Identification of candidate reference genes for quantitative RT-PCR in Miscanthus sinensis subjected to various abiotic stresses
Quantitative real-time PCR (qRT-PCR) has been widely used for studying gene expression at the transcript level. Its accuracy usually relies on the reference genes that are utilized for data normalization. Miscanthus sinensis , a perennial C4 grass with high biomass and strong resistance to adversiti...
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| creator | Zhong, Minyi Yang, Xinying Hu, Yiyue Huang, Linkai Peng, Yan Li, Zhou Liu, Qiuxu Wang, Xia Zhang, Xinquan Nie, Gang |
| description | Quantitative real-time PCR (qRT-PCR) has been widely used for studying gene expression at the transcript level. Its accuracy usually relies on the reference genes that are utilized for data normalization.
Miscanthus sinensis
, a perennial C4 grass with high biomass and strong resistance to adversities, is often utilized as a high value energy crop. However, no reliable reference genes have been investigated for normalizing gene expression for this species. In this study, 12 candidate reference genes were selected to identify their stability under five different abiotic stress treatments (drought, salt, cadmium, chromium and arsenic) by using geNorm, NormFinder, BestKeeper and RefFinder softwares. The results showed that
18S rRNA
and
Unigene33312
were the best reference genes under drought treatments.
Unigene33312
and
Unigene33024
were found to be the most stably expressed genes under salt stress and Cd stress. Moreover,
Unigene33024
and
PP2A
were the most suitable reference genes under Cr stress and
Unigene33024
and
Sb09g019750
were deemed more suitable reference genes under As stress. In total, considering all the samples,
Unigene33024
and
PP2A
were the most stable genes while
ACTIN
and
Unigene26576
were the least stable reference genes for internal control. The expression patterns of two target genes (
Cu
/
Zn SOD
and
CAT
) were used to further verify those selected reference genes under different conditions. The results showed that the most and the least stable reference genes had clearly different expression patterns. This work comprehensively estimated the stability of reference genes in
M. sinensis
which may give insight to the reference genes selection in other tissues as well as other related varieties. These suggested reference genes would assist in further putative gene expression validation in
M. sinensis. |
| doi_str_mv | 10.1007/s11033-020-05392-9 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2384499962</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2384499962</sourcerecordid><originalsourceid>FETCH-LOGICAL-c375t-670b7846b8b87a2a8cbfcded570e7c82cb7024faff2697c71ff5159683bac1083</originalsourceid><addsrcrecordid>eNp9kU9rVDEUxYModqx-ARcScOMmmr8vyVKGqoWKUuo6JHk3NcNMXpvkFdz50Y1OVXBhNgnc3zn3kIPQc0ZfM0r1m8YYFYJQTglVwnJiH6ANU1oQabV5iDZUUEakUewEPWltRymVTKvH6ETwcSzTG_T9fIbSc8rR97wUvCQcfZnz7DvgCgkqlAj4Ggo0nJaKb1c_-D7oO8CXV-Tz9hLngj_mNnT969pwywVKy-Oxhh3EDjPuC77zNS9j6kNeeo649QqtQXuKHiW_b_Ds_j5FX96dXW0_kItP78-3by9IFFp1MmkatJFTMMFoz72JIcUZZqUp6Gh4DJpymXxKfLI6apaSYspORgQfGTXiFL06-t7U5XaF1t1hRIb93hcYuRwXRkpr7cQH-vIfdLestYx0jiuttVRWskHxIxXr0tr4KndT88HXb45R97Mfd-zHjX7cr36cHaIX99ZrOMD8R_K7kAGII9DGqFxD_bv7P7Y_AN5JnQQ</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2577745941</pqid></control><display><type>article</type><title>Identification of candidate reference genes for quantitative RT-PCR in Miscanthus sinensis subjected to various abiotic stresses</title><source>MEDLINE</source><source>SpringerNature Journals</source><creator>Zhong, Minyi ; Yang, Xinying ; Hu, Yiyue ; Huang, Linkai ; Peng, Yan ; Li, Zhou ; Liu, Qiuxu ; Wang, Xia ; Zhang, Xinquan ; Nie, Gang</creator><creatorcontrib>Zhong, Minyi ; Yang, Xinying ; Hu, Yiyue ; Huang, Linkai ; Peng, Yan ; Li, Zhou ; Liu, Qiuxu ; Wang, Xia ; Zhang, Xinquan ; Nie, Gang</creatorcontrib><description>Quantitative real-time PCR (qRT-PCR) has been widely used for studying gene expression at the transcript level. Its accuracy usually relies on the reference genes that are utilized for data normalization.
