Analysis of gene co-expression networks of phosphate starvation and aluminium toxicity responses in Populus spp.
Identifieur interne : 000B32 ( Main/Exploration ); précédent : 000B31; suivant : 000B33Analysis of gene co-expression networks of phosphate starvation and aluminium toxicity responses in Populus spp.
Auteurs : Thiago Bergamo Cardoso [Brésil] ; Renan Terassi Pinto [Brésil] ; Luciano Vilela Paiva [Brésil]Source :
- PloS one [ 1932-6203 ] ; 2019.
Descripteurs français
- KwdFr :
- Adaptation physiologique (génétique), Aluminium (toxicité), Engrais (toxicité), Humains (MeSH), Inanition (génétique), Phosphates (métabolisme), Populus (effets des médicaments et des substances chimiques), Populus (génétique), Populus (métabolisme), Produits agricoles (MeSH), Régulation de l'expression des gènes végétaux (effets des médicaments et des substances chimiques), Réseaux de régulation génique (effets des médicaments et des substances chimiques), Sol (composition chimique), Stress physiologique (génétique), Transcriptome (effets des médicaments et des substances chimiques), Transcriptome (génétique).
- MESH :
- composition chimique : Sol.
- effets des médicaments et des substances chimiques : Populus, Régulation de l'expression des gènes végétaux, Réseaux de régulation génique, Transcriptome.
- génétique : Adaptation physiologique, Inanition, Populus, Stress physiologique, Transcriptome.
- métabolisme : Phosphates, Populus.
- toxicité : Aluminium, Engrais.
- Humains, Produits agricoles.
English descriptors
- KwdEn :
- Adaptation, Physiological (genetics), Aluminum (toxicity), Crops, Agricultural (MeSH), Fertilizers (toxicity), Gene Expression Regulation, Plant (drug effects), Gene Regulatory Networks (drug effects), Humans (MeSH), Phosphates (metabolism), Populus (drug effects), Populus (genetics), Populus (metabolism), Soil (chemistry), Starvation (genetics), Stress, Physiological (genetics), Transcriptome (drug effects), Transcriptome (genetics).
- MESH :
- chemical , chemistry : Soil.
- chemical , metabolism : Phosphates.
- chemical , toxicity : Aluminum, Fertilizers.
- drug effects : Gene Expression Regulation, Plant, Gene Regulatory Networks, Populus, Transcriptome.
- genetics : Adaptation, Physiological, Populus, Starvation, Stress, Physiological, Transcriptome.
- metabolism : Populus.
- Crops, Agricultural, Humans.
Abstract
The adaptation of crops to acid soils is needed for the maintenance of food security in a sustainable way, as decreasing fertilizers use and mechanical interventions in the soil would favor the reduction of agricultural practices' environmental impact. Phosphate deficiency and the presence of reactive aluminum affect vital processes to the plant in this soil, mostly water and nutrient absorption. From this, the understanding of the molecular response to these stresses can foster strategies for genetic improvement, so the aim was to broadly analyze the transcriptional variations in Poupulus spp. in response to these abiotic stresses, as a plant model for woody crops. A co-expression network was constructed among 3,180 genes differentially expressed in aluminum-stressed plants with 34,988 connections. Of this total, 344 genes presented two-fold transcriptional variation and the group of genes associated with those regulated after 246 hours of stress had higher number of connections per gene, with some already characterized genes related to this stress as main hubs. Another co-expression network was made up of 8,380 connections between 550 genes regulated by aluminum stress and phosphate deficiency, in which 380 genes had similar profile in both stresses and only eight with transcriptional variation higher than 20%. All the transcriptomic data are presented here with functional enrichment and homology comparisons with already characterized genes in another species that are related to the explored stresses, in order to provide a broad analysis of the co-opted responses for both the stresses as well as some specificity. This approach improves our understanding regarding the plants adaptation to acid soils and may contribute to strategies of crop genetic improvement for this condition that is widely present in regions of high agricultural activity.
