Assessment of reference gene stability in Rice stripe virus and Rice black streaked dwarf virus infection rice by quantitative Real-time PCR
Identifieur interne : 000978 ( Main/Exploration ); précédent : 000977; suivant : 000979Assessment of reference gene stability in Rice stripe virus and Rice black streaked dwarf virus infection rice by quantitative Real-time PCR
Auteurs : Peng Fang [République populaire de Chine] ; Rongfei Lu [République populaire de Chine] ; Feng Sun [République populaire de Chine] ; Ying Lan [République populaire de Chine] ; Wenbiao Shen [République populaire de Chine] ; Linlin Du [République populaire de Chine] ; Yijun Zhou [République populaire de Chine] ; Tong Zhou [République populaire de Chine]Source :
- Virology Journal [ 1743-422X ] ; 2015.
Abstract
Stably expressed reference gene(s) normalization is important for the understanding of gene expression patterns by quantitative Real-time PCR (RT-qPCR), particularly for
The expression of fourteen common used reference genes of Oryza sativa L. were evaluated by RT-qPCR in RSV and RBSDV infected rice plants. Suitable normalization reference gene(s) were identified by geNorm and NormFinder algorithms.
We proposed that the combination of two reference genes could obtain more accurate and reliable normalization of RT-qPCR results in RSV- and RBSDV-infected plants. This work therefore sheds light on establishing a standardized RT-qPCR procedure in RSV- and RBSDV-infected rice plants, and might serve as an important point for discovering complex regulatory networks and identifying genes relevant to biological processes or implicated in virus.
The online version of this article (doi:10.1186/s12985-015-0405-2) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12985-015-0405-2
PubMed: 26497487
PubMed Central: 4619528
Affiliations:
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Fang</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing, 210014 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff3">College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Sciences, Nanjing Agricultural University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Lu, Rongfei" sort="Lu, Rongfei" uniqKey="Lu R" first="Rongfei" last="Lu">Rongfei Lu</name><affiliation wicri:level="1"><nlm:aff id="Aff3">College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Sciences, Nanjing Agricultural University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Sun, Feng" sort="Sun, Feng" uniqKey="Sun F" first="Feng" last="Sun">Feng Sun</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing, 210014 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Lan, Ying" sort="Lan, Ying" uniqKey="Lan Y" first="Ying" last="Lan">Ying Lan</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing, 210014 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Shen, Wenbiao" sort="Shen, Wenbiao" uniqKey="Shen W" first="Wenbiao" last="Shen">Wenbiao Shen</name><affiliation wicri:level="1"><nlm:aff id="Aff3">College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Sciences, Nanjing Agricultural University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Du, Linlin" sort="Du, Linlin" uniqKey="Du L" first="Linlin" last="Du">Linlin Du</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing, 210014 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Zhou, Yijun" sort="Zhou, Yijun" uniqKey="Zhou Y" first="Yijun" last="Zhou">Yijun Zhou</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing, 210014 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Zhou, Tong" sort="Zhou, Tong" uniqKey="Zhou T" first="Tong" last="Zhou">Tong Zhou</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing, 210014 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Scientific Observing and Experimental Station of Crop Pests in Nanjing, Ministry of Agriculture, China, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author></analytic><series><title level="j">Virology Journal</title><idno type="eISSN">1743-422X</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Stably expressed reference gene(s) normalization is important for the understanding of gene expression patterns by quantitative Real-time PCR (RT-qPCR), particularly for <italic>Rice stripe virus</italic> (RSV) and <italic>Rice black streaked dwarf virus</italic> (RBSDV) that caused seriously damage on rice plants in China and Southeast Asia.</p></sec><sec><title>Methods</title><p>The expression of fourteen common used reference genes of Oryza sativa L. were evaluated by RT-qPCR in RSV and RBSDV infected rice plants. Suitable normalization reference gene(s) were identified by geNorm and NormFinder algorithms.</p></sec><sec><title>Results</title><p><italic>UBQ 10</italic> + <italic>GAPDH</italic> and <italic>UBC</italic> + <italic>Actin1</italic> were identified as suitable reference genes for RT-qPCR normalization under RSV and RBSDV infection, respectively. When using multiple reference genes, the expression patterns of <italic>OsPRIb</italic> and <italic>OsWRKY</italic>, two virus resistance genes, were approximately similar with that reported previously. Comparatively, by using single reference gene (<italic>TIP41-Like</italic>), a weaker inducible response was observed.</p></sec><sec><title>Conclusions</title><p>We proposed that the combination of two reference genes could obtain more accurate and reliable normalization of RT-qPCR results in RSV- and RBSDV-infected plants. This work therefore sheds light on establishing a standardized RT-qPCR procedure in RSV- and RBSDV-infected rice plants, and might serve as an important point for discovering complex regulatory networks and identifying genes relevant to biological processes or implicated in virus.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12985-015-0405-2) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Hibino, H" uniqKey="Hibino H">H Hibino</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kuribayashi, K" uniqKey="Kuribayashi K">K Kuribayashi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shikata, E" uniqKey="Shikata E">E Shikata</name></author><author><name sortKey="Kitagawa, Y" uniqKey="Kitagawa Y">Y 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last="Fang">Peng Fang</name></noRegion><name sortKey="Du, Linlin" sort="Du, Linlin" uniqKey="Du L" first="Linlin" last="Du">Linlin Du</name><name sortKey="Du, Linlin" sort="Du, Linlin" uniqKey="Du L" first="Linlin" last="Du">Linlin Du</name><name sortKey="Fang, Peng" sort="Fang, Peng" uniqKey="Fang P" first="Peng" last="Fang">Peng Fang</name><name sortKey="Fang, Peng" sort="Fang, Peng" uniqKey="Fang P" first="Peng" last="Fang">Peng Fang</name><name sortKey="Lan, Ying" sort="Lan, Ying" uniqKey="Lan Y" first="Ying" last="Lan">Ying Lan</name><name sortKey="Lan, Ying" sort="Lan, Ying" uniqKey="Lan Y" first="Ying" last="Lan">Ying Lan</name><name sortKey="Lu, Rongfei" sort="Lu, Rongfei" uniqKey="Lu R" first="Rongfei" last="Lu">Rongfei Lu</name><name sortKey="Shen, Wenbiao" sort="Shen, Wenbiao" uniqKey="Shen W" first="Wenbiao" last="Shen">Wenbiao Shen</name><name sortKey="Sun, Feng" sort="Sun, Feng" uniqKey="Sun F" first="Feng" last="Sun">Feng Sun</name><name sortKey="Sun, Feng" sort="Sun, Feng" uniqKey="Sun F" first="Feng" last="Sun">Feng Sun</name><name sortKey="Zhou, Tong" sort="Zhou, Tong" uniqKey="Zhou T" first="Tong" last="Zhou">Tong Zhou</name><name sortKey="Zhou, Tong" sort="Zhou, Tong" uniqKey="Zhou T" first="Tong" last="Zhou">Tong Zhou</name><name sortKey="Zhou, Yijun" sort="Zhou, Yijun" uniqKey="Zhou Y" first="Yijun" last="Zhou">Yijun Zhou</name><name sortKey="Zhou, Yijun" sort="Zhou, Yijun" uniqKey="Zhou Y" first="Yijun" last="Zhou">Yijun Zhou</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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