Validation of potential reference genes for qPCR in maize across abiotic stresses, hormone treatments, and tissue types
The reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a powerful and widely used technique for the measurement of gene expression. Reference genes, which serve as endogenous controls ensure that the results are accurate and reproducible, are vital for data normalization. To b...
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| description | The reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a powerful and widely used technique for the measurement of gene expression. Reference genes, which serve as endogenous controls ensure that the results are accurate and reproducible, are vital for data normalization. To bolster the literature on reference gene selection in maize, ten candidate reference genes, including eight traditionally used internal control genes and two potential candidate genes from our microarray datasets, were evaluated for expression level in maize across abiotic stresses (cold, heat, salinity, and PEG), phytohormone treatments (abscisic acid, salicylic acid, jasmonic acid, ethylene, and gibberellins), and different tissue types. Three analytical software packages, geNorm, NormFinder, and Bestkeeper, were used to assess the stability of reference gene expression. The results revealed that elongation factor 1 alpha (EF1α), tubulin beta (β-TUB), cyclophilin (CYP), and eukaryotic initiation factor 4A (EIF4A) were the most reliable reference genes for overall gene expression normalization in maize, while GRP (Glycine-rich RNA-binding protein), GLU1(beta-glucosidase), and UBQ9 (ubiquitin 9) were the least stable and most unsuitable genes. In addition, the suitability of EF1α, β-TUB, and their combination as reference genes was confirmed by validating the expression of WRKY50 in various samples. The current study indicates the appropriate reference genes for the urgent requirement of gene expression normalization in maize across certain abiotic stresses, hormones, and tissue types. |
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Reference genes, which serve as endogenous controls ensure that the results are accurate and reproducible, are vital for data normalization. To bolster the literature on reference gene selection in maize, ten candidate reference genes, including eight traditionally used internal control genes and two potential candidate genes from our microarray datasets, were evaluated for expression level in maize across abiotic stresses (cold, heat, salinity, and PEG), phytohormone treatments (abscisic acid, salicylic acid, jasmonic acid, ethylene, and gibberellins), and different tissue types. Three analytical software packages, geNorm, NormFinder, and Bestkeeper, were used to assess the stability of reference gene expression. The results revealed that elongation factor 1 alpha (EF1α), tubulin beta (β-TUB), cyclophilin (CYP), and eukaryotic initiation factor 4A (EIF4A) were the most reliable reference genes for overall gene expression normalization in maize, while GRP (Glycine-rich RNA-binding protein), GLU1(beta-glucosidase), and UBQ9 (ubiquitin 9) were the least stable and most unsuitable genes. In addition, the suitability of EF1α, β-TUB, and their combination as reference genes was confirmed by validating the expression of WRKY50 in various samples. The current study indicates the appropriate reference genes for the urgent requirement of gene expression normalization in maize across certain abiotic stresses, hormones, and tissue types.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0095445</identifier><identifier>PMID: 24810581</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Abiotic stress ; Abscisic acid ; Abscisic Acid - pharmacology ; Acids ; Algorithms ; Biology and life sciences ; Cold treatment ; Corn ; Cyclopentanes - pharmacology ; Cyclophilins - genetics ; Cytochrome P-450 ; DNA microarrays ; Droughts ; Ecology and Environmental Sciences ; Elongation ; Ethylenes - pharmacology ; Eukaryotic Initiation Factor-4A - genetics ; Gene expression ; Gene Expression Regulation, Plant - drug effects ; Genes ; Genes, Essential - drug effects ; Genes, Plant ; Genomes ; Gibberellins ; Gibberellins - pharmacology ; Glucosidase ; Glycine ; Hormones ; Initiation factor eIF-4A ; Jasmonic acid ; Laboratories ; Lolium perenne ; Molecular biology ; Oryza ; Oxylipins - pharmacology ; Peptide Elongation Factor 1 - genetics ; Plant biology ; Plant hormones ; Plant sciences ; Polyethylene glycol ; Polymerase chain reaction ; Protein binding ; Real-Time Polymerase Chain Reaction - methods ; Researchers ; Reverse transcription ; Ribonucleic acid ; RNA ; RNA-binding protein ; Salicylic acid ; Salicylic Acid - pharmacology ; Software packages ; Stability analysis ; Stresses ; Studies ; Transcription factors ; Tubulin ; Ubiquitin ; Zea mays - genetics</subject><ispartof>PloS one, 2014-05, Vol.9 (5), p.e95445</ispartof><rights>COPYRIGHT 2014 Public Library of Science</rights><rights>2014 Lin et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2014 Lin et al 2014 Lin et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-ceff888f606c8bb3828ca156b9c96e137fb804cb3eec4ce73082eaab0f69d6a33</citedby><cites>FETCH-LOGICAL-c692t-ceff888f606c8bb3828ca156b9c96e137fb804cb3eec4ce73082eaab0f69d6a33</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014480/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014480/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24810581$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lin, Yueai</creatorcontrib><creatorcontrib>Zhang, Chenlu</creatorcontrib><creatorcontrib>Lan, Hai</creatorcontrib><creatorcontrib>Gao, Shibin</creatorcontrib><creatorcontrib>Liu, Hailan</creatorcontrib><creatorcontrib>Liu, Jian</creatorcontrib><creatorcontrib>Cao, Moju</creatorcontrib><creatorcontrib>Pan, Guangtang</creatorcontrib><creatorcontrib>Rong, Tingzhao</creatorcontrib><creatorcontrib>Zhang, Suzhi</creatorcontrib><title>Validation of potential reference genes for qPCR in maize across abiotic stresses, hormone treatments, and tissue types</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a powerful and widely used technique for the measurement of gene expression. Reference genes, which serve as endogenous controls ensure that the results are accurate and reproducible, are vital for data normalization. To bolster the literature on reference gene selection in maize, ten candidate reference genes, including eight traditionally used internal control genes and two potential candidate genes from our microarray datasets, were evaluated for expression level in maize across abiotic stresses (cold, heat, salinity, and PEG), phytohormone treatments (abscisic acid, salicylic acid, jasmonic acid, ethylene, and gibberellins), and different tissue types. Three analytical software packages, geNorm, NormFinder, and Bestkeeper, were used to assess the stability of reference gene expression. The results revealed that elongation factor 1 alpha (EF1α), tubulin beta (β-TUB), cyclophilin (CYP), and eukaryotic initiation factor 4A (EIF4A) were the most reliable reference genes for overall gene expression normalization in maize, while GRP (Glycine-rich RNA-binding protein), GLU1(beta-glucosidase), and UBQ9 (ubiquitin 9) were the least stable and most unsuitable genes. In addition, the suitability of EF1α, β-TUB, and their combination as reference genes was confirmed by validating the expression of WRKY50 in various samples. The current study indicates the appropriate reference genes for the urgent requirement of gene expression normalization in maize across certain abiotic stresses, hormones, and tissue types.</description><subject>Abiotic stress</subject><subject>Abscisic acid</subject><subject>Abscisic Acid - pharmacology</subject><subject>Acids</subject><subject>Algorithms</subject><subject>Biology and life sciences</subject><subject>Cold treatment</subject><subject>Corn</subject><subject>Cyclopentanes - pharmacology</subject><subject>Cyclophilins - genetics</subject><subject>Cytochrome P-450</subject><subject>DNA microarrays</subject><subject>Droughts</subject><subject>Ecology and Environmental Sciences</subject><subject>Elongation</subject><subject>Ethylenes - pharmacology</subject><subject>Eukaryotic Initiation Factor-4A - genetics</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Plant - drug effects</subject><subject>Genes</subject><subject>Genes, Essential - drug effects</subject><subject>Genes, Plant</subject><subject>Genomes</subject><subject>Gibberellins</subject><subject>Gibberellins - pharmacology</subject><subject>Glucosidase</subject><subject>Glycine</subject><subject>Hormones</subject><subject>Initiation factor eIF-4A</subject><subject>Jasmonic acid</subject><subject>Laboratories</subject><subject>Lolium perenne</subject><subject>Molecular biology</subject><subject>Oryza</subject><subject>Oxylipins - pharmacology</subject><subject>Peptide