Reference genes selection for transcript normalization in kenaf (<i>Hibiscus cannabinus</i>L.) under salinity and drought stress

Niu, Xiaoping; Qi, Jianmin; Chen, Meixia; Zhang, Gaoyang; Tao, Aifen; Fang, Pingping; Xu, Jie; Onyedinma, Sandra A.; Su, Jianguang

doi:10.7717/peerj.1347

Cited by 28 publications

(34 citation statements)

References 40 publications

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“…The expression stabilities of these genes were found to be different in different species as well as different experimental conditions in the same species [5,9,20,22]. The expression stabilities of these genes were found to be different in different species as well as different experimental conditions in the same species [5,9,20,22].…”

Section: Discussionmentioning

confidence: 99%

“…The expression stabilities of these genes were found to be different in different species as well as different experimental conditions in the same species [5,9,20,22]. UQT was considered as an unstable reference gene in kenaf [22]. UQT was considered as an unstable reference gene in kenaf [22].…”

Section: Discussionmentioning

confidence: 99%

“…species, such as rice [14], rubber tree [15], sunflower [16], black locust [17], grapevine [18], and annual ryegrass [19]. Ubiquitin (UBQ) and actin (ACT) were the most stable reference genes in different developing seeds and cultivars in the tung tree [21], while 18S ribosomal RNA (18S rRNA) was the optimum reference gene under the salinity and drought conditions in kenaf [22]. For instance, elongation factor 1-alpha (EF1-a) was the best reference gene to normalize gene expression under heat stress, waterlogging, and across different tissues in Amorphophallus [20].…”

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confidence: 99%

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RNA‐seq‐based selection of reference genes for RT‐qPCR analysis of pitaya

et al. 2019

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Reverse‐transcription quantitative real‐time PCR (RT‐qPCR) is a primary tool for measuring gene expression levels, and selection of appropriate reference genes is crucial for accurate and reproducible results of gene expression under various experimental conditions. However, no systematic evaluation of reference genes in pitaya (Hylocereus undatus Britt.) has been performed. Here, we examined the expression of five candidate reference genes, namely elongation factor 1‐alpha (HuEF1‐α), 18S ribosomal RNA (Hu18S rRNA), ubiquitin (HuUBQ), actin (HuACT), and ubiquitin‐conjugating enzyme (HuUQT), under different conditions in pitaya. The expression stabilities of these five genes were evaluated using two computation programs: geNorm and NormFinder. The results were further validated by normalizing the expression of the phosphoglycerate kinase (HuPGK) and ethylene‐responsive transcription factor (HuERF) genes. Our results indicate that combined use of HuUBQ and HuUQT is the most stable reference under all of the experimental conditions examined. HuEF1‐α, HuUBQ, and HuUQT are the top three most stable reference genes under salt stress, drought stress, and heat stress, and across different cultivars. HuEF1‐α, HuACT, and HuUQT exhibited the most stable expression patterns across different tissues. Our results will allow researchers to select the most appropriate reference genes for gene expression studies of pitaya under different conditions.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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RNA‐seq‐based selection of reference genes for RT‐qPCR analysis of pitaya

et al. 2019

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“…Kenaf is an appealing fiber source for the paper manufacture, owing to its environmentally friendly nature, such as biodegradability, renewability, and low energy consumption (Bhardwaj et al, 2005; Villar et al, 2009; Niu et al, 2015a). It has also a great potential for utilization in oil absorption, animal feed, and value-added industrial products (Ayadi et al, 2011; Niu et al, 2015a).…”

Section: Introductionmentioning

confidence: 99%

Reference Gene Selection for qRT-PCR Normalization Analysis in kenaf (Hibiscus cannabinus L.) under Abiotic Stress and Hormonal Stimuli

et al. 2017

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Kenaf (Hibiscus cannabinus L.), an environmental friendly and economic fiber crop, has a certain tolerance to abiotic stresses. Identification of reliable reference genes for transcript normalization of stress responsive genes expression by quantitative real-time PCR (qRT-PCR) is important for exploring the molecular mechanisms of plants response to abiotic stresses. In this study, nine candidate reference genes were cloned, and their expression stabilities were assessed in 132 abiotic stress and hormonal stimuli samples of kenaf using geNorm, NormFinder, and BestKeeper algorithms. Results revealed that HcPP2A (Protein phosphatase 2A) and HcACT7 (Actin 7) were the optimum reference genes across all samples; HcUBC (Ubiquitin-conjugating enzyme like protein) was the worst reference gene for transcript normalization. The reliability of the selected reference genes was further confirmed by evaluating the expression profile of HcWRKY28 gene at different stress durations. This work will benefit future studies on discovery of stress-tolerance genes and stress-signaling pathways in this important fiber crop.

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“…The output of each software program permitted us to rank the expression stability of RGs in different treatment groups. A comprehensive ranking of RGs was also generated as described previously [35,36].…”

Section: Gene Expression Stability Analysismentioning

confidence: 99%

Selection and Validation of Appropriate Reference Genes for Real-Time Quantitative PCR Analysis in Needles of Larix olgensis under Abiotic Stresses

Zeng

et al. 2020

Forests

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Larix olgensis Henry is an important afforestation species in northeastern China because of its fast juvenile growth, high-quality timber, and significant economic and ecological values. The selection of appropriate reference genes is necessary for the normalization of gene expression determination during quantitative real-time polymerase chain reaction (qRT-PCR) experiments. In this study, qRT-PCR was used to study gene expression. Three software packages geNorm, NormFinder, BestKeeper were used, and a comprehensive ranking of candidate reference genes was produced based on their output to evaluate the expression stability of 16 candidate reference genes from L. olgensis under drought, salt, cold, and heat stress. PP2A-1 and GAPDH ranked as the most stable reference genes under drought and cold stress, PP2A-1 and UBQ10 were most stable under salt stress, and TIP41 and ACT2 were most stable under heat stress. The least stable gene was ADP, which ranked the last under all treatments. Expression profile analysis of the antioxidant gene CAT using the two most stable and the single least stable reference genes under each stress further verified that the selected reference genes were suitable for gene expression normalization. This study provides an important foundation for the selection of suitable reference genes for the normalization and quantification of L. olgensis gene expression under abiotic stress conditions.

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Reference genes selection for transcript normalization in kenaf (Hibiscus cannabinusL.) under salinity and drought stress

Cited by 28 publications

References 40 publications

RNA‐seq‐based selection of reference genes for RT‐qPCR analysis of pitaya

RNA‐seq‐based selection of reference genes for RT‐qPCR analysis of pitaya

Reference Gene Selection for qRT-PCR Normalization Analysis in kenaf (Hibiscus cannabinus L.) under Abiotic Stress and Hormonal Stimuli

Selection and Validation of Appropriate Reference Genes for Real-Time Quantitative PCR Analysis in Needles of Larix olgensis under Abiotic Stresses

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