Validation of reference genes for quantitative gene expression in the Lippia alba polyploid complex (Verbenaceae)

Lopes, Juliana Mainenti Leal; Matos, Elyabe Monteiro de; Nascimento, Laís Stehling de Queiroz; Viccini, Lyderson Facio

doi:10.1007/s11033-021-06183-6

Cited by 8 publications

(9 citation statements)

References 45 publications

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“…Dorak et al [ 36 ] reported a comparison of efficiencies in optimized qPCR reactions for nine different real-time PCR kits, finding an average value of 103% (94–128%), which confirms that the efficiency obtained in this work is in the valid range for such a test. Reference genes have already been characterized for allopolyploid and autopolyploid species; however, this is the first time that they have been determined from a population of plants of the genus Vaccinium regenerated on a colchicine-supplemented medium [ 37 , 38 , 39 , 40 , 41 ]. Another study in Arabidopsis thaliana [ 42 ], using representative mitochondrial genes, atp1, rps4, nad6 and cox1, as targets for quantitative qPCR analysis where the selected genes represent mitochondrial chondrome-dependent functions of ATP synthesis, electron transport and gene expression, found similar results in these reference genes.…”

Section: Discussionmentioning

confidence: 99%

Validation of Reference Genes in a Population of Blueberry (Vaccinium corymbosum) Plants Regenerated in Colchicine

Valenzuela

D’Afonseca

Hernández

et al. 2022

Plants

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For the first time we report the validation of reference genes in plants from a population of blueberry (Vaccinium corymbosum) clones cultured in vitro on a colchicine-supplemented medium. Nodal segment explants of the cultivar Duke were regenerated by organogenesis under different periods of colchicine 1 mg/L exposure (1, 2, 3, 5, 30 days). The clones selected for the study showed variability for phenotypic traits after 2 years of adaptation to field conditions, compared to plants of the donor genotype that were regenerated on a medium without colchicine. Vaccinium myrtillus (GAPDH) and Vaccinium macrocarpon (ATP1, NADH, RPOB and COX2) were used as reference genomes for primer design. The results show that colchicine treatments can cause genomic changes in blueberry plants. At the molecular level, exposure of plants to colchicine in early periods could promote an increase in gene expression of specific genes such as ATP1, COX2, GAPDH, MATK, NADH and RPOB. However, prolonged exposure (30 days) could decrease gene expression of the genes studied. For qPCR assays, the primers designed for ATP1, COX2, GAPDH and MATK genes showed high efficiency. In addition, the GAPDH, ATP1, NADH and COX2 genes showed high stability and could be recommended as potential reference genes for gene expression assays in Vaccinium.

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Section: Discussionmentioning

confidence: 99%

Validation of Reference Genes in a Population of Blueberry (Vaccinium corymbosum) Plants Regenerated in Colchicine

Valenzuela

D’Afonseca

Hernández

et al. 2022

Plants

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“…Assuming that an absolutely stable reference gene (under all experimental conditions, tissues and species) does not exist, an ideal reference gene should have a stable expression in a wide range of environmental conditions, tissues and growth stages. At the present time, only four studies have investigated reference genes for allopolyploid species [10,11,37,38], and only one has focused on autopolyploid species [23].…”

Section: Reference Gene Stability Among Tissues and Ploidy Levelsmentioning

confidence: 99%

“…In this study, special emphasis has been placed on the selected reference gene maintaining a stable profile expression at different ploidy levels. Polyploidy events may influence the regulation of gene expression due to epigenetic control, genomic rearrangement or dosage effects [23]. Several studies suggest that the stability of the reference genes is influenced by the ploidy level, especially dosage effects or compensations are triggered by genome duplication [23].…”

Section: Gene Expression Attenuation Enable the Comparison Among The ...mentioning

confidence: 99%

“…Polyploidy events may influence the regulation of gene expression due to epigenetic control, genomic rearrangement or dosage effects [23]. Several studies suggest that the stability of the reference genes is influenced by the ploidy level, especially dosage effects or compensations are triggered by genome duplication [23]. Although duplication by polyploidy increases the dosage of all genes and so should not affect the balance, for every gene duplicated by polyploidy, a diversity of transcriptional dosage responses (changes in expression associated with changes in gene dosage) is feasible [45].…”

