Selection of Reliable Reference Genes for Gene Expression Analysis under Abiotic Stresses in the Desert Biomass Willow, Salix psammophila.
Identifieur interne : 000B22 ( Main/Corpus ); précédent : 000B21; suivant : 000B23Selection of Reliable Reference Genes for Gene Expression Analysis under Abiotic Stresses in the Desert Biomass Willow, Salix psammophila.
Auteurs : Jianbo Li ; Huixia Jia ; Xiaojiao Han ; Jin Zhang ; Pei Sun ; Mengzhu Lu ; Jianjun HuSource :
- Frontiers in plant science [ 1664-462X ] ; 2016.
Abstract
Salix psammophila is a desert shrub willow that has extraordinary adaptation to abiotic stresses and plays an important role in maintaining local ecosystems. Moreover, S. psammophila is regarded as a promising biomass feedstock because of its high biomass yields and short rotation coppice cycle. However, few suitable reference genes (RGs) for quantitative real-time polymerase chain reaction (qRT-PCR) constrain the study on normalization of gene expression in S. psammophila until now. Here, we investigated the expression stabilities of 14 candidate RGs across tissue types and under four abiotic stress treatments, including heat, cold, salt, and drought treatments. After calculation of PCR efficiencies, three different software, NormFinder, geNorm, and BestKeeper were employed to analyze systematically the qRT-PCR data, and the outputs were merged by RankAggreg software. The optimal RGs selected for gene expression analysis were EF1α (Elongation factor-1 alpha) and OTU (OTU-like cysteine protease family protein) for different tissue types, UBC (Ubiquitin-conjugating enzyme E2) and LTA4H (Leukotriene A-4 hydrolase homolog) for heat treatment, HIS (Histone superfamily protein H3) and ARF2 (ADP-ribosylation factor 2) for cold treatment, OTU and ACT7 (Actin 7) for salt treatment, UBC and LTA4H for drought treatment. The expression of UBC, ARF2, and VHAC (V-type proton ATPase subunit C) varied the least across tissue types and under abiotic stresses. Furthermore, the relative genes expression profiles of one tissue-specific gene WOX1a (WUSCHEL-related homeobox 1a), and four stress-inducible genes, including Hsf-A2 (Heat shock transcription factors A2), CBF3 (C-repeat binding factor 3), HKT1 (High-Affinity K+ Transporter 1), and GST (Glutathione S-transferase), were conducted to confirm the validity of the RGs in this study. These results provided an important RGs application guideline for gene expression characterization in S. psammophila.
DOI: 10.3389/fpls.2016.01505
PubMed: 27761137
PubMed Central: PMC5050224
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Selection of Reliable Reference Genes for Gene Expression Analysis under Abiotic Stresses in the Desert Biomass Willow, <i>Salix psammophila</i>.</title><author><name sortKey="Li, Jianbo" sort="Li, Jianbo" uniqKey="Li J" first="Jianbo" last="Li">Jianbo Li</name><affiliation><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Jia, Huixia" sort="Jia, Huixia" uniqKey="Jia H" first="Huixia" last="Jia">Huixia Jia</name><affiliation><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry UniversityNanjing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Han, Xiaojiao" sort="Han, Xiaojiao" uniqKey="Han X" first="Xiaojiao" last="Han">Xiaojiao Han</name><affiliation><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Jin" sort="Zhang, Jin" uniqKey="Zhang J" first="Jin" last="Zhang">Jin Zhang</name><affiliation><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Sun, Pei" sort="Sun, Pei" uniqKey="Sun P" first="Pei" last="Sun">Pei Sun</name><affiliation><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Lu, Mengzhu" sort="Lu, Mengzhu" uniqKey="Lu M" first="Mengzhu" last="Lu">Mengzhu Lu</name><affiliation><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry UniversityNanjing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Hu, Jianjun" sort="Hu, Jianjun" uniqKey="Hu J" first="Jianjun" last="Hu">Jianjun Hu</name><affiliation><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry UniversityNanjing, China.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:27761137</idno><idno type="pmid">27761137</idno><idno type="doi">10.3389/fpls.2016.01505</idno><idno type="pmc">PMC5050224</idno><idno type="wicri:Area/Main/Corpus">000B22</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000B22</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Selection of Reliable Reference Genes for Gene Expression Analysis under Abiotic Stresses in the Desert Biomass Willow, <i>Salix psammophila</i>.</title><author><name sortKey="Li, Jianbo" sort="Li, Jianbo" uniqKey="Li J" first="Jianbo" last="Li">Jianbo Li</name><affiliation><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Jia, Huixia" sort="Jia, Huixia" uniqKey="Jia H" first="Huixia" last="Jia">Huixia Jia</name><affiliation><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry UniversityNanjing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Han, Xiaojiao" sort="Han, Xiaojiao" uniqKey="Han X" first="Xiaojiao" last="Han">Xiaojiao Han</name><affiliation><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Jin" sort="Zhang, Jin" uniqKey="Zhang J" first="Jin" last="Zhang">Jin Zhang</name><affiliation><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Sun, Pei" sort="Sun, Pei" uniqKey="Sun P" first="Pei" last="Sun">Pei Sun</name><affiliation><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Lu, Mengzhu" sort="Lu, Mengzhu" uniqKey="Lu M" first="Mengzhu" last="Lu">Mengzhu Lu</name><affiliation><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry UniversityNanjing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Hu, Jianjun" sort="Hu, Jianjun" uniqKey="Hu J" first="Jianjun" last="Hu">Jianjun Hu</name><affiliation><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry UniversityNanjing, China.