GeneChip profiling of transcriptional responses to soybean cyst nematode, Heterodera glycines, colonization of soybean roots
Soybean cyst nematode (SCN) is currently the most devastating pathogen of soybean. SCN penetrates the root and migrates toward the central vascular bundle where it establishes a complex multinucleated feeding structure that provides plant-derived nutrients to support the development and growth of th...
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| Veröffentlicht in: | Journal of experimental botany 2007, Vol.58 (12), p.3407-3418 |
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| creator | Puthoff, David P Ehrenfried, Mindy L Vinyard, Bryan T Tucker, Mark L |
| description | Soybean cyst nematode (SCN) is currently the most devastating pathogen of soybean. SCN penetrates the root and migrates toward the central vascular bundle where it establishes a complex multinucleated feeding structure that provides plant-derived nutrients to support the development and growth of the nematode. To identify host genes that play significant roles in SCN development in susceptible roots, RNA from SCN-inoculated and non-inoculated root pieces were hybridized to the Affymetrix soybean genome GeneChips. RNA was collected at 8, 12, and 16 d post-inoculation from root pieces that displayed multiple swollen female SCN and similar root pieces from non-inoculated roots. Branch roots and root tips were trimmed from the root pieces to minimize the amount of RNA contributed by these organs. Of the 35 593 transcripts represented on the GeneChip, approximately 26 500 were expressed in the SCN-colonized root pieces. ANOVA followed by False Discovery Rate analysis indicated that the expression levels of 4616 transcripts changed significantly (Q-value ≤0.05) in response to SCN. In this set of 4616 transcripts, 1404 transcripts increased >2-fold and 739 decreased >2-fold. Of the transcripts to which a function could be assigned, a large proportion was associated with cell wall structure. Other functional categories that included a large number of up-regulated transcripts were defence, metabolism, and histones, and a smaller group of transcripts associated with signal transduction and transcription. |
| doi_str_mv | 10.1093/jxb/erm211 |
| format | Article |
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SCN penetrates the root and migrates toward the central vascular bundle where it establishes a complex multinucleated feeding structure that provides plant-derived nutrients to support the development and growth of the nematode. To identify host genes that play significant roles in SCN development in susceptible roots, RNA from SCN-inoculated and non-inoculated root pieces were hybridized to the Affymetrix soybean genome GeneChips. RNA was collected at 8, 12, and 16 d post-inoculation from root pieces that displayed multiple swollen female SCN and similar root pieces from non-inoculated roots. Branch roots and root tips were trimmed from the root pieces to minimize the amount of RNA contributed by these organs. Of the 35 593 transcripts represented on the GeneChip, approximately 26 500 were expressed in the SCN-colonized root pieces. ANOVA followed by False Discovery Rate analysis indicated that the expression levels of 4616 transcripts changed significantly (Q-value ≤0.05) in response to SCN. In this set of 4616 transcripts, 1404 transcripts increased >2-fold and 739 decreased >2-fold. Of the transcripts to which a function could be assigned, a large proportion was associated with cell wall structure. Other functional categories that included a large number of up-regulated transcripts were defence, metabolism, and histones, and a smaller group of transcripts associated with signal transduction and transcription.</description><identifier>ISSN: 0022-0957</identifier><identifier>EISSN: 1460-2431</identifier><identifier>DOI: 10.1093/jxb/erm211</identifier><identifier>PMID: 17977850</identifier><identifier>CODEN: JEBOA6</identifier><language>eng</language><publisher>Oxford: Oxford University Press</publisher><subject>Affymetrix ; Agronomy. Soil science and plant productions ; Animals ; Biological and medical sciences ; cell wall ; Cell walls ; Cellular structures ; cyst nematode ; Cyst nematodes ; Economic plant physiology ; False Discovery Rate ; Fundamental and applied biological sciences. Psychology ; Gene Expression Profiling ; GeneChip ; Genes ; Glycine max ; Glycine max - genetics ; Glycine max - parasitology ; Heterodera glycines ; histones ; Metabolic diseases ; Nematoda - physiology ; Nematodes ; plant defence ; Plant roots ; Plant Roots - genetics ; Plant Roots - parasitology ; Plants ; Research Papers ; RNA ; soybean ; Soybeans ; Symbiosis (nodules, symbiotic nitrogen fixation, mycorrhiza...) ; Transcription, Genetic</subject><ispartof>Journal of experimental botany, 2007, Vol.58 (12), p.3407-3418</ispartof><rights>Society for Experimental Biology 2007</rights><rights>2007 The Author(s). 