Identification of novel soybean microRNAs involved in abiotic and biotic stresses
Identifieur interne : 001715 ( Main/Exploration ); précédent : 001714; suivant : 001716Identification of novel soybean microRNAs involved in abiotic and biotic stresses
Auteurs : Franceli R. Kulcheski [Brésil] ; Luiz Fv De Oliveira [Brésil] ; Lorrayne G. Molina [Brésil] ; Maurício P. Almerão [Brésil] ; Fabiana A. Rodrigues [Brésil] ; Juliana Marcolino [Brésil] ; Joice F. Barbosa [Brésil] ; Renata Stolf-Moreira [Brésil] ; Alexandre L. Nepomuceno [Brésil] ; Francismar C. Marcelino-Guimarães [Brésil] ; Ricardo V. Abdelnoor [Brésil] ; Leandro C. Nascimento [Brésil] ; Marcelo F. Carazzolle [Brésil] ; Gonçalo Ag Pereira [Brésil] ; Rogério Margis [Brésil]Source :
- BMC Genomics [ 1471-2164 ] ; 2011.
Abstract
Small RNAs (19-24 nt) are key regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in eukaryotes. Current studies have demonstrated that microRNAs (miRNAs) act in several plant pathways associated with tissue proliferation, differentiation, and development and in response to abiotic and biotic stresses. In order to identify new miRNAs in soybean and to verify those that are possibly water deficit and rust-stress regulated, eight libraries of small RNAs were constructed and submitted to Solexa sequencing.
The libraries were developed from drought-sensitive and tolerant seedlings and rust-susceptible and resistant soybeans with or without stressors. Sequencing the library and subsequent analyses detected 256 miRNAs. From this total, we identified 24 families of novel miRNAs that had not been reported before, six families of conserved miRNAs that exist in other plants species, and 22 families previously reported in soybean. We also observed the presence of several isomiRNAs during our analyses. To validate novel miRNAs, we performed RT-qPCR across the eight different libraries. Among the 11 miRNAs analyzed, all showed different expression profiles during biotic and abiotic stresses to soybean. The majority of miRNAs were up-regulated during water deficit stress in the sensitive plants. However, for the tolerant genotype, most of the miRNAs were down regulated. The pattern of miRNAs expression was also different for the distinct genotypes submitted to the pathogen stress. Most miRNAs were down regulated during the fungus infection in the susceptible genotype; however, in the resistant genotype, most miRNAs did not vary during rust attack. A prediction of the putative targets was carried out for conserved and novel miRNAs families.
Validation of our results with quantitative RT-qPCR revealed that Solexa sequencing is a powerful tool for miRNA discovery. The identification of differentially expressed plant miRNAs provides molecular evidence for the possible involvement of miRNAs in the process of water deficit- and rust-stress responses.
Url:
DOI: 10.1186/1471-2164-12-307
PubMed: 21663675
PubMed Central: 3141666
Affiliations:
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Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification of novel soybean microRNAs involved in abiotic and biotic stresses</title>
<author><name sortKey="Kulcheski, Franceli R" sort="Kulcheski, Franceli R" uniqKey="Kulcheski F" first="Franceli R" last="Kulcheski">Franceli R. Kulcheski</name>
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<author><name sortKey="De Oliveira, Luiz Fv" sort="De Oliveira, Luiz Fv" uniqKey="De Oliveira L" first="Luiz Fv" last="De Oliveira">Luiz Fv De Oliveira</name>
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<author><name sortKey="Rodrigues, Fabiana A" sort="Rodrigues, Fabiana A" uniqKey="Rodrigues F" first="Fabiana A" last="Rodrigues">Fabiana A. Rodrigues</name>
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<author><name sortKey="Barbosa, Joice F" sort="Barbosa, Joice F" uniqKey="Barbosa J" first="Joice F" last="Barbosa">Joice F. Barbosa</name>
<affiliation wicri:level="2"><nlm:aff id="I3">EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR, Brazil</nlm:aff>
<country xml:lang="fr">Brésil</country>
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<author><name sortKey="Stolf Moreira, Renata" sort="Stolf Moreira, Renata" uniqKey="Stolf Moreira R" first="Renata" last="Stolf-Moreira">Renata Stolf-Moreira</name>
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<country xml:lang="fr">Brésil</country>
<wicri:regionArea>EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR</wicri:regionArea>
<placeName><region type="state">Paraná (État)</region>
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<author><name sortKey="Nepomuceno, Alexandre L" sort="Nepomuceno, Alexandre L" uniqKey="Nepomuceno A" first="Alexandre L" last="Nepomuceno">Alexandre L. Nepomuceno</name>
