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Evaluation of Appropriate Reference Genes for Reverse Transcription-Quantitative PCR Studies in Different Tissues of a Desert Poplar via Comparision of Different Algorithms.

Identifieur interne : 001D85 ( Main/Exploration ); précédent : 001D84; suivant : 001D86

Evaluation of Appropriate Reference Genes for Reverse Transcription-Quantitative PCR Studies in Different Tissues of a Desert Poplar via Comparision of Different Algorithms.

Auteurs : Hou-Ling Wang [République populaire de Chine] ; Lan Li [République populaire de Chine] ; Sha Tang [République populaire de Chine] ; Chao Yuan [République populaire de Chine] ; Qianqian Tian [République populaire de Chine] ; Yanyan Su [République populaire de Chine] ; Hui-Guang Li [République populaire de Chine] ; Lin Zhao [République populaire de Chine] ; Weilun Yin [République populaire de Chine] ; Rui Zhao [République populaire de Chine] ; Xinli Xia [République populaire de Chine]

Source :

RBID : pubmed:26343648

Descripteurs français

English descriptors

Abstract

Despite the unshakable status of reverse transcription-quantitative PCR in gene expression analysis, it has certain disadvantages, including that the results are highly dependent on the reference genes selected for data normalization. Since inappropriate endogenous control genes will lead to inaccurate target gene expression profiles, the validation of suitable internal reference genes is essential. Given the increasing interest in functional genes and genomics of Populus euphratica, a desert poplar showing extraordinary adaptation to salt stress, we evaluated the expression stability of ten candidate reference genes in P. euphratica roots, stems, and leaves under salt stress conditions. We used five algorithms, namely, ΔCt, NormFinder, geNorm, GrayNorm, and a rank aggregation method (RankAggreg) to identify suitable normalizers. To support the suitability of the identified reference genes and to compare the relative merits of these different algorithms, we analyzed and compared the relative expression levels of nine P. euphratica functional genes in different tissues. Our results indicate that a combination of multiple reference genes recommended by GrayNorm algorithm (e.g., a combination of Actin, EF1α, GAPDH, RP, UBQ in root) should be used instead of a single reference gene. These results are valuable for research of gene identification in different P. euphratica tissues.

DOI: 10.3390/ijms160920468
PubMed: 26343648
PubMed Central: PMC4613214


Affiliations:


