene co-expression network analysis identified the clusters of transcription factors (TFs) which may be involved in PXO99A resistance. Additionally, we retrieved 67 differentially expressed TFs and 26 peroxidase responsive genes which may be involved in disease resistance mechanism. DEGs involved in the host-pathogen interaction, e.g., signaling mechanism, cell wall and plant hormones were identified. This data would be a valuable resource for researchers to identify the candidate genes associated with Xoo resistance. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/30842619/Transcriptome_analysis_of_a_rice_cultivar_reveals_the_differentially_expressed_genes_in_response_to_wild_and_mutant_strains_of_Xanthomonas_oryzae_pv__oryzae_ L2 - https://doi.org/10.1038/s41598-019-39928-2 DB - PRIME DP - Unbound Medicine ER -