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<country xml:lang="fr">Brésil</country>
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<country xml:lang="fr">Brésil</country>
<wicri:regionArea>EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR</wicri:regionArea>
<placeName><region type="state">Paraná (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Abdelnoor, Ricardo V" sort="Abdelnoor, Ricardo V" uniqKey="Abdelnoor R" first="Ricardo V" last="Abdelnoor">Ricardo V. Abdelnoor</name>
<affiliation wicri:level="2"><nlm:aff id="I3">EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR, Brazil</nlm:aff>
<country xml:lang="fr">Brésil</country>
<wicri:regionArea>EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR</wicri:regionArea>
<placeName><region type="state">Paraná (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Nascimento, Leandro C" sort="Nascimento, Leandro C" uniqKey="Nascimento L" first="Leandro C" last="Nascimento">Leandro C. Nascimento</name>
<affiliation wicri:level="2"><nlm:aff id="I4">Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, CEP 13083-970, Campinas, SP, Brazil</nlm:aff>
<country xml:lang="fr">Brésil</country>
<wicri:regionArea>Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, CEP 13083-970, Campinas, SP</wicri:regionArea>
<placeName><region type="state">État de São Paulo</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Carazzolle, Marcelo F" sort="Carazzolle, Marcelo F" uniqKey="Carazzolle M" first="Marcelo F" last="Carazzolle">Marcelo F. Carazzolle</name>
<affiliation wicri:level="2"><nlm:aff id="I4">Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, CEP 13083-970, Campinas, SP, Brazil</nlm:aff>
<country xml:lang="fr">Brésil</country>
<wicri:regionArea>Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, CEP 13083-970, Campinas, SP</wicri:regionArea>
<placeName><region type="state">État de São Paulo</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="I5">National Center for High Performance Processing (CENAPAD-SP), State University of Campinas, CEP 13083-970, Campinas, SP, Brazil</nlm:aff>
<country xml:lang="fr">Brésil</country>
<wicri:regionArea>National Center for High Performance Processing (CENAPAD-SP), State University of Campinas, CEP 13083-970, Campinas, SP</wicri:regionArea>
<placeName><region type="state">État de São Paulo</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Pereira, Goncalo Ag" sort="Pereira, Goncalo Ag" uniqKey="Pereira G" first="Gonçalo Ag" last="Pereira">Gonçalo Ag Pereira</name>
<affiliation wicri:level="2"><nlm:aff id="I4">Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, CEP 13083-970, Campinas, SP, Brazil</nlm:aff>
<country xml:lang="fr">Brésil</country>
<wicri:regionArea>Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, CEP 13083-970, Campinas, SP</wicri:regionArea>
<placeName><region type="state">État de São Paulo</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Margis, Rogerio" sort="Margis, Rogerio" uniqKey="Margis R" first="Rogério" last="Margis">Rogério Margis</name>
<affiliation wicri:level="2"><nlm:aff id="I1">Centre of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Population, building 43431, Federal University of Rio Grande do Sul - UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, RS, Brazil</nlm:aff>
<country xml:lang="fr">Brésil</country>
<wicri:regionArea>Centre of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Population, building 43431, Federal University of Rio Grande do Sul - UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, RS</wicri:regionArea>
<placeName><region type="state">Rio Grande do Sul</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="I2">PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil</nlm:aff>
<country xml:lang="fr">Brésil</country>
<wicri:regionArea>PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS</wicri:regionArea>
<placeName><region type="state">Rio Grande do Sul</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">BMC Genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint><date when="2011">2011</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Small RNAs (19-24 nt) are key regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in eukaryotes. Current studies have demonstrated that microRNAs (miRNAs) act in several plant pathways associated with tissue proliferation, differentiation, and development and in response to abiotic and biotic stresses. In order to identify new miRNAs in soybean and to verify those that are possibly water deficit and rust-stress regulated, eight libraries of small RNAs were constructed and submitted to Solexa sequencing.</p>
</sec>
<sec><title>Results</title>
