Comparison of early transcriptome responses to copper and cadmium in rice roots
The phytotoxic effects of copper (Cu) and cadmium (Cd) on plant growth are well documented. However, Cu and Cd toxicity targets and the cellular systems contributing to acquisition of tolerance are not fully understood at the molecular level. We aimed to identify genes and pathways that discriminate...
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description | The phytotoxic effects of copper (Cu) and cadmium (Cd) on plant growth are well documented. However, Cu and Cd toxicity targets and the cellular systems contributing to acquisition of tolerance are not fully understood at the molecular level. We aimed to identify genes and pathways that discriminate the actions of Cu and Cd in rice roots (
Oryza sativa
L. cv. TN67). The transcripts of 1,450 and 1,172 genes were regulated after Cu and Cd treatments, respectively. We identified 882 genes specifically respond to Cu treatment, and 604 unique genes as Cd-responsive by comparison of expression profiles of these two regulated gene groups. Gene ontology analysis for 538 genes involved in primary metabolism, oxidation reduction and response to stimulus was changed in response to both metals. In the individual aspect, Cu specifically altered levels of genes involved in vesicle trafficking transport, fatty acid metabolism and cellular component biogenesis. Cd-regulated genes related to unfolded protein binding and sulfate assimilation. To further characterize the functions of vesicle trafficking transport under Cu stress, interference of excytosis in root tissues was conducted by inhibitors and silencing of
Exo70
genes. It was demonstrated that vesicle-trafficking is required for mediation of Cu-induced reactive oxygen species (ROS) production in root tissues. These results may provide new insights into understanding the molecular basis of the early metal stress response in plants. |
doi_str_mv | 10.1007/s11103-013-0020-9 |
format | Article |
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Oryza sativa
L. cv. TN67). The transcripts of 1,450 and 1,172 genes were regulated after Cu and Cd treatments, respectively. We identified 882 genes specifically respond to Cu treatment, and 604 unique genes as Cd-responsive by comparison of expression profiles of these two regulated gene groups. Gene ontology analysis for 538 genes involved in primary metabolism, oxidation reduction and response to stimulus was changed in response to both metals. In the individual aspect, Cu specifically altered levels of genes involved in vesicle trafficking transport, fatty acid metabolism and cellular component biogenesis. Cd-regulated genes related to unfolded protein binding and sulfate assimilation. To further characterize the functions of vesicle trafficking transport under Cu stress, interference of excytosis in root tissues was conducted by inhibitors and silencing of
Exo70
genes. It was demonstrated that vesicle-trafficking is required for mediation of Cu-induced reactive oxygen species (ROS) production in root tissues. These results may provide new insights into understanding the molecular basis of the early metal stress response in plants.</description><identifier>ISSN: 0167-4412</identifier><identifier>EISSN: 1573-5028</identifier><identifier>DOI: 10.1007/s11103-013-0020-9</identifier><identifier>PMID: 23400832</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Biochemistry ; Biomedical and Life Sciences ; Cadmium ; Cadmium - toxicity ; Copper ; Copper - toxicity ; Gene Expression Profiling ; Gene Expression Regulation, Plant - drug effects ; Gene Silencing - drug effects ; Genes, Plant - genetics ; Life Sciences ; Molecular biology ; Molecular Sequence Annotation ; Nicotiana - drug effects ; Nicotiana - genetics ; Nicotiana - virology ; Oligonucleotide Array Sequence Analysis ; Oryza - drug effects ; Oryza - genetics ; Oryza - growth & development ; Oryza sativa ; Plant biology ; Plant growth ; Plant Pathology ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Plant Roots - drug effects ; Plant Roots - genetics ; Plant Roots - growth & development ; Plant Sciences ; Plant tissues ; Plant Viruses - drug effects ; Plant Viruses - genetics ; Reactive