Section: Gene Expression Attenuation Enable the Comparison Among The ...mentioning

confidence: 99%

“…These phenotypic changes may be due to altered gene expression, increased variation in dosage-regulated gene expression, modified regulatory interaction, epigenetic changes, gene redundancy or heterozygosity [20,21]. Taking this into account, and with the objective of studying these biological processes, additional research focusing on finding stable reference genes between different ploidy levels to perform gene expression analysis is required [22,23].…”

Section: Introductionmentioning

confidence: 99%

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Evaluation of Reference Genes in the Polyploid Complex Dianthus broteri (Caryophyllaceae) Using qPCR

Rodríguez-Parra

Picazo-Aragonés

Balao

2022

Plants

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Dianthus broteri is an endemic complex which is considered the largest polyploid series within the Dianthus genus. This polyploid species involves four cytotypes (2×, 4×, 6× and 12×) with spatial and ecological segregation. The study of gene expression in polyploid species must be very rigorous because of the effects of duplications on gene regulation. In these cases, real-time polymerase chain reaction (qPCR) is the most appropriate technique for determining the gene expression profile because of its high sensitivity. The relative quantification strategy using qPCR requires genes with stable expression, known as reference genes, for normalization. In this work, we evaluated the stability of 13 candidate genes to be considered reference genes in leaf and petal tissues in Dianthus broteri. Several statistical analyses were used to determine the most stable candidate genes: Bayesian analysis, network analysis based on equivalence tests, geNorm and BestKeeper algorithms. In the leaf tissue, the most stable candidate genes were TIP41, TIF5A, PP2A and SAMDC. Similarly, the most adequate reference genes were H3.1, TIP41, TIF5A and ACT7 in the petal tissue. Therefore, we suggest that the best reference genes to compare different ploidy levels for both tissues in D. broteri are TIP41 and TIF5A.

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Impact of Colored Shade Nets on Biomass Production, Essential Oil Composition and Orientin and Isoorientin Content in Lippia gracilis Schauer

Viana,

Alves de Carvalho,

Alves de Assis

et al. 2023

Chemistry & Biodiversity

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The objective of this study was to evaluate the effect of ChromatiNet on vegetative growth, total antioxidant capacity, phenolic and essential oils (EOs) composition of Lippia gracilis. The plants were cultivated under full sunlight, black, blue and red ChromatiNet. The flavonoid content and antioxidant capacity were quantified spectrophotometrically. The C‐glycosylflavone isomers (orientin and isoorientin) were isolated and identified by conventional spectroscopic techniques and measured using high‐performance liquid chromatography‐diode array detection. The EO was analysed by gas chromatography and gas chromatography‐mass spectrometry. Environment influenced growth, total antioxidant capacity and phytochemical levels. Shoot dry weight, thymol, carvacrol and (E)‐caryophyllene were favoured under red and black ChromatiNet. Root growth, EOs, caryophyllene oxide, p‐cymene, flavonoids, orientin and isoorientin were favoured in sunlight. Growth and accumulation of EOs, flavonoids and photosynthetic pigments increased under blue ChromatiNet. Therefore, Lippia gracilis plants have plasticity related to the spectral quality of light and it cultivate depends of the phytochemicals of interest.

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Validation of reference genes for quantitative gene expression in the Lippia alba polyploid complex (Verbenaceae)

Cited by 8 publications

References 45 publications

Validation of Reference Genes in a Population of Blueberry (Vaccinium corymbosum) Plants Regenerated in Colchicine

Validation of Reference Genes in a Population of Blueberry (Vaccinium corymbosum) Plants Regenerated in Colchicine

Evaluation of Reference Genes in the Polyploid Complex Dianthus broteri (Caryophyllaceae) Using qPCR

Impact of Colored Shade Nets on Biomass Production, Essential Oil Composition and Orientin and Isoorientin Content in Lippia gracilis Schauer

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