Evaluation of six commonly used reference genes for gene expression studies in herbicide‐resistant <i>Avena fatua</i> biotypes

Wrzesińska, Barbara; Kierzek, R.; Obrępalska‐Stęplowska, Aleksandra

doi:10.1111/wre.12209

Cited by 25 publications

(35 citation statements)

References 29 publications

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“…This was somewhat consistent with the previous results 18S or 28S is an ideal reference gene for normalisation of qPCR data (Bagnall & Kotze 2010). TBP is as one of the most stably expressed genes in previous study of A. fatua (Wrzesińska et al 2016) as well as the research in Solanum lycopersicum and Lolium multiflorum L. (Expósito-Rodríguez et al 2008;Wang et al 2015). ACT as traditional reference genes is not always stable in different experimental conditions, which was somewhat in accordance with several studies demonstrating ACT as an unsuitable internal control for RT-PCR in other cell types or species (Lord et al 2010).…”

Section: Discussionsupporting

confidence: 92%

“…However, some reports indicated 18S was recommended to validate gene expression data in Solanum melongena L. or Oryza sativa L. (Kim et al 2003;Gantasala et al 2013). GAPDH was one of the most stably expressed genes in our results consistent with the previous results in A. fatua (Wrzesińska et al 2016) as well as other weed species, such as Alopecurus myosuroides Huds and Lolium sp. (Duhoux & Délye 2013).…”

Section: Discussionsupporting

confidence: 91%

“…ACT as traditional reference genes is not always stable in different experimental conditions, which was somewhat in accordance with several studies demonstrating ACT as an unsuitable internal control for RT-PCR in other cell types or species (Lord et al 2010). Recent studies have shown that ACT expression can change in response to a variety of conditions (Ruan & Lai 2007;Zarivi et al 2015;Wrzesińska et al 2016). Thus, these traditionally used reference genes are not persistently and stably expressed in many species or different experimental treatments (Chandna 2012;Cheng et al 2013;Ma et al 2016), which emphasised the need to evaluate reference genes in A. fatua.…”

Section: Discussionsupporting

confidence: 84%

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Selection and evaluation of potential reference genes for gene expression analysis in Avena fatua

Liu¹,

Li²,

Lu³

et al. 2019

Plant Prot. Sci.

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Citation: Liu J., Li P., Lu L., Xie L., Chen X., Zhang B. (2019): Selection and evaluation of potential reference genes for gene expression analysis in Avena fatua. Plant Protect. Sci., 55: 61-71.Abstract: Eight commonly used candidate reference genes, 18S ribosomal RNA (rRNA) (18S), 28S rRNA (28S), actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), elongation factor 1 alpha (EF1α), ribosomal protein L7 (RPL7), Alpha-tubulin (α-TUB), and TATA box binding protein-associated factor (TBP), were evaluated under various experimental conditions to assess their suitability in different developmental stages, tissues and herbicide treatments in Avena fatua. The results indicated the most suitable reference genes for the different experimental conditions. For developmental stages, 28S and EF1α were the optimal reference genes, both EF1α and 28S were suitable for experiments of different tissues, whereas for herbicide treatments, GAPDH and ACT were suitable for normalizations of expression data. In addition, GAPDH and EF1α were the suitable reference genes.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionsupporting

confidence: 91%

Section: Discussionsupporting

confidence: 84%

See 1 more Smart Citation

Selection and evaluation of potential reference genes for gene expression analysis in Avena fatua

Liu¹,

Li²,

Lu³

et al. 2019

Plant Prot. Sci.

