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Selection and validation of reliable reference genes in Gossypium raimondii
Objective To identify reliable reference genes for gene expression analysis in Gossypium raimondii . Results Five different software tools, geNorm, NormFinder, BestKeeper, ReFinder and ∆Ct method were employed to analyze the qRT-PCR data systematically of 12 housekeeping genes. SAD and TUA11 showed...
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| Published in: | Biotechnology letters 2015-07, Vol.37 (7), p.1483-1493 |
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| Main Authors: | , , , |
| Format: | Article |
| Language: | English |
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| cites | cdi_FETCH-LOGICAL-c471t-aed0b3a32c8ec4481211928e9ad640cd6eecaffbefc55084ae8f2f1a5f44af5b3 |
| container_end_page | 1493 |
| container_issue | 7 |
| container_start_page | 1483 |
| container_title | Biotechnology letters |
| container_volume | 37 |
| creator | Sun, Runrun He, Qiuling Zhang, Baohong Wang, Qinglian |
| description | Objective
To identify reliable reference genes for gene expression analysis in
Gossypium raimondii
.
Results
Five different software tools, geNorm, NormFinder, BestKeeper, ReFinder and ∆Ct method were employed to analyze the qRT-PCR data systematically of 12 housekeeping genes. SAD and TUA11 showed relatively stable expression levels in all tissues (i.e. leaves, shoots, buds, and sepals). We then limited our analysis to each plant part and identified tissue-specific reference genes. Our results showed TUA11, TUB6 and EF1a, EF1a, MZA and GAPC2, MZA, GAPC2, SAD and TUA11, and UBQ and MZA were reliable reference genes in leaves, shoots, buds, and sepals, respectively.
Conclusion
Some genes were commonly identified as candidate reference genes in more than two tissue, while others were tissue-specific. Thus, our study allows choosing an appropriate control gene based on sampling for gene expression analysis. |
| doi_str_mv | 10.1007/s10529-015-1810-8 |
| format | article |
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To identify reliable reference genes for gene expression analysis in
Gossypium raimondii
.
Results
Five different software tools, geNorm, NormFinder, BestKeeper, ReFinder and ∆Ct method were employed to analyze the qRT-PCR data systematically of 12 housekeeping genes. SAD and TUA11 showed relatively stable expression levels in all tissues (i.e. leaves, shoots, buds, and sepals). We then limited our analysis to each plant part and identified tissue-specific reference genes. Our results showed TUA11, TUB6 and EF1a, EF1a, MZA and GAPC2, MZA, GAPC2, SAD and TUA11, and UBQ and MZA were reliable reference genes in leaves, shoots, buds, and sepals, respectively.
Conclusion
Some genes were commonly identified as candidate reference genes in more than two tissue, while others were tissue-specific. Thus, our study allows choosing an appropriate control gene based on sampling for gene expression analysis.</description><identifier>ISSN: 0141-5492</identifier><identifier>EISSN: 1573-6776</identifier><identifier>DOI: 10.1007/s10529-015-1810-8</identifier><identifier>PMID: 26003093</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Applied Microbiology ; Biochemistry ; Biomedical and Life Sciences ; Biotechnology ; Buds ; Computer programs ; Gene expression ; Gene Expression Profiling - standards ; Gene Expression Regulation, Plant - genetics ; Genes ; Genes, Plant - genetics ; Gossypium ; Gossypium - genetics ; Gossypium - metabolism ; Leaves ; Life Sciences ; Microbiology ; Original Research Paper ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Plants (organisms) ; Real-Time Polymerase Chain Reaction ; Sampling ; Shoots ; Software</subject><ispartof>Biotechnology letters, 2015-07, Vol.37 (7), p.1483-1493</ispartof><rights>Springer Science+Business Media Dordrecht 2015</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c471t-aed0b3a32c8ec4481211928e9ad640cd6eecaffbefc55084ae8f2f1a5f44af5b3</citedby><cites>FETCH-LOGICAL-c471t-aed0b3a32c8ec4481211928e9ad640cd6eecaffbefc55084ae8f2f1a5f44af5b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26003093$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sun, Runrun</creatorcontrib><creatorcontrib>He, Qiuling</creatorcontrib><creatorcontrib>Zhang, Baohong</creatorcontrib><creatorcontrib>Wang, Qinglian</creatorcontrib><title>Selection and validation of reliable reference genes in Gossypium raimondii</title><title>Biotechnology letters</title><addtitle>Biotechnol Lett</addtitle><addtitle>Biotechnol Lett</addtitle><description>Objective
To identify reliable reference genes for gene expression analysis in
Gossypium raimondii
.
