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De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress
Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alam...
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Published in: | BMC genomics 2021-01, Vol.22 (1), p.82-82, Article 82 |
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description | Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM-314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress.
Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes.
Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm. |
doi_str_mv | 10.1186/s12864-021-07368-w |
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Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes.
Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.</description><identifier>ISSN: 1471-2164</identifier><identifier>EISSN: 1471-2164</identifier><identifier>DOI: 10.1186/s12864-021-07368-w</identifier><identifier>PMID: 33509088</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Abiotic stress ; Agricultural production ; Alkaline salt stress ; Analysis ; Antioxidants ; ASTTI ; BASIC BIOLOGICAL SCIENCES ; biotechnology & applied microbiology ; Cultivation ; Dehydration ; Detoxification ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene regulation ; Gene sequencing ; Genes ; Genetic aspects ; genetics & heredity ; Genomics ; Genotype & phenotype ; Genotypes ; Germplasm ; Gluconeogenesis ; Glycolysis ; Grasses ; Growth ; Heat shock proteins ; Homeostasis ; Kinases ; MAP kinase ; Metabolism ; Network reliability ; Osmosis ; Panicum - genetics ; Panicum virgatum ; Physiological aspects ; Physiological responses ; Physiology ; Plant Roots - genetics ; Protein transport ; Proteins ; Proteolysis ; Reproducibility of Results ; Ribonucleic acid ; RNA ; RNA sequencing ; Roots ; Saline soils ; Salinity tolerance ; Salinization ; Salt ; Salt Stress ; Salt stress (Botany) ; Salt tolerance ; Soil dynamics ; Soil investigations ; Soil salinity ; Soil stresses ; Stress ; Transcription ; Transcriptome ; Transcriptomes ; Ubiquitin ; WGCNA</subject><ispartof>BMC genomics, 2021-01, Vol.22 (1), p.82-82, Article 82</ispartof><rights>COPYRIGHT 2021 BioMed Central Ltd.</rights><rights>2021. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>The Author(s) 2021</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c624t-54e37cbc31eca136c039d6fab400d52f40c3f972670bf5fd59ae91f9b15dc68b3</citedby><cites>FETCH-LOGICAL-c624t-54e37cbc31eca136c039d6fab400d52f40c3f972670bf5fd59ae91f9b15dc68b3</cites><orcidid>0000-0002-3630-4503 ; 0000000236304503</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7841905/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2491026020?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,44590,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33509088$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/servlets/purl/1851072$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhang, Pan</creatorcontrib><creatorcontrib>Duo, Tianqi</creatorcontrib><creatorcontrib>Wang, Fengdan</creatorcontrib><creatorcontrib>Zhang, Xunzhong</creatorcontrib><creatorcontrib>Yang, Zouzhuan</creatorcontrib><creatorcontrib>Hu, Guofu</creatorcontrib><creatorcontrib>Michigan State Univ., East Lansing, MI (United States)</creatorcontrib><title>De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress</title><title>BMC genomics</title><addtitle>BMC Genomics</addtitle><description>Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM-314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress.
Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes.
Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.</description><subject>Abiotic stress</subject><subject>Agricultural production</subject><subject>Alkaline salt stress</subject><subject>Analysis</subject><subject>Antioxidants</subject><subject>ASTTI</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>biotechnology & applied microbiology</subject><subject>Cultivation</subject><subject>Dehydration</subject><subject>Detoxification</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Plant</subject><subject>Gene regulation</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>genetics & heredity</subject><subject>Genomics</subject><subject>Genotype & phenotype</subject><subject>Genotypes</subject><subject>Germplasm</subject><subject>Gluconeogenesis</subject><subject>Glycolysis</subject><subject>Grasses</subject><subject>Growth</subject><subject>Heat shock proteins</subject><subject>Homeostasis</subject><subject>Kinases</subject><subject>MAP kinase</subject><subject>Metabolism</subject><subject>Network reliability</subject><subject>Osmosis</subject><subject>Panicum - genetics</subject><subject>Panicum virgatum</subject><subject>Physiological aspects</subject><subject>Physiological responses</subject><subject>Physiology</subject><subject>Plant Roots - genetics</subject><subject>Protein transport</subject><subject>Proteins</subject><subject>Proteolysis</subject><subject>Reproducibility of Results</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA sequencing</subject><subject>Roots</subject><subject>Saline soils</subject><subject>Salinity tolerance</subject><subject>Salinization</subject><subject>Salt</subject><subject>Salt Stress</subject><subject>Salt stress (Botany)</subject><subject>Salt tolerance</subject><subject>Soil dynamics</subject><subject>Soil investigations</subject><subject>Soil salinity</subject><subject>Soil