2007</rights><rights>2008 INIST-CNRS</rights><rights>2007 The Author(s).</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c492t-7542b372bc684c7032f71297cc96386bbe43eee7d56955ca20733b470cab53db3</citedby><cites>FETCH-LOGICAL-c492t-7542b372bc684c7032f71297cc96386bbe43eee7d56955ca20733b470cab53db3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/24036704$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/24036704$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,776,780,799,1578,4010,27900,27901,27902,57992,58225</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=19880932$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17977850$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Puthoff, David P</creatorcontrib><creatorcontrib>Ehrenfried, Mindy L</creatorcontrib><creatorcontrib>Vinyard, Bryan T</creatorcontrib><creatorcontrib>Tucker, Mark L</creatorcontrib><title>GeneChip profiling of transcriptional responses to soybean cyst nematode, Heterodera glycines, colonization of soybean roots</title><title>Journal of experimental botany</title><addtitle>J Exp Bot</addtitle><description>Soybean cyst nematode (SCN) is currently the most devastating pathogen of soybean. SCN penetrates the root and migrates toward the central vascular bundle where it establishes a complex multinucleated feeding structure that provides plant-derived nutrients to support the development and growth of the nematode. To identify host genes that play significant roles in SCN development in susceptible roots, RNA from SCN-inoculated and non-inoculated root pieces were hybridized to the Affymetrix soybean genome GeneChips. RNA was collected at 8, 12, and 16 d post-inoculation from root pieces that displayed multiple swollen female SCN and similar root pieces from non-inoculated roots. Branch roots and root tips were trimmed from the root pieces to minimize the amount of RNA contributed by these organs. Of the 35 593 transcripts represented on the GeneChip, approximately 26 500 were expressed in the SCN-colonized root pieces. ANOVA followed by False Discovery Rate analysis indicated that the expression levels of 4616 transcripts changed significantly (Q-value ≤0.05) in response to SCN. In this set of 4616 transcripts, 1404 transcripts increased >2-fold and 739 decreased >2-fold. Of the transcripts to which a function could be assigned, a large proportion was associated with cell wall structure. Other functional categories that included a large number of up-regulated transcripts were defence, metabolism, and histones, and a smaller group of transcripts associated with signal transduction and transcription.</description><subject>Affymetrix</subject><subject>Agronomy. Soil science and plant productions</subject><subject>Animals</subject><subject>Biological and medical sciences</subject><subject>cell wall</subject><subject>Cell walls</subject><subject>Cellular structures</subject><subject>cyst nematode</subject><subject>Cyst nematodes</subject><subject>Economic plant physiology</subject><subject>False Discovery Rate</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Expression Profiling</subject><subject>GeneChip</subject><subject>Genes</subject><subject>Glycine max</subject><subject>Glycine max - genetics</subject><subject>Glycine max - parasitology</subject><subject>Heterodera glycines</subject><subject>histones</subject><subject>Metabolic diseases</subject><subject>Nematoda - physiology</subject><subject>Nematodes</subject><subject>plant defence</subject><subject>Plant roots</subject><subject>Plant Roots - genetics</subject><subject>Plant Roots - parasitology</subject><subject>Plants</subject><subject>Research Papers</subject><subject>RNA</subject><subject>soybean</subject><subject>Soybeans</subject><subject>Symbiosis (nodules, symbiotic nitrogen fixation, mycorrhiza...)</subject><subject>Transcription, Genetic</subject><issn>0022-0957</issn><issn>1460-2431</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kcFrFDEUhwdR7Fq9eFeDUA_SsS_JZDJzlMV2haJoLUgvIZN9s2admUyTLHTFP94ss3bBg5ck8L58Ly-_LHtO4R2Fmp-t75oz9D2j9EE2o0UJOSs4fZjNABjLoRbyKHsSwhoABAjxODuispayEjDLfl_ggPMfdiSjd63t7LAiriXR6yEYb8do3aA74jGMbggYSHQkuG2DeiBmGyIZsNfRLfGULDCiTyevyarbGjtgOCXGdW6wv_TOsxP_veudi-Fp9qjVXcBn-_04uz7_8G2-yC8_X3ycv7_MTVGzmEtRsIZL1piyKowEzlpJWS2NqUtelU2DBUdEuRRlLYTRDCTnTSHB6EbwZcOPszeTN814u8EQVW-Dwa7TA7pNUElb1mVdJPD1P-DabXz6gKAYF0BTb5mgtxNkvAvBY6tGb3vtt4qC2gWiUiBqCiTBL_fGTdPj8oDuE0jAyR7QweiuTR9vbDhwdVUlJTtwbjP-v-GLiVuH6Pw9yQrgpYTdiPlUtyHi3X1d-5-qlFwKtfh-o24E-_KJfq3UVeJfTXyrndIrn952fcWAcoCKpQX4H2XIxEQ</recordid><startdate>2007</startdate><enddate>2007</enddate><creator>Puthoff, David P</creator><creator>Ehrenfried, Mindy L</creator><creator>Vinyard, Bryan T</creator><creator>Tucker, Mark L</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>FBQ</scope><scope>BSCLL</scope><scope>IQODW</scope><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>7QO</scope><scope>7QP</scope><scope>8FD</scope><scope>FR3</scope><scope>K9.