Selection of suitable reference genes for normalization of quantitative RT-PCR (RT-qPCR) expression data across twelve tissues of riverine buffaloes (Bubalus bubalis)
Identifieur interne : 000694 ( Main/Exploration ); précédent : 000693; suivant : 000695Selection of suitable reference genes for normalization of quantitative RT-PCR (RT-qPCR) expression data across twelve tissues of riverine buffaloes (Bubalus bubalis)
Auteurs : Ramneek Kaur [Inde] ; Monika Sodhi [Inde] ; Ankita Sharma [Inde] ; Vijay Lakshmi Sharma [Inde] ; Preeti Verma [Inde] ; Shelesh Kumar Swami [Inde] ; Parvesh Kumari [Inde] ; Manishi Mukesh [Inde]Source :
- PLoS ONE [ 1932-6203 ] ; 2018.
Abstract
Selection of reference genes has become an integral step in any real time quantitative PCR (RT-qPCR) based expression studies. The importance of this study stems from the fact that riverine buffaloes are major dairy species of Indian sub-continent and the information generated here will be of great interest to the investigators engaged in functional genomic studies of this important livestock species. In this study, an effort was made to evaluate a panel of 10 candidate reference genes (glyceraldehyde 3-phosphate dehydrogenase (
Url:
DOI: 10.1371/journal.pone.0191558
PubMed: 29509770
PubMed Central: 5839537
Affiliations:
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Resources, Karnal, Haryana, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana</wicri:regionArea><wicri:noRegion>Haryana</wicri:noRegion></affiliation></author><author><name sortKey="Sharma, Vijay Lakshmi" sort="Sharma, Vijay Lakshmi" uniqKey="Sharma V" first="Vijay Lakshmi" last="Sharma">Vijay Lakshmi Sharma</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Department of Zoology, Panjab University, Chandigarh, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Zoology, Panjab University, Chandigarh</wicri:regionArea><wicri:noRegion>Chandigarh</wicri:noRegion></affiliation></author><author><name sortKey="Verma, Preeti" sort="Verma, Preeti" uniqKey="Verma P" first="Preeti" last="Verma">Preeti Verma</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Animal 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wicri:level="1"><nlm:aff id="aff002"><addr-line>Department of Zoology, Panjab University, Chandigarh, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Zoology, Panjab University, Chandigarh</wicri:regionArea><wicri:noRegion>Chandigarh</wicri:noRegion></affiliation></author><author><name sortKey="Sodhi, Monika" sort="Sodhi, Monika" uniqKey="Sodhi M" first="Monika" last="Sodhi">Monika Sodhi</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana</wicri:regionArea><wicri:noRegion>Haryana</wicri:noRegion></affiliation></author><author><name sortKey="Sharma, Ankita" sort="Sharma, Ankita" uniqKey="Sharma A" first="Ankita" last="Sharma">Ankita Sharma</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana</wicri:regionArea><wicri:noRegion>Haryana</wicri:noRegion></affiliation></author><author><name sortKey="Sharma, Vijay Lakshmi" sort="Sharma, Vijay Lakshmi" uniqKey="Sharma V" first="Vijay Lakshmi" last="Sharma">Vijay Lakshmi Sharma</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Department of Zoology, Panjab University, Chandigarh, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Zoology, Panjab University, Chandigarh</wicri:regionArea><wicri:noRegion>Chandigarh</wicri:noRegion></affiliation></author><author><name sortKey="Verma, Preeti" sort="Verma, Preeti" uniqKey="Verma P" first="Preeti" last="Verma">Preeti Verma</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana</wicri:regionArea><wicri:noRegion>Haryana</wicri:noRegion></affiliation></author><author><name sortKey="Swami, Shelesh Kumar" sort="Swami, Shelesh Kumar" uniqKey="Swami S" first="Shelesh Kumar" last="Swami">Shelesh Kumar Swami</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana</wicri:regionArea><wicri:noRegion>Haryana</wicri:noRegion></affiliation></author><author><name sortKey="Kumari, Parvesh" sort="Kumari, Parvesh" uniqKey="Kumari P" first="Parvesh" last="Kumari">Parvesh Kumari</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana</wicri:regionArea><wicri:noRegion>Haryana</wicri:noRegion></affiliation></author><author><name sortKey="Mukesh, Manishi" sort="Mukesh, Manishi" uniqKey="Mukesh M" first="Manishi" last="Mukesh">Manishi Mukesh</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana</wicri:regionArea><wicri:noRegion>Haryana</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2018">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Selection of reference genes has become an integral step in any real time quantitative PCR (RT-qPCR) based expression studies. The importance of this study stems from the fact that riverine buffaloes are major dairy species of Indian