Selection of reference genes for quantitative real-time PCR analysis of photosynthesis-related genes expression in Lilium regale

Du, Wenkai; Hu, Fengrong; Yuan, Suxia; Lei, Chun

doi:10.1007/s12298-019-00707-y

Cited by 9 publications

(6 citation statements)

References 37 publications

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“…TUA ranked in the top two stable genes by BestKeeper, but was ranked fifth by GeNorm and third by NormFinder. The results are similar to many previous studies of different species such as were identified as Cynodon dactylon [31], Chrysanthemum morifolium [12], Lilium regale [37], and Tolypocladium guangdongense [38]. Finally, Ref-Finder was used to combine and validate the results.…”

Section: Discussionsupporting

confidence: 85%

Reference Gene Selection for qRT-PCR Normalization in Iris germanica L.

Wang¹,

Zhang²,

Liu³

et al. 2021

Phyton

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Quantitative real-time PCR (qPCR) is an effective and widely used method to analyze expression patterns of target genes. Selection of stable reference genes is a prerequisite for accurate normalization of target gene expression by qRT-PCR. In Iris germanica L., no studies have yet been published regarding the evaluation of potential reference genes. In this study, nine candidate reference genes were assessed at different flower developmental stages and in different tissues by four different algorithms (GeNorm, NormFinder, BestKeeper, and Ref-Finder). The results revealed that ACT11 (Actin 11) and EF1α (Elongation factor 1 alpha) were the most stable reference genes in different tissues, whereas TUA (Tubulin alpha) and UBC9 (Ubiquitin-protein ligase 9) were the most stable ones in different flower developmental stages. UBC9 and ACT11 were the most stable reference genes in all of the tested samples, while the SAMDC (S-Adenosylmethionine decarboxylase) showed the least stability. Finally, to validate the suitability of the selected reference genes, the relative expression level of IgTPS (beta-caryophyllene synthase) was assessed and highlighted the importance of suitable reference gene selection. This work constitutes the first systematic evaluation of potential reference genes in I. germanica and provides guidelines for future research on gene function and molecular mechanisms on I. germanica and related species.

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Section: Discussionsupporting

confidence: 85%

Reference Gene Selection for qRT-PCR Normalization in Iris germanica L.

Wang¹,

Zhang²,

Liu³

et al. 2021

Phyton

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“…To combine the results of the first three algorithms, an online ranking software RefFinder was used for the overall ranking, which calculated the average gene weight and obtained the final ranking result [ 28 ]. To date, RefFinder has been applied in Lilium regale [ 57 ], Brassica juncea [ 2 ], and Solanum rostratum [ 58 ] for reference gene selection. In our study, according to RefFinder’s ranking, HIS6 was the best reference gene in okra ( Table S2 ).…”

Section: Discussionmentioning

confidence: 99%

Selection and Validation of Reference Genes in Different Tissues of Okra (Abelmoschus esculentus L.) under Different Abiotic Stresses

Zhu

Jian-xiang

Tang

et al. 2023

Genes

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Okra (Abelmoschus esculentus L.) is a particular vegetable with both edible and medicinal values. However, the expression pattern of the okra reference genes in response to abiotic stress has not been explored. In the present study, 18 potential reference genes were selected from okra in various tissues and abiotic stress conditions, and their expression levels were detected by Real-Time quantitative PCR (RT-qPCR). Their expression stabilities were calculated by four algorithms (geNorm, NormFinder, BestKeeper, and RefFinder). Under cold stress, the most stable genes included GAPC1 and CYP (leaf), CYP and ACT7 (root), HIS6 and GAPC1 (stem), and HIS6 and 60s (different tissues). Under salt stress, EF-1α and UBQ (leaf), EF-1α and UBQ (root), TUA4 and Eif (stem), and HIS6 and Eif (different tissues) were the most stable genes. Under drought stress, UBQ and Eif in the leaf, HIS6 and Eif in the root, TUA4 and HIS6 in the stem, and UBQ and Eif in different tissues were most stably expressed in okra. In addition, complete sequencing results by RefFinder showed that HIS6 and ACT7 in the leaf, HIS6 and Eif in the root, UBC5B and 60s in the stem, and HIS6 and Eif in different tissues, were most the suitable reference genes for okra. Furthermore, AeMYB1R1 transcription factor was used to verify the reliability of RT-qPCR values. In summary, this study was carried out to demonstrate the potential reference genes of okra under abiotic stress, aiming to provide a molecular basis for functional gene analysis and regulatory mechanism research of okra.

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“…The melting curve was obtained by heating the amplification products from 60 to 95 ℃ in 5 s intervals. The LrActin2 gene was used as the internal control for normalization (forward primer: CGA TTT ACG AAG GCT ATG CTC; reverse primer: CTC CTT TAT GTC CCT CAC GATT) [28]. The relative expression levels of the target genes were calculated using the 2 −△△ CT method [29] against the internal control.…”

Section: Qrt-pcr Analysesmentioning

confidence: 99%

The identification of key candidate genes mediating yellow seedling lethality in a Lilium regale mutant

Yuan

et al. 2020

Mol Biol Rep

Self Cite

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Leaf color mutants are ideal materials for exploring plant photosynthesis mechanisms, chlorophyll biosynthetic pathways and chloroplast development. The yellow seedling lethal mutant lrysl1 was discovered from self-bred progenies of Lilium regale; however, the mechanism of leaf color mutation remains unclear. In this study, the ultrastructural and physiological features and de novo RNA-Seq data of a L. regale leaf color mutant and wild-type L. regale were investigated. Genetic analysis indicated that the characteristics of the lrysl1 mutant were controlled by a recessive nuclear gene. The chlorophyll a, chlorophyll b and carotenoid contents in the mutant leaves were lower than those in the wild-type leaves. Furthermore, the contents of the chlorophyll precursors aminolevulinic acid (ALA), porphobilinogen (PBG), protoporphyrin IX (ProtoIX), Mg-protoporphyrin IX (Mg-ProtoIX), and protochlorophyll (Pchl) decreased significantly in mutant leaves. Transcriptome data from the mutant and wild type showed that a total of 892 differentially expressed genes were obtained, of which 668 and 224 were upregulated genes and downregulated genes in the mutant, respectively. Almost all genes in the photosynthesis pathway and chlorophyll biosynthetic pathway were downregulated in the mutant, which corroborated the differences in the physiological features mentioned above. Further research indicated that the chloroplasts of the mutant leaves exhibited an abnormal morphology and distribution and that the expression of a gene related to chloroplast development was downregulated. It was concluded that abnormal chloroplast development was the main cause of leaf color mutation in the mutant lrysl1 and that LrGLK was a gene related to chloroplast development in L. regale. This research provides a foundation for further research on the mechanism by which LrGLK regulates chloroplast development in L. regale.

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Selection of reference genes for quantitative real-time PCR analysis of photosynthesis-related genes expression in Lilium regale

Cited by 9 publications

References 37 publications

Reference Gene Selection for qRT-PCR Normalization in Iris germanica L.

Reference Gene Selection for qRT-PCR Normalization in Iris germanica L.

Selection and Validation of Reference Genes in Different Tissues of Okra (Abelmoschus esculentus L.) under Different Abiotic Stresses

The identification of key candidate genes mediating yellow seedling lethality in a Lilium regale mutant

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