DOI: 10.1371/journal.pone.0223217
PubMed: 31600239
PubMed Central: PMC6786596
Affiliations:
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xml:lang="fr"><term>Humains</term><term>Produits agricoles</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The adaptation of crops to acid soils is needed for the maintenance of food security in a sustainable way, as decreasing fertilizers use and mechanical interventions in the soil would favor the reduction of agricultural practices' environmental impact. Phosphate deficiency and the presence of reactive aluminum affect vital processes to the plant in this soil, mostly water and nutrient absorption. From this, the understanding of the molecular response to these stresses can foster strategies for genetic improvement, so the aim was to broadly analyze the transcriptional variations in Poupulus spp. in response to these abiotic stresses, as a plant model for woody crops. A co-expression network was constructed among 3,180 genes differentially expressed in aluminum-stressed plants with 34,988 connections. Of this total, 344 genes presented two-fold transcriptional variation and the group of genes associated with those regulated after 246 hours of stress had higher number of connections per gene, with some already characterized genes related to this stress as main hubs. Another co-expression network was made up of 8,380 connections between 550 genes regulated by aluminum stress and phosphate deficiency, in which 380 genes had similar profile in both stresses and only eight with transcriptional variation higher than 20%. All the transcriptomic data are presented here with functional enrichment and homology comparisons with already characterized genes in another species that are related to the explored stresses, in order to provide a broad analysis of the co-opted responses for both the stresses as well as some specificity. This approach improves our understanding regarding the plants adaptation to acid soils and may contribute to strategies of crop genetic improvement for this condition that is widely present in regions of high agricultural activity.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31600239</PMID><DateCompleted><Year>2020</Year><Month>03</Month><Day>12</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>12</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>14</Volume><Issue>10</Issue><PubDate><Year>2019</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Analysis of gene co-expression networks of phosphate starvation and aluminium toxicity responses in Populus spp.</ArticleTitle><Pagination><MedlinePgn>e0223217</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0223217</ELocationID><Abstract><AbstractText>The adaptation of crops to acid soils is needed for the maintenance of food security in a sustainable way, as decreasing fertilizers use and mechanical interventions in the soil would favor the reduction of agricultural practices' environmental impact. Phosphate deficiency and the presence of reactive aluminum affect vital processes to the plant in this soil, mostly water and nutrient absorption. From this, the understanding of the molecular response to these stresses can foster strategies for genetic improvement, so the aim was to broadly analyze the transcriptional variations in Poupulus spp. in response to these abiotic stresses, as a plant model for woody crops. A co-expression network was constructed among 3,180 genes differentially expressed in aluminum-stressed plants with 34,988 connections. Of this total, 344 genes presented two-fold transcriptional variation and the group of genes associated with those regulated after 246 hours of stress had higher number of connections per gene, with some already characterized genes related to this stress as main hubs. Another co-expression network was made up of 8,380 connections between 550 genes regulated by aluminum stress and phosphate deficiency, in which 380 genes had similar profile in both stresses and only eight with transcriptional variation higher than 20%. All the transcriptomic data are presented here with functional enrichment and homology comparisons with already characterized genes in another species that are related to the explored stresses, in order to provide a broad analysis of the co-opted responses for both the stresses as well as some specificity. This approach improves our understanding regarding the plants adaptation to acid soils and may contribute to strategies of crop genetic improvement for this condition that is widely present in regions of high agricultural activity.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cardoso</LastName><ForeName>Thiago Bergamo</ForeName><Initials>TB</Initials><AffiliationInfo><Affiliation>Central Laboratory of Molecular Biology, Department of Chemistry, Federal University of Lavras, Lavras, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pinto</LastName><ForeName>Renan Terassi</ForeName><Initials>RT</Initials><AffiliationInfo><Affiliation>Central Laboratory of Molecular Biology, Department of Chemistry, Federal University of Lavras, Lavras, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Paiva</LastName><ForeName>Luciano Vilela</ForeName><Initials>LV</Initials><Identifier Source="ORCID">0000-0002-2577-2168</Identifier><AffiliationInfo><Affiliation>Central Laboratory of Molecular Biology, Department of Chemistry, Federal University of Lavras, Lavras, Brazil.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>10</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005308">Fertilizers</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010710">Phosphates</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012987">Soil</NameOfSubstance></Chemical><Chemical><RegistryNumber>CPD4NFA903</RegistryNumber><NameOfSubstance UI="D000535">Aluminum</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000222" MajorTopicYN="N">Adaptation, Physiological</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000535" MajorTopicYN="N">Aluminum</DescriptorName><QualifierName UI="Q000633" MajorTopicYN="Y">toxicity</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018556" MajorTopicYN="N">Crops, Agricultural</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005308" MajorTopicYN="N">Fertilizers</DescriptorName><QualifierName UI="Q000633" MajorTopicYN="N">toxicity</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="N">drug effects</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D053263" MajorTopicYN="N">Gene Regulatory Networks</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="N">drug effects</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010710" MajorTopicYN="N">Phosphates</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="N">drug effects</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012987" MajorTopicYN="N">Soil</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013217" MajorTopicYN="N">Starvation</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013312" MajorTopicYN="N">Stress, Physiological</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="N">Transcriptome</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="N">drug effects</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList><CoiStatement>The authors have declared that no competing interests exist.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate 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