sub-continent and the information generated here will be of great interest to the investigators engaged in functional genomic studies of this important livestock species. In this study, an effort was made to evaluate a panel of 10 candidate reference genes (glyceraldehyde 3-phosphate dehydrogenase (<italic>GAPDH)</italic>, beta- actin (<italic>ACTB</italic>), ubiquitously expressed transcript (<italic>UXT</italic>), ribosomal protein S15 (<italic>RPS15</italic>), ribosomal protein L-4 (<italic>RPL4</italic>), ribosomal protein S9 (<italic>RPS9</italic>), ribosomal protein S23 (<italic>RPS23</italic>), hydroxymethylbilane synthase (<italic>HMBS</italic>), β2 Microglobulin (<italic>β2M</italic>) and eukaryotic translation elongation factor 1 alpha 1 (<italic>EEF1A1</italic>) across 12 tissues (mammary gland, kidney, spleen, liver, heart, intestine, ovary, lung, muscle, brain, subcutaneous fat and testis) of riverine buffaloes. In addition to overall analysis, tissue wise evaluation of expression stability of individual RG was also performed. Three different algorithms provided in geNorm, NormFinder and BestKeeper softwares were used to evaluate the stability of 10 potential reference genes from different functional classes. The M-value given by geNorm ranged from 0.9797 (<italic>RPS9</italic> and <italic>UXT</italic>) to 1.7362 (<italic>RPS15</italic>). From the most stable to the least stable, genes were ranked as: <italic>UXT/RPS9> RPL4> RPS23> EEF1A1> ACTB> HMBS> GAPDH> B2M> RPS15</italic>. While NormFinder analysis ranked the genes as: <italic>UXT> RPS23> RPL4> RPS9> EEF1A1> HMBS> ACTB> β2M> GAPDH> RPS15</italic>. Based on the crossing point SD value and range of fold change expression, BestKeeper analysis ranked the genes as: <italic>RPS9> RPS23/UXT> RPL4> GAPDH> EEF1A1> ACTB> HMBS> β2M> RPS15</italic>. Overall the study has identified <italic>RPS23</italic>, <italic>RPS9</italic>, <italic>RPL4</italic> and <italic>UXT</italic> genes to be the most stable and appropriate RGs that could be utilized for normalization of transcriptional data in various tissues of buffaloes. This manuscript thus provide useful information on panel of reference genes that could be helpful for researchers conducting functional genomic studies in riverine buffaloes.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Livak, Kj" uniqKey="Livak K">KJ Livak</name></author><author><name sortKey="Schmittgen, Td" uniqKey="Schmittgen T">TD Schmittgen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bustin, S A" uniqKey="Bustin S">S.A Bustin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fleige, S" uniqKey="Fleige S">S Fleige</name></author><author><name sortKey="Pfaffl, Mw" uniqKey="Pfaffl M">MW Pfaffl</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lisowski, P" uniqKey="Lisowski P">P Lisowski</name></author><author><name sortKey="Pierzchala, M" uniqKey="Pierzchala M">M 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sortKey="Infascelli, F" uniqKey="Infascelli F">F Infascelli</name></author><author><name sortKey="Stanca, Am" uniqKey="Stanca A">AM Stanca</name></author><author><name sortKey="Faccioli, P" uniqKey="Faccioli P">P Faccioli</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Suzuki, T" uniqKey="Suzuki T">T Suzuki</name></author><author><name sortKey="Higgins, Pj" uniqKey="Higgins P">PJ Higgins</name></author><author><name sortKey="Crawford, Dr" uniqKey="Crawford D">DR Crawford</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Inde</li></country></list><tree><country name="Inde"><noRegion><name sortKey="Kaur, Ramneek" sort="Kaur, Ramneek" uniqKey="Kaur R" first="Ramneek" last="Kaur">Ramneek Kaur</name></noRegion><name sortKey="Kaur, Ramneek" sort="Kaur, Ramneek" uniqKey="Kaur R" first="Ramneek" last="Kaur">Ramneek Kaur</name><name sortKey="Kumari, Parvesh" sort="Kumari, Parvesh" uniqKey="Kumari P" first="Parvesh" last="Kumari">Parvesh Kumari</name><name sortKey="Mukesh, Manishi" sort="Mukesh, Manishi" uniqKey="Mukesh M" first="Manishi" last="Mukesh">Manishi Mukesh</name><name sortKey="Sharma, Ankita" sort="Sharma, Ankita" uniqKey="Sharma A" first="Ankita" last="Sharma">Ankita Sharma</name><name sortKey="Sharma, Vijay Lakshmi" sort="Sharma, Vijay Lakshmi" uniqKey="Sharma V" first="Vijay Lakshmi" last="Sharma">Vijay Lakshmi Sharma</name><name sortKey="Sodhi, Monika" sort="Sodhi, Monika" uniqKey="Sodhi M" first="Monika" last="Sodhi">Monika Sodhi</name><name sortKey="Swami, Shelesh Kumar" sort="Swami, Shelesh Kumar" uniqKey="Swami S" first="Shelesh Kumar" last="Swami">Shelesh Kumar Swami</name><name sortKey="Verma, Preeti" sort="Verma, Preeti" uniqKey="Verma P" first="Preeti" last="Verma">Preeti Verma</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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