Validation of suitable genes for normalization of diurnal gene expression studies in Chenopodium quinoa
Patirange, Dilan S. R.
Schmoeckel, Sandra Manuela
KAUST DepartmentBiological and Environmental Science and Engineering (BESE) Division
Center for Desert Agriculture
King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
KAUST Grant NumberOSR-2016-CRG5-2966-02
Permanent link to this recordhttp://hdl.handle.net/10754/667731
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AbstractQuinoa depicts high nutritional quality and abiotic stress resistance, attracting strong interest in the last years. To unravel the function of candidate genes for agronomically relevant traits, studying their transcriptional activities by RT-qPCR is an important experimental approach. The accuracy of such experiments strongly depends on precise data normalization. To date, validation of potential candidate genes for normalization of diurnal expression studies has not been performed in C. quinoa. We selected eight candidate genes based on transcriptome data and literature survey, including conventionally used reference genes. We used three statistical algorithms (BestKeeper, geNorm and NormFinder) to test their stability and added further validation by a simulation-based strategy. We demonstrated that using different reference genes, including those top ranked by stability, causes significant differences among the resulting diurnal expression patterns. Our results show that isocitrate dehydrogenase enzyme (IDH-A) and polypyrimidine tract-binding protein (PTB) are suitable genes to normalize diurnal expression data of two different quinoa accessions. Moreover, we validated our reference genes by normalizing two known diurnally regulated genes, BTC1 and BBX19. The validated reference genes obtained in this study will improve the accuracy of RT-qPCR data normalization and facilitate gene expression studies in quinoa.
CitationMaldonado-Taipe, N., Patirange, D. S. R., Schmöckel, S. M., Jung, C., & Emrani, N. (2021). Validation of suitable genes for normalization of diurnal gene expression studies in Chenopodium quinoa. PLOS ONE, 16(3), e0233821. doi:10.1371/journal.pone.0233821
SponsorsThis study was partially funded by the Competitive Research Grant of the King Abdullah University of Science and Technology, Saudi Arabia awarded to CJ (Grant number: OSR-2016-CRG5-2966-02). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. There was no additional external funding received for this study. The rest of the costs were covered internally by the institute budget of the Plant Breeding Institute, Kiel University. We acknowledge the financial support by State of Schleswig-Holstein, Germany within the funding program “Open Access Publikationsfonds”.
PublisherPublic Library of Science (PLoS)
PubMed Central IDPMC7951847
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