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show abstract

“…Our results demonstrated that traditional reference gene ACT, involved in cytoskeleton structure, was not usually unchange under diverse experimental treatments. Similar findings were verified in the beetle Tribolium castaneum [34], perigord black truffle [35] and Avena fatua [36]. Therefore, no reference genes in multiple species show unchanged expression across all the tested conditions [37,38], suggesting that it is of particular important to identify suitable reference genes in BGA.…”

Section: Evaluation Of Reference Genes Expression Stabilitysupporting

confidence: 71%

Reference gene selection for quantitative real-time PCR (qRT-PCR) expression analysis in Galium aparine L.

et al. 2020

PLoS ONE

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To accurately evaluate expression levels of target genes, stable internal reference genes is required for normalization of quantitative real-time PCR (qRT-PCR) data. However, there have been no systematical investigation on the stability of reference genes used in the bedstraw weed, Galium aparine L. (BGA). In this study, the expression profiles of seven traditionally used reference genes, namely 18S, 28S, ACT, GAPDH, EF1α, RPL7 and TBP in BGA were assessed under both biotic (developmental time and tissue), and abiotic (temperature, regions and herbicide) conditions. Four analytical algorithms (geNorm, Normfinder, BestKeeper and the ΔCt method) were used to analyze the suitability of these genes as internal reference genes. RefFinder, a comprehensive analytical software, was used to rank the overall stability of the candidate genes. The optimal normalization internal control genes were ranked as: 28S and RPL7 were best for all the different experimental conditions (developmental stages, tissues, temperature, regions and herbicide treatment); 28S and RPL7 for developmental stages; TBP and GAPDH for different tissues; 28S and GAPDH were relatively stable for different temperature; 28S and TBP were suitable for herbicide treatment. A specific set of reference genes were recommended for each experimental condition in BGA.

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“…Avena fatua L. (wild oat) is listed among the most common and economically threatening grass weed species of cereal crops all over the world [ 7 – 10 ]. Several traits may account for wild oat’s success as a weed, among them: high competitiveness, multiple herbicide resistance, crop mimicry (similar phenology) and varied germination strategies [ 8 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

Reference gene selection for molecular studies of dormancy in wild oat (Avena fatua L.) caryopses by RT-qPCR method

Ruduś¹,

Kępczyński²

2018

PLoS ONE

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Molecular studies of primary and secondary dormancy in Avena fatua L., a serious weed of cereal and other crops, are intended to reveal the species-specific details of underlying molecular mechanisms which in turn may be useable in weed management. Among others, quantitative real-time PCR (RT-qPCR) data of comparative gene expression analysis may give some insight into the involvement of particular wild oat genes in dormancy release, maintenance or induction by unfavorable conditions. To assure obtaining biologically significant results using this method, the expression stability of selected candidate reference genes in different data subsets was evaluated using four statistical algorithms i.e. geNorm, NormFinder, Best Keeper and ΔCt method. Although some discrepancies in their ranking outputs were noticed, evidently two ubiquitin-conjugating enzyme homologs, AfUBC1 and AfUBC2, as well as one homolog of glyceraldehyde 3-phosphate dehydrogenase AfGAPDH1 and TATA-binding protein AfTBP2 appeared as more stably expressed than AfEF1a (translation elongation factor 1α), AfGAPDH2 or the least stable α-tubulin homolog AfTUA1 in caryopses and seedlings of A. fatua. Gene expression analysis of a dormancy-related wild oat transcription factor VIVIPAROUS1 (AfVP1) allowed for a validation of candidate reference genes performance. Based on the obtained results it can be recommended that the normalization factor calculated as a geometric mean of Cq values of AfUBC1, AfUBC2 and AfGAPDH1 would be optimal for RT-qPCR results normalization in the experiments comprising A. fatua caryopses of different dormancy status.

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Evaluation of six commonly used reference genes for gene expression studies in herbicide‐resistant Avena fatua biotypes

Cited by 25 publications

References 29 publications

Selection and evaluation of potential reference genes for gene expression analysis in Avena fatua

Selection and evaluation of potential reference genes for gene expression analysis in Avena fatua

Reference gene selection for quantitative real-time PCR (qRT-PCR) expression analysis in Galium aparine L.

Reference gene selection for molecular studies of dormancy in wild oat (Avena fatua L.) caryopses by RT-qPCR method

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