Validation of reference genes for qPCR analysis of Coffea arabica L. somatic embryogenesis-related tissues

Freitas, Natália Chagas; Barreto, Horllys Gomes; Fernandes-Brum, Christiane Noronha; Moreira, Rafael Oliveira; Chalfun-Júnior, Antônio; Paiva, Luciano Vilela

doi:10.1007/s11240-016-1147-6

Cited by 23 publications

(24 citation statements)

References 60 publications

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“…Prior to conducting a study on gene expression associated with Al-induced PCD in peanut, it was vital to carry out detailed research on the stability of candidate reference genes. RefFinder ranked the candidate genes on the basis of output from the different algorithms, including geNorm, NormFinder and BestKeeper, when the results of algorithms were different (Freitas et al 2017). Volland et al (2016) suggested the use of the RefFinder tool as an alternative to a global ranking tool to improve normali-zation of reference genes.…”

Section: Discussionmentioning

confidence: 99%

“…The expression stability of candidate reference genes was evaluated by different algorithms, estimating the stability parameter in each, in order to identify the most appropriate reference gene from different candidates. Several widely-used statistical algorithm packages (BestKeeper, geNorm, Normfinder, and RefFinder) have been recommended for reference gene evaluation in recent years (Patankar et al 2016, Freitas et al 2017.…”

Section: mentioning

confidence: 99%

“…For more reliable and consistent results, the RefFinder was applied to calculate the geometric mean of each candidate gene and to re-rank the stability (Castro-Quezada et al 2013, Zsóri et al 2013. To execute, the ranking of each gene by geNorm, NormFinder and BestKeeper was multiplied by different weighting coefficients and calculated the geometric mean to produce an overall final ranking (Freitas et al 2017).…”

Section: Selection Of Reference Genes and Primer Designmentioning

confidence: 99%

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Identification and validation of reference genes for real-time qPCR normalization during Al-induced programmed cell death in peanut

Yao¹,

Zhan²,

Pan³

et al. 2019

Biol. plant.

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Section: Discussionmentioning

confidence: 99%

Section: mentioning

confidence: 99%

Section: Selection Of Reference Genes and Primer Designmentioning

confidence: 99%

See 1 more Smart Citation

Identification and validation of reference genes for real-time qPCR normalization during Al-induced programmed cell death in peanut

Yao¹,

Zhan²,

Pan³

et al. 2019

Biol. plant.

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“…The specificity of each pair of primers was verified by analysis of the dissociation (melting) curves. The expression data were normalized with reference genes 24S and PP2A (Freitas et al 2017) and relatively quantified by applying Pfaffl formula (Pfaffl et al 2001).…”

Section: Relative Real-time Pcrmentioning

confidence: 99%

In silico and in vivo analysis of ABI3 and VAL2 genes during somatic embryogenesis of Coffea arabica: competence acquisition and developmental marker genes

Freitas

Barreto

Torres

et al. 2019

Plant Cell Tiss Organ Cult

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The employment of biotechnology-based approaches such as somatic embryogenesis has been applied to several plants including Coffea sp. Despite the economic importance of this genus, few information about the role of key regulatory genes in somatic embryogenesis in coffee is available. This work provides information about ABI3 and VAL2 genes performance by RT-qPCR during indirect somatic embryogenesis of Coffea arabica. To achieve this, bioinformatics analysis was performed to identify the genes of the B3 superfamily in the coffee genome. The cell suspensions lines presented similar histological and regeneration patterns, yielding of up to 6.6 embryos per 1 mg of embryogenic aggregates at 7 months. We have identified possible orthologs for VAL2 (Cc06g00410) and ABI3 (Cc01g17380) as well as the other members belonging to superfamily B3. The CaABI3 expression was higher in dedifferentiated competent cells for somatic embryogenesis as compared with non-embryogenic calli. Whereas the expression of VAL2 gene is more active in cotyledonary embryos and plantlets, showing its clear performance in the embryogenesis late stages. The present study suggests that CaABI3 gene could be potentially used as a biomarker for embryogenic process improvement. The good plantlets development obtained from the protocol used may be a reflection of the high expression of CaVAL2 in cotyledonary embryos and plantlets. Key message The activity of CaABI3 is correlated to embryogenic potential with highly expressed in embryogenic masses and expression of the VAL2 gene is increased at the end of the embryogenic process.

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“…An ideal reference gene has to show invariant expression across a range of tissues, developmental stages and environmental conditions. However, expression of the vast majority of genes fluctuates in response to various stresses [ 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 ], circadian rhythms [ 12 , 16 ], or by developmental stage [ 10 , 17 , 18 , 19 , 20 , 21 ]. Furthermore, most genes show substantial differences between gametophyte and sporophyte [ 20 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of reference genes for reverse transcription quantitative real-time PCR (RT-qPCR) studies in Silene vulgaris considering the method of cDNA preparation

2017

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Accurate gene expression measurements are essential in studies of both crop and wild plants. Reverse transcription quantitative real-time PCR (RT-qPCR) has become a preferred tool for gene expression estimation. A selection of suitable reference genes for the normalization of transcript levels is an essential prerequisite of accurate RT-qPCR results. We evaluated the expression stability of eight candidate reference genes across roots, leaves, flower buds and pollen of Silene vulgaris (bladder campion), a model plant for the study of gynodioecy. As random priming of cDNA is recommended for the study of organellar transcripts and poly(A) selection is indicated for nuclear transcripts, we estimated gene expression with both random-primed and oligo(dT)-primed cDNA. Accordingly, we determined reference genes that perform well with oligo(dT)- and random-primed cDNA, making it possible to estimate levels of nucleus-derived transcripts in the same cDNA samples as used for organellar transcripts, a key benefit in studies of cyto-nuclear interactions. Gene expression variance was estimated by RefFinder, which integrates four different analytical tools. The SvACT and SvGAPDH genes were the most stable candidates across various organs of S. vulgaris, regardless of whether pollen was included or not.

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Validation of reference genes for qPCR analysis of Coffea arabica L. somatic embryogenesis-related tissues

Cited by 23 publications

References 60 publications

Identification and validation of reference genes for real-time qPCR normalization during Al-induced programmed cell death in peanut

Identification and validation of reference genes for real-time qPCR normalization during Al-induced programmed cell death in peanut

In silico and in vivo analysis of ABI3 and VAL2 genes during somatic embryogenesis of Coffea arabica: competence acquisition and developmental marker genes

Evaluation of reference genes for reverse transcription quantitative real-time PCR (RT-qPCR) studies in Silene vulgaris considering the method of cDNA preparation

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