</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>2007</creationdate><title>GeneChip profiling of transcriptional responses to soybean cyst nematode, Heterodera glycines, colonization of soybean roots</title><author>Puthoff, David P ; Ehrenfried, Mindy L ; Vinyard, Bryan T ; Tucker, Mark L</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c492t-7542b372bc684c7032f71297cc96386bbe43eee7d56955ca20733b470cab53db3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Affymetrix</topic><topic>Agronomy. Soil science and plant productions</topic><topic>Animals</topic><topic>Biological and medical sciences</topic><topic>cell wall</topic><topic>Cell walls</topic><topic>Cellular structures</topic><topic>cyst nematode</topic><topic>Cyst nematodes</topic><topic>Economic plant physiology</topic><topic>False Discovery Rate</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Expression Profiling</topic><topic>GeneChip</topic><topic>Genes</topic><topic>Glycine max</topic><topic>Glycine max - genetics</topic><topic>Glycine max - parasitology</topic><topic>Heterodera glycines</topic><topic>histones</topic><topic>Metabolic diseases</topic><topic>Nematoda - physiology</topic><topic>Nematodes</topic><topic>plant defence</topic><topic>Plant roots</topic><topic>Plant Roots - genetics</topic><topic>Plant Roots - parasitology</topic><topic>Plants</topic><topic>Research Papers</topic><topic>RNA</topic><topic>soybean</topic><topic>Soybeans</topic><topic>Symbiosis (nodules, symbiotic nitrogen fixation, mycorrhiza...)</topic><topic>Transcription, Genetic</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Puthoff, David P</creatorcontrib><creatorcontrib>Ehrenfried, Mindy L</creatorcontrib><creatorcontrib>Vinyard, Bryan T</creatorcontrib><creatorcontrib>Tucker, Mark L</creatorcontrib><collection>AGRIS</collection><collection>Istex</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of experimental botany</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Puthoff, David P</au><au>Ehrenfried, Mindy L</au><au>Vinyard, Bryan T</au><au>Tucker, Mark L</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>GeneChip profiling of transcriptional responses to soybean cyst nematode, Heterodera glycines, colonization of soybean roots</atitle><jtitle>Journal of experimental botany</jtitle><addtitle>J Exp Bot</addtitle><date>2007</date><risdate>2007</risdate><volume>58</volume><issue>12</issue><spage>3407</spage><epage>3418</epage><pages>3407-3418</pages><issn>0022-0957</issn><eissn>1460-2431</eissn><coden>JEBOA6</coden><abstract>Soybean cyst nematode (SCN) is currently the most devastating pathogen of soybean. SCN penetrates the root and migrates toward the central vascular bundle where it establishes a complex multinucleated feeding structure that provides plant-derived nutrients to support the development and growth of the nematode. To identify host genes that play significant roles in SCN development in susceptible roots, RNA from SCN-inoculated and non-inoculated root pieces were hybridized to the Affymetrix soybean genome GeneChips. RNA was collected at 8, 12, and 16 d post-inoculation from root pieces that displayed multiple swollen female SCN and similar root pieces from non-inoculated roots. Branch roots and root tips were trimmed from the root pieces to minimize the amount of RNA contributed by these organs. Of the 35 593 transcripts represented on the GeneChip, approximately 26 500 were expressed in the SCN-colonized root pieces. ANOVA followed by False Discovery Rate analysis indicated that the expression levels of 4616 transcripts changed significantly (Q-value ≤0.05) in response to SCN. In this set of 4616 transcripts, 1404 transcripts increased >2-fold and 739 decreased >2-fold. Of the transcripts to which a function could be assigned, a large proportion was associated with cell wall structure. Other functional categories that included a large number of up-regulated transcripts were defence, metabolism, and histones, and a smaller group of transcripts associated with signal transduction and transcription.</abstract><cop>Oxford</cop><pub>Oxford University Press</pub><pmid>17977850</pmid><doi>10.1093/jxb/erm211</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Affymetrix Agronomy. Soil science and plant productions Animals Biological and medical sciences cell wall Cell walls Cellular structures cyst nematode Cyst nematodes Economic plant physiology False Discovery Rate Fundamental and applied biological sciences. Psychology Gene Expression Profiling GeneChip Genes Glycine max Glycine max - genetics Glycine max - parasitology Heterodera glycines histones Metabolic diseases Nematoda - physiology Nematodes plant defence Plant roots Plant Roots - genetics Plant Roots - parasitology Plants Research Papers RNA soybean Soybeans Symbiosis (nodules, symbiotic nitrogen fixation, mycorrhiza...) Transcription, Genetic |
| title | GeneChip profiling of transcriptional responses to soybean cyst nematode, Heterodera glycines, colonization of soybean roots |
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