Miscanthus sinensis
, a perennial C4 grass with high biomass and strong resistance to adversities, is often utilized as a high value energy crop. However, no reliable reference genes have been investigated for normalizing gene expression for this species. In this study, 12 candidate reference genes were selected to identify their stability under five different abiotic stress treatments (drought, salt, cadmium, chromium and arsenic) by using geNorm, NormFinder, BestKeeper and RefFinder softwares. The results showed that
18S rRNA
and
Unigene33312
were the best reference genes under drought treatments.
Unigene33312
and
Unigene33024
were found to be the most stably expressed genes under salt stress and Cd stress. Moreover,
Unigene33024
and
PP2A
were the most suitable reference genes under Cr stress and
Unigene33024
and
Sb09g019750
were deemed more suitable reference genes under As stress. In total, considering all the samples,
Unigene33024
and
PP2A
were the most stable genes while
ACTIN
and
Unigene26576
were the least stable reference genes for internal control. The expression patterns of two target genes (
Cu
/
Zn SOD
and
CAT
) were used to further verify those selected reference genes under different conditions. The results showed that the most and the least stable reference genes had clearly different expression patterns. This work comprehensively estimated the stability of reference genes in
M. sinensis
which may give insight to the reference genes selection in other tissues as well as other related varieties. These suggested reference genes would assist in further putative gene expression validation in
M. sinensis.</description><identifier>ISSN: 0301-4851</identifier><identifier>EISSN: 1573-4978</identifier><identifier>DOI: 10.1007/s11033-020-05392-9</identifier><identifier>PMID: 32222917</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Actin ; Animal Anatomy ; Animal Biochemistry ; Arsenic ; Biomedical and Life Sciences ; Cadmium ; Chromium ; Drought ; Droughts ; Gene expression ; Gene Expression - genetics ; Gene Expression Profiling - methods ; Gene Expression Profiling - standards ; Gene Expression Regulation, Plant - genetics ; Genes, Plant - genetics ; Histology ; Life Sciences ; Miscanthus sinensis ; Morphology ; Original Article ; Poaceae - genetics ; Polymerase chain reaction ; Real-Time Polymerase Chain Reaction - methods ; Real-Time Polymerase Chain Reaction - standards ; Reference Standards ; Reverse Transcriptase Polymerase Chain Reaction - methods ; Reverse Transcriptase Polymerase Chain Reaction - standards ; rRNA 18S ; Stress, Physiological - genetics ; Transcription</subject><ispartof>Molecular biology reports, 2020-04, Vol.47 (4), p.2913-2927</ispartof><rights>Springer Nature B.V. 2020</rights><rights>Springer Nature B.V. 2020.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c375t-670b7846b8b87a2a8cbfcded570e7c82cb7024faff2697c71ff5159683bac1083</citedby><cites>FETCH-LOGICAL-c375t-670b7846b8b87a2a8cbfcded570e7c82cb7024faff2697c71ff5159683bac1083</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s11033-020-05392-9$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11033-020-05392-9$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32222917$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhong, Minyi</creatorcontrib><creatorcontrib>Yang, Xinying</creatorcontrib><creatorcontrib>Hu, Yiyue</creatorcontrib><creatorcontrib>Huang, Linkai</creatorcontrib><creatorcontrib>Peng, Yan</creatorcontrib><creatorcontrib>Li, Zhou</creatorcontrib><creatorcontrib>Liu, Qiuxu</creatorcontrib><creatorcontrib>Wang, Xia</creatorcontrib><creatorcontrib>Zhang, Xinquan</creatorcontrib><creatorcontrib>Nie, Gang</creatorcontrib><title>Identification of candidate reference genes for quantitative RT-PCR in Miscanthus sinensis subjected to various abiotic stresses</title><title>Molecular biology reports</title><addtitle>Mol Biol Rep</addtitle><addtitle>Mol Biol Rep</addtitle><description>Quantitative real-time PCR (qRT-PCR) has been widely used for studying gene expression at the transcript level. Its accuracy usually relies on the reference genes that are utilized for data normalization.