stresses</subject><subject>Stress</subject><subject>Transcription</subject><subject>Transcriptome</subject><subject>Transcriptomes</subject><subject>Ubiquitin</subject><subject>WGCNA</subject><issn>1471-2164</issn><issn>1471-2164</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNptkstu1DAYhSMEoqXwAiyQBZt2keJbYmeDVJXbSJVAXNaW4_xJ3Sb21HZm2pfgmfF0Sukg5EWsP985To5PUbwk-JgQWb-NhMqal5iSEgtWy3L9qNgnXJCSkpo_frDfK57FeIExEZJWT4s9xircYCn3i1_vATm_8igF7aIJdpn8BMg6FLxPEfkexbVN5nwIOkZ0-FU7a-YJrWwYdMqbs-MjFGAFeoxoAAcIrpcBYrTeoe7G6ckapF2HtEnIQVr7cIlm10FAerzUo82KqMeEYtqonhdP-uwEL-6eB8XPjx9-nH4uz758WpyenJWmpjyVFQcmTGsYAaMJqw1mTVf3uuUYdxXtOTasbwStBW77qu-qRkND-qYlVWdq2bKDYrH17by-UMtgJx1ulNdW3Q58GJQOyZoRFCNCc1ZJ3UnNBTOyzTaath1ujeCUZ693W6_l3E7QGXA5y3HHdPeNs-dq8CslJCcNrrLB662Bj8mqaGwCc268c2CSIrIiWNAMHd6dEvzVDDGpyUYD46gd-DkqyiWTOQpBMvrmH_TCz8HlPDPVEExrTPFfatD5L63rff44szFVJ3WFeUVELTJ1_B8qrw7yzXoHvc3zHcHRjiAzCa7ToOcY1eL7t12WblkTfIwB-vvQCFabiqttxVWuuLqtuFpn0auHcd9L_nSa_QbDMvdS</recordid><startdate>20210128</startdate><enddate>20210128</enddate><creator>Zhang, 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novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress</title><author>Zhang, Pan ; Duo, Tianqi ; Wang, Fengdan ; Zhang, Xunzhong ; Yang, Zouzhuan ; Hu, Guofu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c624t-54e37cbc31eca136c039d6fab400d52f40c3f972670bf5fd59ae91f9b15dc68b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Abiotic stress</topic><topic>Agricultural production</topic><topic>Alkaline salt stress</topic><topic>Analysis</topic><topic>Antioxidants</topic><topic>ASTTI</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>biotechnology & applied microbiology</topic><topic>Cultivation</topic><topic>Dehydration</topic><topic>Detoxification</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation, Plant</topic><topic>Gene regulation</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>genetics & heredity</topic><topic>Genomics</topic><topic>Genotype & phenotype</topic><topic>Genotypes</topic><topic>Germplasm</topic><topic>Gluconeogenesis</topic><topic>Glycolysis</topic><topic>Grasses</topic><topic>Growth</topic><topic>Heat shock proteins</topic><topic>Homeostasis</topic><topic>Kinases</topic><topic>MAP kinase</topic><topic>Metabolism</topic><topic>Network reliability</topic><topic>Osmosis</topic><topic>Panicum - genetics</topic><topic>Panicum virgatum</topic><topic>Physiological aspects</topic><topic>Physiological responses</topic><topic>Physiology</topic><topic>Plant Roots - genetics</topic><topic>Protein transport</topic><topic>Proteins</topic><topic>Proteolysis</topic><topic>Reproducibility of Results</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA sequencing</topic><topic>Roots</topic><topic>Saline soils</topic><topic>Salinity tolerance</topic><topic>Salinization</topic><topic>Salt</topic><topic>Salt Stress</topic><topic>Salt stress (Botany)</topic><topic>Salt tolerance</topic><topic>Soil dynamics</topic><topic>Soil investigations</topic><topic>Soil salinity</topic><topic>Soil stresses</topic><topic>Stress</topic><topic>Transcription</topic><topic>Transcriptome</topic><topic>Transcriptomes</topic><topic>Ubiquitin</topic><topic>WGCNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhang, Pan</creatorcontrib><creatorcontrib>Duo, Tianqi</creatorcontrib><creatorcontrib>Wang, Fengdan</creatorcontrib><creatorcontrib>Zhang, Xunzhong</creatorcontrib><creatorcontrib>Yang, Zouzhuan</creatorcontrib><creatorcontrib>Hu, Guofu</creatorcontrib><creatorcontrib>Michigan State Univ., East Lansing, MI (United States)</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE 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Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content (ProQuest)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV - Hybrid</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><collection>Directory of Open Access Journals</collection><jtitle>BMC genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Pan</au><au>Duo, Tianqi</au><au>Wang, Fengdan</au><au>Zhang, Xunzhong</au><au>Yang, Zouzhuan</au><au>Hu, Guofu</au><aucorp>Michigan State Univ., East Lansing, MI (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress</atitle><jtitle>BMC genomics</jtitle><addtitle>BMC Genomics</addtitle><date>2021-01-28</date><risdate>2021</risdate><volume>22</volume><issue>1</issue><spage>82</spage><epage>82</epage><pages>82-82</pages><artnum>82</artnum><issn>1471-2164</issn><eissn>1471-2164</eissn><abstract>Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM-314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress.
Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes.
Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>33509088</pmid><doi>10.1186/s12864-021-07368-w</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0002-3630-4503</orcidid><orcidid>https://orcid.org/0000000236304503</orcidid><oa>free_for_read</oa></addata></record> |
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recordid | cdi_doaj_primary_oai_doaj_org_article_317a4358ad8a473c8b9b1a2bd0bc7424 |
source | Publicly Available Content (ProQuest); PubMed Central |
subjects | Abiotic stress Agricultural production Alkaline salt stress Analysis Antioxidants ASTTI BASIC BIOLOGICAL SCIENCES biotechnology & applied microbiology Cultivation Dehydration Detoxification Gene expression Gene Expression Profiling Gene Expression Regulation, Plant Gene regulation Gene sequencing Genes Genetic aspects genetics & heredity Genomics Genotype & phenotype Genotypes Germplasm Gluconeogenesis Glycolysis Grasses Growth Heat shock proteins Homeostasis Kinases MAP kinase Metabolism Network reliability Osmosis Panicum - genetics Panicum virgatum Physiological aspects Physiological responses Physiology Plant Roots - genetics Protein transport Proteins Proteolysis Reproducibility of Results Ribonucleic acid RNA RNA sequencing Roots Saline soils Salinity tolerance Salinization Salt Salt Stress Salt stress (Botany) Salt tolerance Soil dynamics Soil investigations Soil salinity Soil stresses Stress Transcription Transcriptome Transcriptomes Ubiquitin WGCNA |
title | De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress |
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