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<term>Algorithms (MeSH)</term>
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<term>Desert Climate (MeSH)</term>
<term>Gene Expression Profiling (methods)</term>
<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Genes, Plant (MeSH)</term>
<term>Organ Specificity (genetics)</term>
<term>Populus (genetics)</term>
<term>RNA Stability (MeSH)</term>
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<term>Sensitivity and Specificity (MeSH)</term>
<term>Stress, Physiological (genetics)</term>
<term>Transcriptome (MeSH)</term>
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<term>Algorithmes (MeSH)</term>
<term>Analyse de profil d'expression de gènes (méthodes)</term>
<term>Biologie informatique (méthodes)</term>
<term>Climat désertique (MeSH)</term>
<term>Gènes de plante (MeSH)</term>
<term>Populus (génétique)</term>
<term>Reproductibilité des résultats (MeSH)</term>
<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
<term>Sensibilité et spécificité (MeSH)</term>
<term>Spécificité d'organe (génétique)</term>
<term>Stabilité de l'ARN (MeSH)</term>
<term>Stress physiologique (génétique)</term>
<term>Transcriptome (MeSH)</term>
</keywords>
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<term>Organ Specificity</term>
<term>Populus</term>
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<term>Populus</term>
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</keywords>
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<term>Computational Biology</term>
<term>Gene Expression Profiling</term>
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<term>Algorithms</term>
<term>Desert Climate</term>
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<term>Algorithmes</term>
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<term>Régulation de l'expression des gènes végétaux</term>
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<div type="abstract" xml:lang="en">Despite the unshakable status of reverse transcription-quantitative PCR in gene expression analysis, it has certain disadvantages, including that the results are highly dependent on the reference genes selected for data normalization. Since inappropriate endogenous control genes will lead to inaccurate target gene expression profiles, the validation of suitable internal reference genes is essential. Given the increasing interest in functional genes and genomics of Populus euphratica, a desert poplar showing extraordinary adaptation to salt stress, we evaluated the expression stability of ten candidate reference genes in P. euphratica roots, stems, and leaves under salt stress conditions. We used five algorithms, namely, ΔCt, NormFinder, geNorm, GrayNorm, and a rank aggregation method (RankAggreg) to identify suitable normalizers. To support the suitability of the identified reference genes and to compare the relative merits of these different algorithms, we analyzed and compared the relative expression levels of nine P. euphratica functional genes in different tissues. Our results indicate that a combination of multiple reference genes recommended by GrayNorm algorithm (e.g., a combination of Actin, EF1α, GAPDH, RP, UBQ in root) should be used instead of a single reference gene. These results are valuable for research of gene identification in different P. euphratica tissues.</div>
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<ISOAbbreviation>Int J Mol Sci</ISOAbbreviation>
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<ArticleTitle>Evaluation of Appropriate Reference Genes for Reverse Transcription-Quantitative PCR Studies in Different Tissues of a Desert Poplar via Comparision of Different Algorithms.</ArticleTitle>
<Pagination>
<MedlinePgn>20468-91</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.3390/ijms160920468</ELocationID>
<Abstract>
<AbstractText>Despite the unshakable status of reverse transcription-quantitative PCR in gene expression analysis, it has certain disadvantages, including that the results are highly dependent on the reference genes selected for data normalization. Since inappropriate endogenous control genes will lead to inaccurate target gene expression profiles, the validation of suitable internal reference genes is essential. Given the increasing interest in functional genes and genomics of Populus euphratica, a desert poplar showing extraordinary adaptation to salt stress, we evaluated the expression stability of ten candidate reference genes in P. euphratica roots, stems, and leaves under salt stress conditions. We used five algorithms, namely, ΔCt, NormFinder, geNorm, GrayNorm, and a rank aggregation method (RankAggreg) to identify suitable normalizers. To support the suitability of the identified reference genes and to compare the relative merits of these different algorithms, we analyzed and compared the relative expression levels of nine P. euphratica functional genes in different tissues. Our results indicate that a combination of multiple reference genes recommended by GrayNorm algorithm (e.g., a combination of Actin, EF1α, GAPDH, RP, UBQ in root) should be used instead of a single reference gene. These results are valuable for research of gene identification in different P. euphratica tissues.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Wang</LastName>
<ForeName>Hou-Ling</ForeName>
<Initials>HL</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. whling@bjfu.edu.cn.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>The Key Laboratory for Silviculture and Conservation of Ministry Education, College of Forestry, Beijing Forestry University, Beijing 100083, China. whling@bjfu.edu.cn.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Li</LastName>
<ForeName>Lan</ForeName>
<Initials>L</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. lilan@bjfu.edu.cn.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Tang</LastName>
<ForeName>Sha</ForeName>
<Initials>S</Initials>
<AffiliationInfo>
<Affiliation>Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China. tangsha@caas.cn.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Yuan</LastName>
<ForeName>Chao</ForeName>
<Initials>C</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. yuanchao@bjfu.edu.cn.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Tian</LastName>
<ForeName>Qianqian</ForeName>
<Initials>Q</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. tqqetqq@bjfu.edu.cn.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Su</LastName>
<ForeName>Yanyan</ForeName>
<Initials>Y</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. yanyansu@bjfu.edu.cn.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Li</LastName>
<ForeName>Hui-Guang</ForeName>
<Initials>HG</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. hg_li@bjfu.edu.cn.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Zhao</LastName>
<ForeName>Lin</ForeName>
<Initials>L</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. lynnzhao@bjfu.edu.cn.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Yin</LastName>
<ForeName>Weilun</ForeName>
<Initials>W</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. yinwl@bjfu.edu.cn.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>The Key Laboratory for Silviculture and Conservation of Ministry Education, College of Forestry, Beijing Forestry University, Beijing 100083, China. yinwl@bjfu.edu.cn.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Zhao</LastName>
<ForeName>Rui</ForeName>
<Initials>R</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. ruizhao@bjfu.edu.cn.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Xia</LastName>
<ForeName>Xinli</ForeName>
<Initials>X</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. xiaxl@bjfu.edu.cn.</Affiliation>
</AffiliationInfo>
</Author>
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<Language>eng</Language>
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<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
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<ArticleDate DateType="Electronic">
<Year>2015</Year>
<Month>08</Month>
<Day>28</Day>
</ArticleDate>
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<Country>Switzerland</Country>
<MedlineTA>Int J Mol Sci</MedlineTA>
<NlmUniqueID>101092791</NlmUniqueID>
<ISSNLinking>1422-0067</ISSNLinking>
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<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName UI="D000465" MajorTopicYN="Y">Algorithms</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D003889" MajorTopicYN="Y">Desert Climate</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D020869" MajorTopicYN="Y">Gene Expression Profiling</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D009928" MajorTopicYN="N">Organ Specificity</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D020871" MajorTopicYN="N">RNA Stability</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D012680" MajorTopicYN="N">Sensitivity and Specificity</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D013312" MajorTopicYN="N">Stress, Physiological</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
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<MeshHeading>
<DescriptorName UI="D059467" MajorTopicYN="N">Transcriptome</DescriptorName>
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<Keyword MajorTopicYN="N">Populus euphratica</Keyword>
<Keyword MajorTopicYN="N">normalization</Keyword>
<Keyword MajorTopicYN="N">reference genes</Keyword>
<Keyword MajorTopicYN="N">reverse transcription-quantitative PCR</Keyword>
<Keyword MajorTopicYN="N">salt stress</Keyword>
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<name sortKey="Tang, Sha" sort="Tang, Sha" uniqKey="Tang S" first="Sha" last="Tang">Sha Tang</name>
<name sortKey="Tian, Qianqian" sort="Tian, Qianqian" uniqKey="Tian Q" first="Qianqian" last="Tian">Qianqian Tian</name>
<name sortKey="Wang, Hou Ling" sort="Wang, Hou Ling" uniqKey="Wang H" first="Hou-Ling" last="Wang">Hou-Ling Wang</name>
<name sortKey="Xia, Xinli" sort="Xia, Xinli" uniqKey="Xia X" first="Xinli" last="Xia">Xinli Xia</name>
<name sortKey="Yin, Weilun" sort="Yin, Weilun" uniqKey="Yin W" first="Weilun" last="Yin">Weilun Yin</name>
<name sortKey="Yin, Weilun" sort="Yin, Weilun" uniqKey="Yin W" first="Weilun" last="Yin">Weilun Yin</name>
<name sortKey="Yuan, Chao" sort="Yuan, Chao" uniqKey="Yuan C" first="Chao" last="Yuan">Chao Yuan</name>
<name sortKey="Zhao, Lin" sort="Zhao, Lin" uniqKey="Zhao L" first="Lin" last="Zhao">Lin Zhao</name>
<name sortKey="Zhao, Rui" sort="Zhao, Rui" uniqKey="Zhao R" first="Rui" last="Zhao">Rui Zhao</name>
</country>
</tree>
</affiliations>
</record>

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