Results
Five different software tools, geNorm, NormFinder, BestKeeper, ReFinder and ∆Ct method were employed to analyze the qRT-PCR data systematically of 12 housekeeping genes. SAD and TUA11 showed relatively stable expression levels in all tissues (i.e. leaves, shoots, buds, and sepals). We then limited our analysis to each plant part and identified tissue-specific reference genes. Our results showed TUA11, TUB6 and EF1a, EF1a, MZA and GAPC2, MZA, GAPC2, SAD and TUA11, and UBQ and MZA were reliable reference genes in leaves, shoots, buds, and sepals, respectively.
Conclusion
Some genes were commonly identified as candidate reference genes in more than two tissue, while others were tissue-specific. Thus, our study allows choosing an appropriate control gene based on sampling for gene expression analysis.</description><subject>Applied Microbiology</subject><subject>Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Buds</subject><subject>Computer programs</subject><subject>Gene expression</subject><subject>Gene Expression Profiling - standards</subject><subject>Gene Expression Regulation, Plant - genetics</subject><subject>Genes</subject><subject>Genes, Plant - genetics</subject><subject>Gossypium</subject><subject>Gossypium - genetics</subject><subject>Gossypium - metabolism</subject><subject>Leaves</subject><subject>Life Sciences</subject><subject>Microbiology</subject><subject>Original Research Paper</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Plants (organisms)</subject><subject>Real-Time Polymerase Chain Reaction</subject><subject>Sampling</subject><subject>Shoots</subject><subject>Software</subject><issn>0141-5492</issn><issn>1573-6776</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><recordid>eNqNkU-LFDEQxYMo7rj6AbxIgxcvrVX530dZdBUXPKjnkE5Xlizd6TGZFvbbm3FWEUH0lAr51avUe4w9RXiJAOZVRVB86AFVjxaht_fYDpURvTZG32c7QIm9kgM_Y49qvQGAwYB5yM64BhAwiB378IlmCoe05s7nqfvm5zT5H9c1doXm5MeZWhGpUA7UXVOm2qXcXa613u7TtnTFp2XNU0qP2YPo50pP7s5z9uXtm88X7_qrj5fvL15f9UEaPPSeJhiFFzxYClJa5IgDtzT4SUsIkyYKPsaRYlAKrPRkI4_oVZTSRzWKc_bipLsv69eN6sEtqQaaZ59p3apDg3YQilvxH2jzyBor-L9RbbVsf1VH9Pkf6M26ldx2PlJKW6mEbhSeqFCaV81Cty9p8eXWIbhjfu6Un2v5uWN-zraeZ3fK27jQ9KvjZ2AN4Cegtqd8TeW30X9V_Q4vmKTP</recordid><startdate>20150701</startdate><enddate>20150701</enddate><creator>Sun, Runrun</creator><creator>He, Qiuling</creator><creator>Zhang, Baohong</creator><creator>Wang, Qinglian</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QL</scope><scope>7QR</scope><scope>7T7</scope><scope>7TB</scope><scope>7U5</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>L6V</scope><scope>L7M</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>Q9U</scope><scope>7X8</scope><scope>7QO</scope></search><sort><creationdate>20150701</creationdate><title>Selection and validation of reliable reference genes in Gossypium raimondii</title><author>Sun, Runrun ; He, Qiuling ; Zhang, Baohong ; Wang, Qinglian</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c471t-aed0b3a32c8ec4481211928e9ad640cd6eecaffbefc55084ae8f2f1a5f44af5b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Applied Microbiology</topic><topic>Biochemistry</topic><topic>Biomedical and Life Sciences</topic><topic>Biotechnology</topic><topic>Buds</topic><topic>Computer programs</topic><topic>Gene expression</topic><topic>Gene Expression Profiling - standards</topic><topic>Gene Expression Regulation, Plant - genetics</topic><topic>Genes</topic><topic>Genes, Plant - genetics</topic><topic>Gossypium</topic><topic>Gossypium - genetics</topic><topic>Gossypium - metabolism</topic><topic>Leaves</topic><topic>Life