Oxygen Species - metabolism ; Reproducibility of Results ; Reverse Transcriptase Polymerase Chain Reaction ; Rice ; Roots ; Seedlings - drug effects ; Seedlings - genetics ; Seedlings - growth & development ; Stress, Physiological - drug effects ; Stress, Physiological - genetics ; Transcriptome - drug effects ; Transcriptome - genetics ; Transport Vesicles - drug effects ; Transport Vesicles - metabolism</subject><ispartof>Plant molecular biology, 2013-03, Vol.81 (4-5), p.507-522</ispartof><rights>Springer Science+Business Media Dordrecht 2013</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c471t-48466e11da81b4dfd6bc1379d32ec13eb50fcb06fe1f1b459595628f6879e0da3</citedby><cites>FETCH-LOGICAL-c471t-48466e11da81b4dfd6bc1379d32ec13eb50fcb06fe1f1b459595628f6879e0da3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s11103-013-0020-9$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11103-013-0020-9$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27923,27924,41487,42556,51318</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23400832$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lin, Chung-Yi</creatorcontrib><creatorcontrib>Trinh, Ngoc Nam</creatorcontrib><creatorcontrib>Fu, Shih-Feng</creatorcontrib><creatorcontrib>Hsiung, Yu-Chyuan</creatorcontrib><creatorcontrib>Chia, Li-Chiao</creatorcontrib><creatorcontrib>Lin, Chung-Wen</creatorcontrib><creatorcontrib>Huang, Hao-Jen</creatorcontrib><title>Comparison of early transcriptome responses to copper and cadmium in rice roots</title><title>Plant molecular biology</title><addtitle>Plant Mol Biol</addtitle><addtitle>Plant Mol Biol</addtitle><description>The phytotoxic effects of copper (Cu) and cadmium (Cd) on plant growth are well documented. However, Cu and Cd toxicity targets and the cellular systems contributing to acquisition of tolerance are not fully understood at the molecular level. We aimed to identify genes and pathways that discriminate the actions of Cu and Cd in rice roots (
Oryza sativa
L. cv. TN67). The transcripts of 1,450 and 1,172 genes were regulated after Cu and Cd treatments, respectively. We identified 882 genes specifically respond to Cu treatment, and 604 unique genes as Cd-responsive by comparison of expression profiles of these two regulated gene groups. Gene ontology analysis for 538 genes involved in primary metabolism, oxidation reduction and response to stimulus was changed in response to both metals. In the individual aspect, Cu specifically altered levels of genes involved in vesicle trafficking transport, fatty acid metabolism and cellular component biogenesis. Cd-regulated genes related to unfolded protein binding and sulfate assimilation. To further characterize the functions of vesicle trafficking transport under Cu stress, interference of excytosis in root tissues was conducted by inhibitors and silencing of
Exo70
genes. It was demonstrated that vesicle-trafficking is required for mediation of Cu-induced reactive oxygen species (ROS) production in root tissues. These results may provide new insights into understanding the molecular basis of the early metal stress response in plants.</description><subject>Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Cadmium</subject><subject>Cadmium - toxicity</subject><subject>Copper</subject><subject>Copper - toxicity</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Plant - drug effects</subject><subject>Gene Silencing - drug effects</subject><subject>Genes, Plant - genetics</subject><subject>Life Sciences</subject><subject>Molecular biology</subject><subject>Molecular Sequence Annotation</subject><subject>Nicotiana - drug effects</subject><subject>Nicotiana - genetics</subject><subject>Nicotiana - virology</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Oryza - drug effects</subject><subject>Oryza - genetics</subject><subject>Oryza - growth & development</subject><subject>Oryza sativa</subject><subject>Plant biology</subject><subject>Plant growth</subject><subject>Plant Pathology</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Plant Roots - drug effects</subject><subject>Plant Roots - genetics</subject><subject>Plant Roots - growth & development</subject><subject>Plant Sciences</subject><subject>Plant