Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomics.
Identifieur interne : 001152 ( Main/Corpus ); précédent : 001151; suivant : 001153Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomics.
Auteurs : Feng Lin ; Meixia Zhao ; Douglas D. Baumann ; Jieqing Ping ; Lianjun Sun ; Yunfeng Liu ; Biao Zhang ; Zongxiang Tang ; Elisa Hughes ; Rebecca W. Doerge ; Teresa J. Hughes ; Jianxin MaSource :
- BMC genomics [ 1471-2164 ] ; 2014.
English descriptors
- KwdEn :
- Alleles (MeSH), Cluster Analysis (MeSH), Genes, Plant (MeSH), High-Throughput Nucleotide Sequencing (MeSH), Phytophthora (isolation & purification), Phytophthora (physiology), Plant Growth Regulators (genetics), Plant Growth Regulators (metabolism), Plant Proteins (chemistry), Plant Proteins (genetics), Plant Proteins (metabolism), Plant Roots (genetics), Plant Roots (metabolism), Plant Roots (parasitology), Plant Stems (genetics), Plant Stems (metabolism), Plant Stems (parasitology), Signal Transduction (genetics), Soybeans (genetics), Soybeans (metabolism), Soybeans (parasitology), Transcriptome (MeSH).
- MESH :
- chemical , chemistry : Plant Proteins.
- chemical , genetics : Plant Growth Regulators, Plant Proteins.
- genetics : Plant Roots, Plant Stems, Signal Transduction, Soybeans.
- isolation & purification : Phytophthora.
- chemical , metabolism : Plant Growth Regulators, Plant Proteins, Plant Roots, Plant Stems, Soybeans.
- parasitology : Plant Roots, Plant Stems, Soybeans.
- physiology : Phytophthora.
- Alleles, Cluster Analysis, Genes, Plant, High-Throughput Nucleotide Sequencing, Transcriptome.
Abstract
BACKGROUND
Phytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is controlled by Rps genes. However, little is known regarding the Rps-induced molecular responses to P. sojae and how they actually overlap. We thus sequenced, analyzed, and compared the transcriptomes of 10 near isogenic lines (NILs), each with a unique Rps gene/allele, and the susceptible parent Williams, pre- and post-inoculation with the pathogen.
RESULTS
A total of 4,330 differentially expressed genes (DEGs) were identified in Williams versus 2,014 to 5,499 DEGs in individual NILs upon inoculation with the pathogen. Comparisons of the DEGs between the NILs and Williams identified incompatible interaction genes (IIGs) and compatible interaction genes (CIGs). Hierarchical cluster and heatmap analyses consistently grouped the NILs into three clusters: Cluster I (Rps1-a), Cluster II (Rps1-b, 1-c and 1-k) and Cluster III (Rps3-a, 3-b, 3-c, 4, 5, and 6), suggesting an overlap in Rps-induced defense signaling among certain NILs. Gene ontology (GO) analysis revealed associations between members of the WRKY family and incompatible reactions and between a number of phytohormone signaling pathways and incompatible/compatible interactions. These associations appear to be distinguished according to the NIL clusters.
CONCLUSIONS
This study characterized genes and multiple branches of putative regulatory networks associated with resistance to P. sojae in ten soybean NILs, and depicted functional "fingerprints" of individual Rps-mediated resistance responses through comparative transcriptomic analysis. Of particular interest are dramatic variations of detected DEGs, putatively involved in ethylene (ET)-, jasmonic acid (JA)-, (reactive oxygen species) ROS-, and (MAP-kinase) MAPK- signaling, among these soybean NILs, implicating their important roles of these signaling in differentiating molecular defense responses. We hypothesize that different timing and robustness in defense signaling to the same pathogen may be largely responsible for such variations.
