Internal Reference Gene Selection under Different Hormone Stresses in Multipurpose Timber Yielding Tree Neolamarckia cadamba

Deng, Zixin; Li, Jingjian; Li, Buye; Li, Chunmei; Ouyang, Kang

doi:10.3390/f11091014

Cited by 3 publications

(4 citation statements)

References 42 publications

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“…The RNA isolation, cDNA synthesis, qRT-PCR and the selection of reference genes followed the methods described previously [ 21 , 26 ]. qRT-PCR amplification was performed on a LC480 instrument (Roche Diagnostics, Basel, Switzerland) with three technical replicates under the conditions as follows: 95 °C for 30 s, followed by 40 cycles (95 °C for 5 s, annealing at 60 °C for 30 s, and 72 °C for 30 s).…”

Section: Methodsmentioning

confidence: 99%

Evolution and Expression Patterns of the Fructose 1,6-Bisphosptase Gene Family in a Miracle Tree (Neolamarckia cadamba)

Que

Liang

Song

et al. 2022

Genes

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Neolamarckia cadamba (N. cadamba) is a fast-growing tree species with tremendous economic and ecological value; the study of the key genes regulating photosynthesis and sugar accumulation is very important for the breeding of N. cadamba. Fructose 1,6-bisphosptase (FBP) gene has been found to play a key role in plant photosynthesis, sugar accumulation and other growth processes. However, no systemic analysis of FBPs has been reported in N. cadamba. A total of six FBP genes were identifed and cloned based on the N. cadamba genome, and these FBP genes were sorted into four groups. The characteristics of the NcFBP gene family were analyzed such as phylogenetic relationships, gene structures, conserved motifs, and expression patterns. A cis-acting element related to circadian control was first found in the promoter region of FBP gene. Phylogenetic and quantitative real-time PCR analyses showed that NcFBP5 and NcFBP6 may be chloroplast type 1 FBP and cytoplasmic FBP, respectively. FBP proteins from N. cadamba and 22 other plant species were used for phylogenetic analyses, indicating that FBP family may have expanded during the evolution of algae to mosses and differentiated cpFBPase1 proteins in mosses. This work analyzes the internal relationship between the evolution and expression of the six NcFBPs, providing a scientific basis for the evolutionary pattern of plant FBPs, and promoting the functional studies of FBP genes.

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Section: Methodsmentioning

confidence: 99%

Evolution and Expression Patterns of the Fructose 1,6-Bisphosptase Gene Family in a Miracle Tree (Neolamarckia cadamba)

Que

Liang

Song

et al. 2022

Genes

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“…The expression of TMV was quantified as described previously (Hao et al 2018;Zhang et al 2020). TMV expression was determined by quantitative polymerase chain reaction (qPCR).…”

Section: Quantitative Real-time Pcrmentioning

confidence: 99%

“…RT-qPCR was performed on an LC480 instrument (Roche, CA, USA) 96-well plate using SYBR ® Premix Ex Taq ™ (TaKaRa, Guangzhou, China). Total RNA was separated from TMV-infected leaves for cDNA synthesis (Zhang et al 2020). The 20 µL real-time PCR volume consisted of 10 µL 2×SYBR Premix Ex Taq II, 1 µL primer F (5 µmol/L), 1 µL primer R (5 µmol/L), 1.5 µL cDNA, and 6.5 µL ddH 2 O.…”

Section: Quantitative Real-time Pcrmentioning

confidence: 99%

Biosynthesis of cupric oxide nanoparticles: its antiviral activities against TMV by directly destroying virion and inducing plant resistance