tissues</subject><subject>Plant Viruses - drug effects</subject><subject>Plant Viruses - genetics</subject><subject>Reactive Oxygen Species - metabolism</subject><subject>Reproducibility of Results</subject><subject>Reverse Transcriptase Polymerase Chain Reaction</subject><subject>Rice</subject><subject>Roots</subject><subject>Seedlings - drug effects</subject><subject>Seedlings - genetics</subject><subject>Seedlings - growth & development</subject><subject>Stress, Physiological - drug effects</subject><subject>Stress, Physiological - genetics</subject><subject>Transcriptome - drug effects</subject><subject>Transcriptome - genetics</subject><subject>Transport Vesicles - drug effects</subject><subject>Transport Vesicles - metabolism</subject><issn>0167-4412</issn><issn>1573-5028</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNp1kE9LwzAYh4Mobk4_gBcJePFSfd-kS9ujDP_BYBc9hzR9Kx1rU5P2sG9vRlVEMCEkkOf3S3gYu0S4RYDsLiAiyAQwLhCQFEdsjstMJksQ-TGbA6osSVMUM3YWwhYgpqQ6ZTMhU4BcijnbrFzbG98E13FXczJ-t-eDN12wvukH1xL3FHrXBQp8cNy6vifPTVdxa6q2GVvedNw3NnLODeGcndRmF-jia1-wt8eH19Vzst48vazu14lNMxySNE-VIsTK5FimVV2p0qLMikoKigcql1DbElRNWEdgWcSpRF6rPCsIKiMX7Gbq7b37GCkMum2Cpd3OdOTGoDGSKo5URfT6D7p1o-_i7zTKqAjzXBwonCjrXQieat37pjV-rxH0wbaebOtoWx9s6yJmrr6ax7Kl6ifxrTcCYgJCvOreyf96-t_WT3aNiXY</recordid><startdate>20130301</startdate><enddate>20130301</enddate><creator>Lin, Chung-Yi</creator><creator>Trinh, Ngoc Nam</creator><creator>Fu, Shih-Feng</creator><creator>Hsiung, Yu-Chyuan</creator><creator>Chia, Li-Chiao</creator><creator>Lin, Chung-Wen</creator><creator>Huang, Hao-Jen</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>RC3</scope><scope>7U7</scope><scope>C1K</scope></search><sort><creationdate>20130301</creationdate><title>Comparison of early transcriptome responses to copper and cadmium in rice roots</title><author>Lin, Chung-Yi ; Trinh, Ngoc Nam ; Fu, Shih-Feng ; Hsiung, Yu-Chyuan ; Chia, Li-Chiao ; Lin, Chung-Wen ; Huang, Hao-Jen</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c471t-48466e11da81b4dfd6bc1379d32ec13eb50fcb06fe1f1b459595628f6879e0da3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Biochemistry</topic><topic>Biomedical and Life Sciences</topic><topic>Cadmium</topic><topic>Cadmium - toxicity</topic><topic>Copper</topic><topic>Copper - toxicity</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation, Plant - drug effects</topic><topic>Gene Silencing - drug effects</topic><topic>Genes, Plant - genetics</topic><topic>Life Sciences</topic><topic>Molecular biology</topic><topic>Molecular Sequence Annotation</topic><topic>Nicotiana - drug effects</topic><topic>Nicotiana - genetics</topic><topic>Nicotiana - virology</topic><topic>Oligonucleotide Array Sequence Analysis</topic><topic>Oryza - drug effects</topic><topic>Oryza - genetics</topic><topic>Oryza - growth & development</topic><topic>Oryza sativa</topic><topic>Plant biology</topic><topic>Plant growth</topic><topic>Plant Pathology</topic><topic>Plant Proteins - genetics</topic><topic>Plant Proteins - metabolism</topic><topic>Plant Roots - drug effects</topic><topic>Plant Roots - genetics</topic><topic>Plant Roots - growth & development</topic><topic>Plant Sciences</topic><topic>Plant tissues</topic><topic>Plant Viruses - drug effects</topic><topic>Plant Viruses - genetics</topic><topic>Reactive Oxygen Species - metabolism</topic><topic>Reproducibility of Results</topic><topic>Reverse Transcriptase Polymerase Chain Reaction</topic><topic>Rice</topic><topic>Roots</topic><topic>Seedlings - drug effects</topic><topic>Seedlings - genetics</topic><topic>Seedlings - growth & development</topic><topic>Stress, Physiological - drug effects</topic><topic>Stress, Physiological - genetics</topic><topic>Transcriptome - drug effects</topic><topic>Transcriptome - genetics</topic><topic>Transport Vesicles - drug effects</topic><topic>Transport Vesicles - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lin, Chung-Yi</creatorcontrib><creatorcontrib>Trinh, Ngoc Nam</creatorcontrib><creatorcontrib>Fu, Shih-Feng</creatorcontrib><creatorcontrib>Hsiung, Yu-Chyuan</creatorcontrib><creatorcontrib>Chia, Li-Chiao</creatorcontrib><creatorcontrib>Lin, Chung-Wen</creatorcontrib><creatorcontrib>Huang, Hao-Jen</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Nucleic