Sciences</topic><topic>Microbiology</topic><topic>Original Research Paper</topic><topic>Plant Proteins - genetics</topic><topic>Plant Proteins - metabolism</topic><topic>Plants (organisms)</topic><topic>Real-Time Polymerase Chain Reaction</topic><topic>Sampling</topic><topic>Shoots</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sun, Runrun</creatorcontrib><creatorcontrib>He, Qiuling</creatorcontrib><creatorcontrib>Zhang, Baohong</creatorcontrib><creatorcontrib>Wang, Qinglian</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Chemoreception Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>Health & Medical Collection (Proquest)</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Engineering Collection</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>Science Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>ProQuest Biological Science Journals</collection><collection>Engineering Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>Biotechnology Research Abstracts</collection><jtitle>Biotechnology letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sun, Runrun</au><au>He, Qiuling</au><au>Zhang, Baohong</au><au>Wang, Qinglian</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Selection and validation of reliable reference genes in Gossypium raimondii</atitle><jtitle>Biotechnology letters</jtitle><stitle>Biotechnol Lett</stitle><addtitle>Biotechnol Lett</addtitle><date>2015-07-01</date><risdate>2015</risdate><volume>37</volume><issue>7</issue><spage>1483</spage><epage>1493</epage><pages>1483-1493</pages><issn>0141-5492</issn><eissn>1573-6776</eissn><abstract>Objective
To identify reliable reference genes for gene expression analysis in
Gossypium raimondii
.
Results
Five different software tools, geNorm, NormFinder, BestKeeper, ReFinder and ∆Ct method were employed to analyze the qRT-PCR data systematically of 12 housekeeping genes. SAD and TUA11 showed relatively stable expression levels in all tissues (i.e. leaves, shoots, buds, and sepals). We then limited our analysis to each plant part and identified tissue-specific reference genes. Our results showed TUA11, TUB6 and EF1a, EF1a, MZA and GAPC2, MZA, GAPC2, SAD and TUA11, and UBQ and MZA were reliable reference genes in leaves, shoots, buds, and sepals, respectively.
Conclusion
Some genes were commonly identified as candidate reference genes in more than two tissue, while others were tissue-specific. Thus, our study allows choosing an appropriate control gene based on sampling for gene expression analysis.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>26003093</pmid><doi>10.1007/s10529-015-1810-8</doi><tpages>11</tpages></addata></record> |
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| identifier | ISSN: 0141-5492 |
| ispartof | Biotechnology letters, 2015-07, Vol.37 (7), p.1483-1493 |
| issn | 0141-5492 1573-6776 |
| language | eng |
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| source | Springer Nature |
| subjects | Applied Microbiology Biochemistry Biomedical and Life Sciences Biotechnology Buds Computer programs Gene expression Gene Expression Profiling - standards Gene Expression Regulation, Plant - genetics Genes Genes, Plant - genetics Gossypium Gossypium - genetics Gossypium - metabolism Leaves Life Sciences Microbiology Original Research Paper Plant Proteins - genetics Plant Proteins - metabolism Plants (organisms) Real-Time Polymerase Chain Reaction Sampling Shoots Software |
| title | Selection and validation of reliable reference genes in Gossypium raimondii |
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