Miscanthus sinensis
, a perennial C4 grass with high biomass and strong resistance to adversities, is often utilized as a high value energy crop. However, no reliable reference genes have been investigated for normalizing gene expression for this species. In this study, 12 candidate reference genes were selected to identify their stability under five different abiotic stress treatments (drought, salt, cadmium, chromium and arsenic) by using geNorm, NormFinder, BestKeeper and RefFinder softwares. The results showed that
18S rRNA
and
Unigene33312
were the best reference genes under drought treatments.
Unigene33312
and
Unigene33024
were found to be the most stably expressed genes under salt stress and Cd stress. Moreover,
Unigene33024
and
PP2A
were the most suitable reference genes under Cr stress and
Unigene33024
and
Sb09g019750
were deemed more suitable reference genes under As stress. In total, considering all the samples,
Unigene33024
and
PP2A
were the most stable genes while
ACTIN
and
Unigene26576
were the least stable reference genes for internal control. The expression patterns of two target genes (
Cu
/
Zn SOD
and
CAT
) were used to further verify those selected reference genes under different conditions. The results showed that the most and the least stable reference genes had clearly different expression patterns. This work comprehensively estimated the stability of reference genes in
M. sinensis
which may give insight to the reference genes selection in other tissues as well as other related varieties. These suggested reference genes would assist in further putative gene expression validation in
M. sinensis.</description><subject>Actin</subject><subject>Animal Anatomy</subject><subject>Animal Biochemistry</subject><subject>Arsenic</subject><subject>Biomedical and Life Sciences</subject><subject>Cadmium</subject><subject>Chromium</subject><subject>Drought</subject><subject>Droughts</subject><subject>Gene expression</subject><subject>Gene Expression - genetics</subject><subject>Gene Expression Profiling - methods</subject><subject>Gene Expression Profiling - standards</subject><subject>Gene Expression Regulation, Plant - genetics</subject><subject>Genes, Plant - genetics</subject><subject>Histology</subject><subject>Life Sciences</subject><subject>Miscanthus sinensis</subject><subject>Morphology</subject><subject>Original Article</subject><subject>Poaceae - genetics</subject><subject>Polymerase chain reaction</subject><subject>Real-Time Polymerase Chain Reaction - methods</subject><subject>Real-Time Polymerase Chain Reaction - standards</subject><subject>Reference Standards</subject><subject>Reverse Transcriptase Polymerase Chain Reaction - methods</subject><subject>Reverse Transcriptase Polymerase Chain Reaction - standards</subject><subject>rRNA 18S</subject><subject>Stress, Physiological - genetics</subject><subject>Transcription</subject><issn>0301-4851</issn><issn>1573-4978</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kU9rVDEUxYModqx-ARcScOMmmr8vyVKGqoWKUuo6JHk3NcNMXpvkFdz50Y1OVXBhNgnc3zn3kIPQc0ZfM0r1m8YYFYJQTglVwnJiH6ANU1oQabV5iDZUUEakUewEPWltRymVTKvH6ETwcSzTG_T9fIbSc8rR97wUvCQcfZnz7DvgCgkqlAj4Ggo0nJaKb1c_-D7oO8CXV-Tz9hLngj_mNnT969pwywVKy-Oxhh3EDjPuC77zNS9j6kNeeo649QqtQXuKHiW_b_Ds_j5FX96dXW0_kItP78-3by9IFFp1MmkatJFTMMFoz72JIcUZZqUp6Gh4DJpymXxKfLI6apaSYspORgQfGTXiFL06-t7U5XaF1t1hRIb93hcYuRwXRkpr7cQH-vIfdLestYx0jiuttVRWskHxIxXr0tr4KndT88HXb45R97Mfd-zHjX7cr36cHaIX99ZrOMD8R_K7kAGII9DGqFxD_bv7P7Y_AN5JnQQ</recordid><startdate>20200401</startdate><enddate>20200401</enddate><creator>Zhong, Minyi</creator><creator>Yang, Xinying</creator><creator>Hu, Yiyue</creator><creator>Huang, Linkai</creator><creator>Peng, Yan</creator><creator>Li, Zhou</creator><creator>Liu, Qiuxu</creator><creator>Wang, Xia</creator><creator>Zhang, Xinquan</creator><creator>Nie, Gang</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>7TK</scope><scope>7TM</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>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</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>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20200401</creationdate><title>Identification of candidate reference genes for quantitative RT-PCR in Miscanthus sinensis subjected to various abiotic stresses</title><author>Zhong, Minyi ; Yang, Xinying ; Hu, Yiyue ; Huang, Linkai ; Peng, Yan ; Li, Zhou ; Liu, Qiuxu ; Wang, Xia ; Zhang, Xinquan ; Nie, Gang</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c375t-670b7846b8b87a2a8cbfcded570e7c82cb7024faff2697c71ff5159683bac1083</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Actin</topic><topic>Animal Anatomy</topic><topic>Animal Biochemistry</topic><topic>Arsenic</topic><topic>Biomedical and Life Sciences</topic><topic>Cadmium</topic><topic>Chromium</topic><topic>Drought</topic><topic>Droughts</topic><topic>Gene expression</topic><topic>Gene Expression - 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Academic</collection><jtitle>Molecular biology reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhong, Minyi</au><au>Yang, Xinying</au><au>Hu, Yiyue</au><au>Huang, Linkai</au><au>Peng, Yan</au><au>Li, Zhou</au><au>Liu, Qiuxu</au><au>Wang, Xia</au><au>Zhang, Xinquan</au><au>Nie, Gang</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of candidate reference genes for quantitative RT-PCR in Miscanthus sinensis subjected to various abiotic stresses</atitle><jtitle>Molecular biology reports</jtitle><stitle>Mol Biol Rep</stitle><addtitle>Mol Biol Rep</addtitle><date>2020-04-01</date><risdate>2020</risdate><volume>47</volume><issue>4</issue><spage>2913</spage><epage>2927</epage><pages>2913-2927</pages><issn>0301-4851</issn><eissn>1573-4978</eissn><abstract>Quantitative real-time PCR (qRT-PCR) has been widely used for studying gene expression at the transcript level. Its accuracy usually relies on the reference genes that are utilized for data normalization.
Miscanthus sinensis
, a perennial C4 grass with high biomass and strong resistance to adversities, is often utilized as a high value energy crop. However, no reliable reference genes have been investigated for normalizing gene expression for this species. In this study, 12 candidate reference genes were selected to identify their stability under five different abiotic stress treatments (drought, salt, cadmium, chromium and arsenic) by using geNorm, NormFinder, BestKeeper and RefFinder softwares. The results showed that
18S rRNA
and
Unigene33312
were the best reference genes under drought treatments.
Unigene33312
and
Unigene33024
were found to be the most stably expressed genes under salt stress and Cd stress. Moreover,
Unigene33024
and
PP2A
were the most suitable reference genes under Cr stress and
Unigene33024
and
Sb09g019750
were deemed more suitable reference genes under As stress. In total, considering all the samples,
Unigene33024
and
PP2A
were the most stable genes while
ACTIN
and
Unigene26576
were the least stable reference genes for internal control. The expression patterns of two target genes (
Cu
/
Zn SOD
and
CAT
) were used to further verify those selected reference genes under different conditions. The results showed that the most and the least stable reference genes had clearly different expression patterns. This work comprehensively estimated the stability of reference genes in
M. sinensis
which may give insight to the reference genes selection in other tissues as well as other related varieties. These suggested reference genes would assist in further putative gene expression validation in
M. sinensis.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>32222917</pmid><doi>10.1007/s11033-020-05392-9</doi><tpages>15</tpages></addata></record> |
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| ispartof | Molecular biology reports, 2020-04, Vol.47 (4), p.2913-2927 |
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| subjects | Actin Animal Anatomy Animal Biochemistry Arsenic Biomedical and Life Sciences Cadmium Chromium Drought Droughts Gene expression Gene Expression - genetics Gene Expression Profiling - methods Gene Expression Profiling - standards Gene Expression Regulation, Plant - genetics Genes, Plant - genetics Histology Life Sciences Miscanthus sinensis Morphology Original Article Poaceae - genetics Polymerase chain reaction Real-Time Polymerase Chain Reaction - methods Real-Time Polymerase Chain Reaction - standards Reference Standards Reverse Transcriptase Polymerase Chain Reaction - methods Reverse Transcriptase Polymerase Chain Reaction - standards rRNA 18S Stress, Physiological - genetics Transcription |
| title | Identification of candidate reference genes for quantitative RT-PCR in Miscanthus sinensis subjected to various abiotic stresses |
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