DOI: 10.1186/1471-2164-15-18
PubMed: 24410936
PubMed Central: PMC3893405
Links to Exploration step
pubmed:24410936Le document en format XML
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Baumann</name></author><author><name sortKey="Ping, Jieqing" sort="Ping, Jieqing" uniqKey="Ping J" first="Jieqing" last="Ping">Jieqing Ping</name></author><author><name sortKey="Sun, Lianjun" sort="Sun, Lianjun" uniqKey="Sun L" first="Lianjun" last="Sun">Lianjun Sun</name></author><author><name sortKey="Liu, Yunfeng" sort="Liu, Yunfeng" uniqKey="Liu Y" first="Yunfeng" last="Liu">Yunfeng Liu</name></author><author><name sortKey="Zhang, Biao" sort="Zhang, Biao" uniqKey="Zhang B" first="Biao" last="Zhang">Biao Zhang</name></author><author><name sortKey="Tang, Zongxiang" sort="Tang, Zongxiang" uniqKey="Tang Z" first="Zongxiang" last="Tang">Zongxiang Tang</name></author><author><name sortKey="Hughes, Elisa" sort="Hughes, Elisa" uniqKey="Hughes E" first="Elisa" last="Hughes">Elisa Hughes</name></author><author><name sortKey="Doerge, Rebecca W" sort="Doerge, Rebecca W" uniqKey="Doerge R" first="Rebecca W" last="Doerge">Rebecca W. 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Hughes</name><affiliation><nlm:affiliation>Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA. hughestj@purdue.edu.</nlm:affiliation></affiliation></author><author><name sortKey="Ma, Jianxin" sort="Ma, Jianxin" uniqKey="Ma J" first="Jianxin" last="Ma">Jianxin Ma</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24410936</idno><idno type="pmid">24410936</idno><idno type="doi">10.1186/1471-2164-15-18</idno><idno type="pmc">PMC3893405</idno><idno type="wicri:Area/Main/Corpus">001152</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001152</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomics.</title><author><name sortKey="Lin, Feng" sort="Lin, Feng" uniqKey="Lin F" first="Feng" last="Lin">Feng Lin</name></author><author><name sortKey="Zhao, Meixia" sort="Zhao, Meixia" uniqKey="Zhao M" first="Meixia" last="Zhao">Meixia Zhao</name></author><author><name sortKey="Baumann, Douglas D" sort="Baumann, Douglas D" uniqKey="Baumann D" first="Douglas D" last="Baumann">Douglas D. Baumann</name></author><author><name sortKey="Ping, Jieqing" sort="Ping, Jieqing" uniqKey="Ping J" first="Jieqing" last="Ping">Jieqing Ping</name></author><author><name sortKey="Sun, Lianjun" sort="Sun, Lianjun" uniqKey="Sun L" first="Lianjun" last="Sun">Lianjun Sun</name></author><author><name sortKey="Liu, Yunfeng" sort="Liu, Yunfeng" uniqKey="Liu Y" first="Yunfeng" last="Liu">Yunfeng Liu</name></author><author><name sortKey="Zhang, Biao" sort="Zhang, Biao" uniqKey="Zhang B" first="Biao" last="Zhang">Biao Zhang</name></author><author><name sortKey="Tang, Zongxiang" sort="Tang, Zongxiang" uniqKey="Tang Z" first="Zongxiang" last="Tang">Zongxiang Tang</name></author><author><name sortKey="Hughes, Elisa" sort="Hughes, Elisa" uniqKey="Hughes E" first="Elisa" last="Hughes">Elisa Hughes</name></author><author><name sortKey="Doerge, Rebecca W" sort="Doerge, Rebecca W" uniqKey="Doerge R" first="Rebecca W" last="Doerge">Rebecca W. Doerge</name></author><author><name sortKey="Hughes, Teresa J" sort="Hughes, Teresa J" uniqKey="Hughes T" first="Teresa J" last="Hughes">Teresa J. Hughes</name><affiliation><nlm:affiliation>Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA. hughestj@purdue.edu.</nlm:affiliation></affiliation></author><author><name sortKey="Ma, Jianxin" sort="Ma, Jianxin" uniqKey="Ma J" first="Jianxin" last="Ma">Jianxin Ma</name></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles (MeSH)</term><term>Cluster Analysis (MeSH)</term><term>Genes, Plant (MeSH)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Phytophthora (isolation & purification)</term><term>Phytophthora (physiology)</term><term>Plant Growth Regulators (genetics)</term><term>Plant Growth Regulators (metabolism)</term><term>Plant Proteins (chemistry)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</term><term>Plant Roots (genetics)</term><term>Plant Roots (metabolism)</term><term>Plant Roots (parasitology)</term><term>Plant Stems (genetics)</term><term>Plant Stems (metabolism)</term><term>Plant Stems (parasitology)</term><term>Signal Transduction (genetics)</term><term>Soybeans (genetics)</term><term>Soybeans (metabolism)</term><term>Soybeans (parasitology)</term><term>Transcriptome (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Growth Regulators</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Plant Roots</term><term>Plant Stems</term><term>Signal Transduction</term><term>Soybeans</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Phytophthora</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Growth Regulators</term><term>Plant Proteins</term><term>Plant Roots</term><term>Plant Stems</term><term>Soybeans</term></keywords><keywords scheme="MESH" qualifier="parasitology" xml:lang="en"><term>Plant Roots</term><term>Plant Stems</term><term>Soybeans</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Phytophthora</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Cluster Analysis</term><term>Genes, Plant</term><term>High-Throughput Nucleotide Sequencing</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Phytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is controlled by Rps genes. However, little is known regarding the Rps-induced molecular responses to P. sojae and how they actually overlap. We thus sequenced, analyzed, and compared the transcriptomes of 10 near isogenic lines (NILs), each with a unique Rps gene/allele, and the susceptible parent Williams, pre- and post-inoculation with the pathogen.