Selection of suitable reference genes for qRT-PCR studies during SE initial dedifferentiation in cotton of different SE capability
- Published
- Accepted
- Subject Areas
- Agricultural Science, Genomics
- Keywords
- qRT-PCR, reference gene, gene expression analysis, RNA sequencing, Gossypium hirsutum L
- Copyright
- © 2018 Ping et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. Selection of suitable reference genes for qRT-PCR studies during SE initial dedifferentiation in cotton of different SE capability. PeerJ Preprints 6:e27138v1 https://doi.org/10.7287/peerj.preprints.27138v1
Abstract
Analysis of gene expression level by RNA sequencing (RNA-seq ) has a wide range of biological purposes in various species. Real-time fluorescent quantitative PCR (qRT-PCR) evaluated gene expression levels and validated transcriptomic, which will depend on the stably expressed reference genes for normalization of the gene expression level under specific situations. In this study, 15 candidate genes were selected from transcriptome datasets during somatic embryogenesis (SE) initial dedifferentiation in Gossypium hirsutum L. of different SE capability. To evaluate the stability of those genes, geNorm, NormFinder and BestKeeper were used. The results revealed that ENDO4 and 18srRNA could be as appropriate reference genes under all conditions. The stability and reliability of the reference genes were further tested through comparison of qRT-PCR results and RNA-seq data, as well as evaluation of the expression profiles of auxin-responsive protein (AUX22) and ethylene-responsive transcription factor (ERF17). In summary, the results of our study indicate the most suitable reference genes for qRT-PCR during three induction stages in four cotton species.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Datase 1
Transcriptome data of 15 candidate genes across all of samples.