ArticleBMC plant biology2019
Genome wide search to identify reference genes candidates for gene expression analysis in Gossypium hirsutum.
Article in BMC plant biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 24 citations in OpenAlex.
- Identification and Validation of Reference Genes for Reliable RT-qPCR Normalization inPlants (Basel, Switzerland) · 2026Article
- Transcriptome-Based Identification of Reference Genes for Expression Analysis in Cassava UnderPlants (Basel, Switzerland) · 2025Article
- Selection of stable reference genes for accurate reverse-transcription quantitative PCR in cotton-herbivore studies using virus-induced gene silencing.Scientific reports · 2025Article
- Selection and validation of reference genes for qRT-PCR normalization in dayflower (Commelina communis) based on the transcriptome profiling.BMC plant biology · 2024Article
- Transcriptome-guided selection of stable reference genes for expression analysis in spinach.Scientific reports · 2024Article
- A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol.Plant communications · 2023Article
- Genome-wide screening of novel RT-qPCR reference genes for study of GLRaV-3 infection in wine grapes and refinement of an RNA isolation protocol for grape berries.Plant methods · 2021Article
- Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling.Scientific reports · 2021Article
- Correlation of Cry1Ac mRNA and protein abundance in transgenic3 Biotech · 2021Article
- Genome-wide association analysis of chickpea germplasms differing for salinity tolerance based on DArTseq markers.PloS one · 2021Article
- Selection and validation of reference genes for measuring gene expression in Toona ciliata under different experimental conditions by quantitative real-time PCR analysis.BMC plant biology · 2020Article
- Article
- Relative quantification of BCL2 mRNA for diagnostic usage needs stable uncontrolled genes as reference.PloS one · 2020Observational
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Authors and funding
8 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCotton is one of the most important commercial crops as the source of natural fiber, oil and fodder. To protect it from harmful pest populations number of newer transgenic lines have been developed. For quick expression checks in successful agriculture qPCR (quantitative polymerase chain reaction) have become extremely popular. The selection of appropriate reference genes plays a critical role in the outcome of such experiments as the method quantifies expression of the target gene in comparison with the reference. Traditionally most commonly used reference genes are the "house-keeping genes", involved in basic cellular processes. However, expression levels of such genes often vary in response to experimental conditions, forcing the researchers to validate the reference genes for every experimental platform. This study presents a data science driven unbiased genome-wide search for the selection of reference genes by assessing variation of > 50,000 genes in a publicly available RNA-seq dataset of cotton species Gossypium hirsutum.
resultFive genes (TMN5, TBL6, UTR5B, AT1g65240 and CYP76B6) identified by data-science driven analysis, along with two commonly used reference genes found in literature (PP2A1 and UBQ14) were taken through qPCR in a set of 33 experimental samples consisting of different tissues (leaves, square, stem and root), different stages of leaf (young and mature) and square development (small, medium and large) in both transgenic and non-transgenic plants. Expression stability of the genes was evaluated using four algorithms - geNorm, BestKeeper, NormFinder and RefFinder.
conclusionBased on the results we recommend the usage of TMN5 and TBL6 as the optimal candidate reference genes in qPCR experiments with normal and transgenic cotton plant tissues. AT1g65240 and PP2A1 can also be used if expression study includes squares. This study, for the first time successfully displays a data science driven genome-wide search method followed by experimental validation as a method of choice for selection of stable reference genes over the selection based on function alone.
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