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>A total of 4,330 differentially expressed genes (DEGs) were identified in Williams versus 2,014 to 5,499 DEGs in individual NILs upon inoculation with the pathogen. Comparisons of the DEGs between the NILs and Williams identified incompatible interaction genes (IIGs) and compatible interaction genes (CIGs). Hierarchical cluster and heatmap analyses consistently grouped the NILs into three clusters: Cluster I (Rps1-a), Cluster II (Rps1-b, 1-c and 1-k) and Cluster III (Rps3-a, 3-b, 3-c, 4, 5, and 6), suggesting an overlap in Rps-induced defense signaling among certain NILs. Gene ontology (GO) analysis revealed associations between members of the WRKY family and incompatible reactions and between a number of phytohormone signaling pathways and incompatible/compatible interactions. These associations appear to be distinguished according to the NIL clusters.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>This study characterized genes and multiple branches of putative regulatory networks associated with resistance to P. sojae in ten soybean NILs, and depicted functional "fingerprints" of individual Rps-mediated resistance responses through comparative transcriptomic analysis. Of particular interest are dramatic variations of detected DEGs, putatively involved in ethylene (ET)-, jasmonic acid (JA)-, (reactive oxygen species) ROS-, and (MAP-kinase) MAPK- signaling, among these soybean NILs, implicating their important roles of these signaling in differentiating molecular defense responses. We hypothesize that different timing and robustness in defense signaling to the same pathogen may be largely responsible for such variations.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24410936</PMID><DateCompleted><Year>2014</Year><Month>08</Month><Day>29</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>15</Volume><PubDate><Year>2014</Year><Month>Jan</Month><Day>10</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomics.</ArticleTitle><Pagination><MedlinePgn>18</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-15-18</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Phytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is controlled by Rps genes. However, little is known regarding the Rps-induced molecular responses to P. sojae and how they actually overlap. We thus sequenced, analyzed, and compared the transcriptomes of 10 near isogenic lines (NILs), each with a unique Rps gene/allele, and the susceptible parent Williams, pre- and post-inoculation with the pathogen.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">A total of 4,330 differentially expressed genes (DEGs) were identified in Williams versus 2,014 to 5,499 DEGs in individual NILs upon inoculation with the pathogen. Comparisons of the DEGs between the NILs and Williams identified incompatible interaction genes (IIGs) and compatible interaction genes (CIGs). Hierarchical cluster and heatmap analyses consistently grouped the NILs into three clusters: Cluster I (Rps1-a), Cluster II (Rps1-b, 1-c and 1-k) and Cluster III (Rps3-a, 3-b, 3-c, 4, 5, and 6), suggesting an overlap in Rps-induced defense signaling among certain NILs. Gene ontology (GO) analysis revealed associations between members of the WRKY family and incompatible reactions and between a number of phytohormone signaling pathways and incompatible/compatible interactions. These associations appear to be distinguished according to the NIL clusters.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">This study characterized genes and multiple branches of putative regulatory networks associated with resistance to P. sojae in ten soybean NILs, and depicted functional "fingerprints" of individual Rps-mediated resistance responses through comparative transcriptomic analysis. Of particular interest are dramatic variations of detected DEGs, putatively involved in ethylene (ET)-, jasmonic acid (JA)-, (reactive oxygen species) ROS-, and (MAP-kinase) MAPK- signaling, among these soybean NILs, implicating their important roles of these signaling in differentiating molecular defense responses. We hypothesize that different timing and robustness in defense signaling to the same pathogen may be largely responsible for such variations.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lin</LastName><ForeName>Feng</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Meixia</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Baumann</LastName><ForeName>Douglas D</ForeName><Initials>DD</Initials></Author><Author ValidYN="Y"><LastName>Ping</LastName><ForeName>Jieqing</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Lianjun</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Yunfeng</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Biao</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Tang</LastName><ForeName>Zongxiang</ForeName><Initials>Z</Initials></Author><Author ValidYN="Y"><LastName>Hughes</LastName><ForeName>Elisa</ForeName><Initials>E</Initials></Author><Author ValidYN="Y"><LastName>Doerge</LastName><ForeName>Rebecca W</ForeName><Initials>RW</Initials></Author><Author ValidYN="Y"><LastName>Hughes</LastName><ForeName>Teresa J</ForeName><Initials>TJ</Initials><AffiliationInfo><Affiliation>Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA. hughestj@purdue.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Jianxin</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>01</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010937">Plant Growth Regulators</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000483" MajorTopicYN="N">Alleles</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="N">Phytophthora</DescriptorName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010937" MajorTopicYN="N">Plant Growth Regulators</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName><QualifierName UI="Q000469" MajorTopicYN="N">parasitology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018547" MajorTopicYN="N">Plant Stems</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName><QualifierName UI="Q000469" MajorTopicYN="N">parasitology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015398" MajorTopicYN="N">Signal Transduction</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013025" MajorTopicYN="N">Soybeans</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName><QualifierName UI="Q000469" 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