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><i>Salix psammophila</i> is a desert shrub willow that has extraordinary adaptation to abiotic stresses and plays an important role in maintaining local ecosystems. Moreover, <i>S. psammophila</i> is regarded as a promising biomass feedstock because of its high biomass yields and short rotation coppice cycle. However, few suitable reference genes (RGs) for quantitative real-time polymerase chain reaction (qRT-PCR) constrain the study on normalization of gene expression in <i>S. psammophila</i> until now. Here, we investigated the expression stabilities of 14 candidate RGs across tissue types and under four abiotic stress treatments, including heat, cold, salt, and drought treatments. After calculation of PCR efficiencies, three different software, NormFinder, geNorm, and BestKeeper were employed to analyze systematically the qRT-PCR data, and the outputs were merged by RankAggreg software. The optimal RGs selected for gene expression analysis were <i>EF1</i>α (<i>Elongation factor-1 alpha</i>) and <i>OTU</i> (<i>OTU-like cysteine protease family protein</i>) for different tissue types, <i>UBC</i> (<i>Ubiquitin-conjugating enzyme E2</i>) and <i>LTA4H</i> (<i>Leukotriene A-4 hydrolase homolog</i>) for heat treatment, <i>HIS</i> (<i>Histone superfamily protein H3</i>) and <i>ARF2</i> (<i>ADP-ribosylation factor 2</i>) for cold treatment, <i>OTU</i> and <i>ACT7</i> (<i>Actin 7</i>) for salt treatment, <i>UBC</i> and <i>LTA4H</i> for drought treatment. The expression of <i>UBC</i>, <i>ARF2</i>, and <i>VHAC</i> (<i>V-type proton ATPase subunit C</i>) varied the least across tissue types and under abiotic stresses. Furthermore, the relative genes expression profiles of one tissue-specific gene <i>WOX1a</i> (<i>WUSCHEL-related homeobox 1a</i>), and four stress-inducible genes, including <i>Hsf-A2</i> (<i>Heat shock transcription factors A2</i>), <i>CBF3</i> (<i>C-repeat binding factor 3</i>), <i>HKT1</i> (<i>High-Affinity K<sup>+</sup> Transporter 1</i>), and <i>GST</i> (<i>Glutathione S-transferase</i>), were conducted to confirm the validity of the RGs in this study. These results provided an important RGs application guideline for gene expression characterization in <i>S. psammophila</i>.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">27761137</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>7</Volume><PubDate><Year>2016</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Selection of Reliable Reference Genes for Gene Expression Analysis under Abiotic Stresses in the Desert Biomass Willow, <i>Salix psammophila</i>.</ArticleTitle><Pagination><MedlinePgn>1505</MedlinePgn></Pagination><Abstract><AbstractText><i>Salix psammophila</i> is a desert shrub willow that has extraordinary adaptation to abiotic stresses and plays an important role in maintaining local ecosystems. Moreover, <i>S. psammophila</i> is regarded as a promising biomass feedstock because of its high biomass yields and short rotation coppice cycle. However, few suitable reference genes (RGs) for quantitative real-time polymerase chain reaction (qRT-PCR) constrain the study on normalization of gene expression in <i>S. psammophila</i> until now. Here, we investigated the expression stabilities of 14 candidate RGs across tissue types and under four abiotic stress treatments, including heat, cold, salt, and drought treatments. After calculation of PCR efficiencies, three different software, NormFinder, geNorm, and BestKeeper were employed to analyze systematically the qRT-PCR data, and the outputs were merged by RankAggreg software. The optimal RGs selected for gene expression analysis were <i>EF1</i>α (<i>Elongation factor-1 alpha</i>) and <i>OTU</i> (<i>OTU-like cysteine protease family protein</i>) for different tissue types, <i>UBC</i> (<i>Ubiquitin-conjugating enzyme E2</i>) and <i>LTA4H</i> (<i>Leukotriene A-4 hydrolase homolog</i>) for heat treatment, <i>HIS</i> (<i>Histone superfamily protein H3</i>) and <i>ARF2</i> (<i>ADP-ribosylation factor 2</i>) for cold treatment, <i>OTU</i> and <i>ACT7</i> (<i>Actin 7</i>) for salt treatment, <i>UBC</i> and <i>LTA4H</i> for drought treatment. The expression of <i>UBC</i>, <i>ARF2</i>, and <i>VHAC</i> (<i>V-type proton ATPase subunit C</i>) varied the least across tissue types and under abiotic stresses. Furthermore, the relative genes expression profiles of one tissue-specific gene <i>WOX1a</i> (<i>WUSCHEL-related homeobox 1a</i>), and four stress-inducible genes, including <i>Hsf-A2</i> (<i>Heat shock transcription factors A2</i>), <i>CBF3</i> (<i>C-repeat binding factor 3</i>), <i>HKT1</i> (<i>High-Affinity K<sup>+</sup> Transporter 1</i>), and <i>GST</i> (<i>Glutathione S-transferase</i>), were conducted to confirm the validity of the RGs in this study. These results provided an important RGs application guideline for gene expression characterization in <i>S. psammophila</i>.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Jianbo</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jia</LastName><ForeName>Huixia</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry UniversityNanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Han</LastName><ForeName>Xiaojiao</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Jin</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Pei</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>Mengzhu</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry UniversityNanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Jianjun</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry UniversityNanjing, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>10</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Salix psammophila</Keyword><Keyword MajorTopicYN="N">abiotic stresses</Keyword><Keyword MajorTopicYN="N">quantitative real-time PCR</Keyword><Keyword MajorTopicYN="N">reference genes</Keyword><Keyword MajorTopicYN="N">tissue types</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate 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