<p>The libraries were developed from drought-sensitive and tolerant seedlings and rust-susceptible and resistant soybeans with or without stressors. Sequencing the library and subsequent analyses detected 256 miRNAs. From this total, we identified 24 families of novel miRNAs that had not been reported before, six families of conserved miRNAs that exist in other plants species, and 22 families previously reported in soybean. We also observed the presence of several isomiRNAs during our analyses. To validate novel miRNAs, we performed RT-qPCR across the eight different libraries. Among the 11 miRNAs analyzed, all showed different expression profiles during biotic and abiotic stresses to soybean. The majority of miRNAs were up-regulated during water deficit stress in the sensitive plants. However, for the tolerant genotype, most of the miRNAs were down regulated. The pattern of miRNAs expression was also different for the distinct genotypes submitted to the pathogen stress. Most miRNAs were down regulated during the fungus infection in the susceptible genotype; however, in the resistant genotype, most miRNAs did not vary during rust attack. A prediction of the putative targets was carried out for conserved and novel miRNAs families.</p>
</sec>
<sec><title>Conclusions</title>
<p>Validation of our results with quantitative RT-qPCR revealed that Solexa sequencing is a powerful tool for miRNA discovery. The identification of differentially expressed plant miRNAs provides molecular evidence for the possible involvement of miRNAs in the process of water deficit- and rust-stress responses.</p>
</sec>
</div>
</front>
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</div1>
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</TEI>
<affiliations><list><country><li>Brésil</li>
</country>
<region><li>Paraná (État)</li>
<li>Rio Grande do Sul</li>
<li>État de São Paulo</li>
</region>
</list>
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</region>
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<name sortKey="Almerao, Mauricio P" sort="Almerao, Mauricio P" uniqKey="Almerao M" first="Maurício P" last="Almerão">Maurício P. Almerão</name>
<name sortKey="Barbosa, Joice F" sort="Barbosa, Joice F" uniqKey="Barbosa J" first="Joice F" last="Barbosa">Joice F. Barbosa</name>
<name sortKey="Carazzolle, Marcelo F" sort="Carazzolle, Marcelo F" uniqKey="Carazzolle M" first="Marcelo F" last="Carazzolle">Marcelo F. Carazzolle</name>
<name sortKey="Carazzolle, Marcelo F" sort="Carazzolle, Marcelo F" uniqKey="Carazzolle M" first="Marcelo F" last="Carazzolle">Marcelo F. Carazzolle</name>
<name sortKey="De Oliveira, Luiz Fv" sort="De Oliveira, Luiz Fv" uniqKey="De Oliveira L" first="Luiz Fv" last="De Oliveira">Luiz Fv De Oliveira</name>
<name sortKey="De Oliveira, Luiz Fv" sort="De Oliveira, Luiz Fv" uniqKey="De Oliveira L" first="Luiz Fv" last="De Oliveira">Luiz Fv De Oliveira</name>
<name sortKey="Marcelino Guimaraes, Francismar C" sort="Marcelino Guimaraes, Francismar C" uniqKey="Marcelino Guimaraes F" first="Francismar C" last="Marcelino-Guimarães">Francismar C. Marcelino-Guimarães</name>
<name sortKey="Marcolino, Juliana" sort="Marcolino, Juliana" uniqKey="Marcolino J" first="Juliana" last="Marcolino">Juliana Marcolino</name>
<name sortKey="Margis, Rogerio" sort="Margis, Rogerio" uniqKey="Margis R" first="Rogério" last="Margis">Rogério Margis</name>
<name sortKey="Margis, Rogerio" sort="Margis, Rogerio" uniqKey="Margis R" first="Rogério" last="Margis">Rogério Margis</name>
<name sortKey="Molina, Lorrayne G" sort="Molina, Lorrayne G" uniqKey="Molina L" first="Lorrayne G" last="Molina">Lorrayne G. Molina</name>
<name sortKey="Molina, Lorrayne G" sort="Molina, Lorrayne G" uniqKey="Molina L" first="Lorrayne G" last="Molina">Lorrayne G. Molina</name>
<name sortKey="Nascimento, Leandro C" sort="Nascimento, Leandro C" uniqKey="Nascimento L" first="Leandro C" last="Nascimento">Leandro C. Nascimento</name>
<name sortKey="Nepomuceno, Alexandre L" sort="Nepomuceno, Alexandre L" uniqKey="Nepomuceno A" first="Alexandre L" last="Nepomuceno">Alexandre L. Nepomuceno</name>
<name sortKey="Pereira, Goncalo Ag" sort="Pereira, Goncalo Ag" uniqKey="Pereira G" first="Gonçalo Ag" last="Pereira">Gonçalo Ag Pereira</name>
<name sortKey="Rodrigues, Fabiana A" sort="Rodrigues, Fabiana A" uniqKey="Rodrigues F" first="Fabiana A" last="Rodrigues">Fabiana A. Rodrigues</name>
<name sortKey="Stolf Moreira, Renata" sort="Stolf Moreira, Renata" uniqKey="Stolf Moreira R" first="Renata" last="Stolf-Moreira">Renata Stolf-Moreira</name>
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</tree>
</affiliations>
</record>
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