Elongation Factor 1 - genetics</subject><subject>Plant biology</subject><subject>Plant hormones</subject><subject>Plant sciences</subject><subject>Polyethylene glycol</subject><subject>Polymerase chain reaction</subject><subject>Protein binding</subject><subject>Real-Time Polymerase Chain Reaction - methods</subject><subject>Researchers</subject><subject>Reverse transcription</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA-binding protein</subject><subject>Salicylic acid</subject><subject>Salicylic Acid - pharmacology</subject><subject>Software packages</subject><subject>Stability analysis</subject><subject>Stresses</subject><subject>Studies</subject><subject>Transcription factors</subject><subject>Tubulin</subject><subject>Ubiquitin</subject><subject>Zea mays - 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Reference genes, which serve as endogenous controls ensure that the results are accurate and reproducible, are vital for data normalization. To bolster the literature on reference gene selection in maize, ten candidate reference genes, including eight traditionally used internal control genes and two potential candidate genes from our microarray datasets, were evaluated for expression level in maize across abiotic stresses (cold, heat, salinity, and PEG), phytohormone treatments (abscisic acid, salicylic acid, jasmonic acid, ethylene, and gibberellins), and different tissue types. Three analytical software packages, geNorm, NormFinder, and Bestkeeper, were used to assess the stability of reference gene expression. The results revealed that elongation factor 1 alpha (EF1α), tubulin beta (β-TUB), cyclophilin (CYP), and eukaryotic initiation factor 4A (EIF4A) were the most reliable reference genes for overall gene expression normalization in maize, while GRP (Glycine-rich RNA-binding protein), GLU1(beta-glucosidase), and UBQ9 (ubiquitin 9) were the least stable and most unsuitable genes. In addition, the suitability of EF1α, β-TUB, and their combination as reference genes was confirmed by validating the expression of WRKY50 in various samples. The current study indicates the appropriate reference genes for the urgent requirement of gene expression normalization in maize across certain abiotic stresses, hormones, and tissue types.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24810581</pmid><doi>10.1371/journal.pone.0095445</doi><oa>free_for_read</oa></addata></record> |
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| recordid | cdi_plos_journals_1522726453 |
| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Abiotic stress Abscisic acid Abscisic Acid - pharmacology Acids Algorithms Biology and life sciences Cold treatment Corn Cyclopentanes - pharmacology Cyclophilins - genetics Cytochrome P-450 DNA microarrays Droughts Ecology and Environmental Sciences Elongation Ethylenes - pharmacology Eukaryotic Initiation Factor-4A - genetics Gene expression Gene Expression Regulation, Plant - drug effects Genes Genes, Essential - drug effects Genes, Plant Genomes Gibberellins Gibberellins - pharmacology Glucosidase Glycine Hormones Initiation factor eIF-4A Jasmonic acid Laboratories Lolium perenne Molecular biology Oryza Oxylipins - pharmacology Peptide Elongation Factor 1 - genetics Plant biology Plant hormones Plant sciences Polyethylene glycol Polymerase chain reaction Protein binding Real-Time Polymerase Chain Reaction - methods Researchers Reverse transcription Ribonucleic acid RNA RNA-binding protein Salicylic acid Salicylic Acid - pharmacology Software packages Stability analysis Stresses Studies Transcription factors Tubulin Ubiquitin Zea mays - genetics |
| title | Validation of potential reference genes for qPCR in maize across abiotic stresses, hormone treatments, and tissue types |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-05T06%3A54%3A20IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Validation%20of%20potential%20reference%20genes%20for%20qPCR%20in%20maize%20across%20abiotic%20stresses,%20hormone%20treatments,%20and%20tissue%20types&rft.jtitle=PloS%20one&rft.au=Lin,%20Yueai&rft.date=2014-05-08&rft.volume=9&rft.issue=5&rft.spage=e95445&rft.pages=e95445-&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0095445&rft_dat=%3Cgale_plos_%3EA418634562%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1522726453&rft_id=info:pmid/24810581&rft_galeid=A418634562&rft_doaj_id=oai_doaj_org_article_5c27e05f413c489b859590e17d08dfae&rfr_iscdi=true |