Acids Abstracts</collection><collection>ProQuest Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biological Sciences</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>ProQuest Research Library</collection><collection>Biological Science Database</collection><collection>Research Library (Corporate)</collection><collection>Biotechnology and BioEngineering Abstracts</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 Basic</collection><collection>Genetics Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Environmental Sciences and Pollution Management</collection><jtitle>Plant molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lin, Chung-Yi</au><au>Trinh, Ngoc Nam</au><au>Fu, Shih-Feng</au><au>Hsiung, Yu-Chyuan</au><au>Chia, Li-Chiao</au><au>Lin, Chung-Wen</au><au>Huang, Hao-Jen</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparison of early transcriptome responses to copper and cadmium in rice roots</atitle><jtitle>Plant molecular biology</jtitle><stitle>Plant Mol Biol</stitle><addtitle>Plant Mol Biol</addtitle><date>2013-03-01</date><risdate>2013</risdate><volume>81</volume><issue>4-5</issue><spage>507</spage><epage>522</epage><pages>507-522</pages><issn>0167-4412</issn><eissn>1573-5028</eissn><abstract>The phytotoxic effects of copper (Cu) and cadmium (Cd) on plant growth are well documented. However, Cu and Cd toxicity targets and the cellular systems contributing to acquisition of tolerance are not fully understood at the molecular level. We aimed to identify genes and pathways that discriminate the actions of Cu and Cd in rice roots (
Oryza sativa
L. cv. TN67). The transcripts of 1,450 and 1,172 genes were regulated after Cu and Cd treatments, respectively. We identified 882 genes specifically respond to Cu treatment, and 604 unique genes as Cd-responsive by comparison of expression profiles of these two regulated gene groups. Gene ontology analysis for 538 genes involved in primary metabolism, oxidation reduction and response to stimulus was changed in response to both metals. In the individual aspect, Cu specifically altered levels of genes involved in vesicle trafficking transport, fatty acid metabolism and cellular component biogenesis. Cd-regulated genes related to unfolded protein binding and sulfate assimilation. To further characterize the functions of vesicle trafficking transport under Cu stress, interference of excytosis in root tissues was conducted by inhibitors and silencing of
Exo70
genes. It was demonstrated that vesicle-trafficking is required for mediation of Cu-induced reactive oxygen species (ROS) production in root tissues. These results may provide new insights into understanding the molecular basis of the early metal stress response in plants.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>23400832</pmid><doi>10.1007/s11103-013-0020-9</doi><tpages>16</tpages></addata></record> |
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subjects | Biochemistry Biomedical and Life Sciences Cadmium Cadmium - toxicity Copper Copper - toxicity Gene Expression Profiling Gene Expression Regulation, Plant - drug effects Gene Silencing - drug effects Genes, Plant - genetics Life Sciences Molecular biology Molecular Sequence Annotation Nicotiana - drug effects Nicotiana - genetics Nicotiana - virology Oligonucleotide Array Sequence Analysis Oryza - drug effects Oryza - genetics Oryza - growth & development Oryza sativa Plant biology Plant growth Plant Pathology Plant Proteins - genetics Plant Proteins - metabolism Plant Roots - drug effects Plant Roots - genetics Plant Roots - growth & development Plant Sciences Plant tissues Plant Viruses - drug effects Plant Viruses - genetics Reactive Oxygen Species - metabolism Reproducibility of Results Reverse Transcriptase Polymerase Chain Reaction Rice Roots Seedlings - drug effects Seedlings - genetics Seedlings - growth & development Stress, Physiological - drug effects Stress, Physiological - genetics Transcriptome - drug effects Transcriptome - genetics Transport Vesicles - drug effects Transport Vesicles - metabolism |
title | Comparison of early transcriptome responses to copper and cadmium in rice roots |
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