Integrative systems biology analysis of barley transcriptome ─ hormonal signaling against biotic stress
Biotic stresses are pests and pathogens that cause a variety of crop diseases and damages. In response to these agents, crops trigger specific defense signal transduction pathways in which hormones play a central role. To recognize hormonal signaling, we integrated barley transcriptome datasets rela...
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| Veröffentlicht in: | PloS one 2023-04, Vol.18 (4), p.e0281470-e0281470 |
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| description | Biotic stresses are pests and pathogens that cause a variety of crop diseases and damages. In response to these agents, crops trigger specific defense signal transduction pathways in which hormones play a central role. To recognize hormonal signaling, we integrated barley transcriptome datasets related to hormonal treatments and biotic stresses. In the meta-analysis of each dataset, 308 hormonal and 1232 biotic DEGs were identified respectively. According to the results, 24 biotic TFs belonging to 15 conserved families and 6 hormonal TFs belonging to 6 conserved families were identified, with the NF-YC, GNAT, and WHIRLY families being the most prevalent. Additionally, gene enrichment and pathway analyses revealed that over-represented cis-acting elements were recognized in response to pathogens and hormones. Based on the co-expression analysis, 6 biotic and 7 hormonal modules were uncovered. Finally, the hub genes of PKT3, PR1, SSI2, LOX2, OPR3, and AOS were candidates for further study in JA- or SA-mediated plant defense. The qPCR confirmed that the expression of these genes was induced from 3 to 6 h following exposure to 100 μM MeJA, with peak expression occurring between 12 h and 24 h and decreasing after 48 h. Overexpression of PR1 was one of the first steps toward SAR. As well as regulating SAR, NPR1 has also been shown to be involved in the activation of ISR by the SSI2. LOX2 catalyzes the first step of JA biosynthesis, PKT3 plays an important role in wound-activated responses, and OPR3 and AOS are involved in JA biosynthesis. In addition, many unknown genes were introduced that can be used by crop biotechnologists to accelerate barley genetic engineering. |
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In response to these agents, crops trigger specific defense signal transduction pathways in which hormones play a central role. To recognize hormonal signaling, we integrated barley transcriptome datasets related to hormonal treatments and biotic stresses. In the meta-analysis of each dataset, 308 hormonal and 1232 biotic DEGs were identified respectively. According to the results, 24 biotic TFs belonging to 15 conserved families and 6 hormonal TFs belonging to 6 conserved families were identified, with the NF-YC, GNAT, and WHIRLY families being the most prevalent. Additionally, gene enrichment and pathway analyses revealed that over-represented cis-acting elements were recognized in response to pathogens and hormones. Based on the co-expression analysis, 6 biotic and 7 hormonal modules were uncovered. Finally, the hub genes of PKT3, PR1, SSI2, LOX2, OPR3, and AOS were candidates for further study in JA- or SA-mediated plant defense. The qPCR confirmed that the expression of these genes was induced from 3 to 6 h following exposure to 100 μM MeJA, with peak expression occurring between 12 h and 24 h and decreasing after 48 h. Overexpression of PR1 was one of the first steps toward SAR. As well as regulating SAR, NPR1 has also been shown to be involved in the activation of ISR by the SSI2. LOX2 catalyzes the first step of JA biosynthesis, PKT3 plays an important role in wound-activated responses, and OPR3 and AOS are involved in JA biosynthesis. In addition, many unknown genes were introduced that can be used by crop biotechnologists to accelerate barley genetic engineering.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0281470</identifier><identifier>PMID: 37104505</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Barley ; Biology ; Biology and Life Sciences ; Biosynthesis ; Cellular signal transduction ; Cereals ; Crop damage ; Crop diseases ; Crops ; Crops, Agricultural - genetics ; Cyclopentanes - pharmacology ; Datasets ; Fungi ; Gene expression ; Gene Expression Regulation, Plant ; Genes ; Genetic aspects ; Genetic engineering ; Genetically modified organisms ; Hordeum - genetics ; Hordeum - metabolism ; Hormones ; Humans ; Kinases ; Meta-analysis ; MicroRNAs ; Oxylipins - metabolism ; Pathogens ; Pests ; Physiological aspects ; Plant diseases ; Plant growth ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Proteins ; Research and Analysis Methods ; Signal Transduction ; Signaling ; Stress, Physiological - genetics ; Stresses ; Systems Biology ; Transcriptome ; Transcriptomes</subject><ispartof>PloS one, 2023-04, Vol.18 (4), p.e0281470-e0281470</ispartof><rights>Copyright: © 2023 Soltani et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</rights><rights>COPYRIGHT 2023 Public Library of Science</rights><rights>2023 Soltani et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2023 Soltani et al 2023 Soltani et al</rights><rights>2023 Soltani et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Soltani, Zahra</au><au>Moghadam, Ali</au><au>Tahmasebi, Ahmad</au><au>Niazi, Ali</au><au>Amancio, Sara</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Integrative systems biology analysis of barley transcriptome ─ hormonal signaling against biotic stress</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2023-04-27</date><risdate>2023</risdate><volume>18</volume><issue>4</issue><spage>e0281470</spage><epage>e0281470</epage><pages>e0281470-e0281470</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Biotic stresses are pests and pathogens that cause a variety of crop diseases and damages. In response to these agents, crops trigger specific defense signal transduction pathways in which hormones play a central role. To recognize hormonal signaling, we integrated barley transcriptome datasets related to hormonal treatments and biotic stresses. In the meta-analysis of each dataset, 308 hormonal and 1232 biotic DEGs were identified respectively. According to the results, 24 biotic TFs belonging to 15 conserved families and 6 hormonal TFs belonging to 6 conserved families were identified, with the NF-YC, GNAT, and WHIRLY families being the most prevalent. Additionally, gene enrichment and pathway analyses revealed that over-represented cis-acting elements were recognized in response to pathogens and hormones. Based on the co-expression analysis, 6 biotic and 7 hormonal modules were uncovered. Finally, the hub genes of PKT3, PR1, SSI2, LOX2, OPR3, and AOS were candidates for further study in JA- or SA-mediated plant defense. The qPCR confirmed that the expression of these genes was induced from 3 to 6 h following exposure to 100 μM MeJA, with peak expression occurring between 12 h and 24 h and decreasing after 48 h. Overexpression of PR1 was one of the first steps toward SAR. As well as regulating SAR, NPR1 has also been shown to be involved in the activation of ISR by the SSI2. LOX2 catalyzes the first step of JA biosynthesis, PKT3 plays an important role in wound-activated responses, and OPR3 and AOS are involved in JA biosynthesis. In addition, many unknown genes were introduced that can be used by crop biotechnologists to accelerate barley genetic engineering.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>37104505</pmid><doi>10.1371/journal.pone.0281470</doi><tpages>e0281470</tpages><orcidid>https://orcid.org/0000-0002-8011-7721</orcidid><orcidid>https://orcid.org/0000-0002-4626-9481</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Analysis Barley Biology Biology and Life Sciences Biosynthesis Cellular signal transduction Cereals Crop damage Crop diseases Crops Crops, Agricultural - genetics Cyclopentanes - pharmacology Datasets Fungi Gene expression Gene Expression Regulation, Plant Genes Genetic aspects Genetic engineering Genetically modified organisms Hordeum - genetics Hordeum - metabolism Hormones Humans Kinases Meta-analysis MicroRNAs Oxylipins - metabolism Pathogens Pests Physiological aspects Plant diseases Plant growth Plant Proteins - genetics Plant Proteins - metabolism Proteins Research and Analysis Methods Signal Transduction Signaling Stress, Physiological - genetics Stresses Systems Biology Transcriptome Transcriptomes |
| title | Integrative systems biology analysis of barley transcriptome ─ hormonal signaling against biotic stress |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-01T15%3A16%3A57IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Integrative%20systems%20biology%20analysis%20of%20barley%20transcriptome%20%E2%94%80%20hormonal%20signaling%20against%20biotic%20stress&rft.jtitle=PloS%20one&rft.au=Soltani,%20Zahra&rft.date=2023-04-27&rft.volume=18&rft.issue=4&rft.spage=e0281470&rft.epage=e0281470&rft.pages=e0281470-e0281470&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0281470&rft_dat=%3Cgale_plos_%3EA747216122%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2806918723&rft_id=info:pmid/37104505&rft_galeid=A747216122&rft_doaj_id=oai_doaj_org_article_968d9f65d74f4207987fcfcfbf8be988&rfr_iscdi=true |