Liu,

Tian,

Liu

et al. 2024

Phytopathol Res

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Tobacco mosaic virus (TMV) is widely recognized as one of the most important plant viruses, causing significant agricultural losses in terms of both quality and yield worldwide each year. This study demonstrated the biosynthesis of copper oxide nanoparticles (CuONPs) using orange peel extract for effective control of TMV infection both in vitro and in vivo. After treatment with CuONPs (100 mg/L) for 2 h, TMV particles exhibited evident fragmentation in vitro, reducing infectivity on tobacco plants. Similarly, the application of CuONPs on Nicotiana benthamiana (N. benthamiana) positively impeded viral replication and accumulation in vivo. Interestingly, the expression of systemic resistance-related genes (PR1, PR2, ERF1, and JAZ3) in the host plant was up-regulated by CuONPs treatment, supporting that CuONPs activated plant immunity to inhibit TMV. Importantly, the application of CuONPs (100 mg/L) did not exhibit any toxic effects on tobacco and, instead, resulted in the promotion of chlorophyll content, as well as an increase in the fresh weight and dry weight of the plant when compared to the control treatment. Overall, we proposed that the appropriate concentration of CuONPs (100 mg/L) can directly break viral particles by passivating, boost plant immunity by stimulating systemic acquired resistance (SAR), and provide nutritional supplements to promote plant growth.

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“…Therefore, the selection of appropriate reference genes for the calibration and standardization of expression levels according to specific species and different processing methods is necessary to improve the accuracy of RT-qPCR [ 30 ]. At present, geNorm, NormFinder, and BestKeeper are common methods for the screening of stable reference genes and authoritative methods in this part [ 31 , 32 ], which were widely used in the stable reference genes of various plants, such as larch [ 33 ] and jujube [ 34 ]. Despite the screening methods of reference genes being relatively mature and developed, few studies detail the screening of reference genes in plateau garlic and its specific tissues under different treatments, which greatly limits the efficacy of reference genes in garlic.…”

Section: Introductionmentioning

confidence: 99%

Screening and Verification of Reference Genes for Analysis of Gene Expression in Garlic (Allium sativum L.) under Cold and Drought Stress

Wang

Guo

Yang

et al. 2023

Plants

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The principal objective of this study was to screen and verify reference genes appropriate for gene expression evaluation during plant growth and development under distinct growth conditions. Nine candidate reference genes were screened based on garlic transcriptome sequence data. RT-qPCR was used to detect the expression levels of the aforementioned reference genes in specific tissues under drought and cold stress. Then, geNorm, NormFinder, BestKeeper, and ReFinder were used to consider the consistency of the expression levels of candidate reference genes. Finally, the stress-responsive gene expression of ascorbate peroxidase (APX) was quantitatively evaluated to confirm the chosen reference genes. Our results indicated that there were variations in the abundance and stability of nine reference gene transcripts underneath cold and drought stress, among which ACT and UBC-E2 had the highest transcript abundance, and 18S rRNA and HIS3 had the lowest transcript abundance. UBC and UBC-E2 were the most stably expressed genes throughout all samples; UBC and UBC-E2 were the most stably expressed genes during cold stress, and ACT and UBC were the most stably expressed genes under drought stress. The most stably expressed genes in roots, pseudostems, leaves, and cloves were EF1, ACT, HIS3, UBC, and UBC-E2, respectively, while GAPDH was the most unstable gene during drought and cold stress conditions and in exclusive tissues. Taking the steady reference genes UBC-E2, UBC, and ACT as references during drought and cold stress, the reliability of the expression levels was further demonstrated by detecting the expression of AsAPX. Our work thereby offers a theoretical reference for the evaluation of gene expression in garlic in various tissues and under stress conditions.

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Internal Reference Gene Selection under Different Hormone Stresses in Multipurpose Timber Yielding Tree Neolamarckia cadamba

Cited by 3 publications

References 42 publications

Evolution and Expression Patterns of the Fructose 1,6-Bisphosptase Gene Family in a Miracle Tree (Neolamarckia cadamba)

Evolution and Expression Patterns of the Fructose 1,6-Bisphosptase Gene Family in a Miracle Tree (Neolamarckia cadamba)

Biosynthesis of cupric oxide nanoparticles: its antiviral activities against TMV by directly destroying virion and inducing plant resistance

Screening and Verification of Reference Genes for Analysis of Gene Expression in Garlic (Allium sativum L.) under Cold and Drought Stress

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