Reference genes selection for quantitative gene expression studies in Pinus massoniana L.

Hu, Chen; Yang, Zhangqi; Hu, Ying; Tan, Jason; Jia, Jie; Xu, Hulan; Chen, Xinhua

doi:10.1007/s00468-015-1311-3

Cited by 29 publications

(21 citation statements)

References 59 publications

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“…However, RPL25 demonstrated the highest expression stability across stress-treated samples of Nicotiana tabacum [37]. CYP was identified as the most stable internal control gene in Petunia hybrida [35], insect-resistant leaves of Pinus massoniana L. [11], and GA-treated samples of Stellera chamaejasme [2]. In a study of Pisum sativum, TUB was suitable for normalization under abiotic stress and biotic stress [34].…”

Section: Discussionmentioning

confidence: 99%

“…Fifteen candidate reference genes were selected for this study, and most of them had been studied previously in different plants such Oryza sativa L. [9], Pinus massoniana L. [11], citrus [33], Pisum sativum [34], Petunia hybrida [35], Linum usitatissimum L. [36], Nicotiana tabacum [37], Camellia sinensis [38], and Populus [39]. In terms of standardization and quality, amplification efficiencies of the candidate reference gene's primer pairs varied from 1.81 to 2.04 ( Table 1).…”

Section: Discussionmentioning

confidence: 99%

“…For example, eIF was chosen as the internal control gene for RT-qPCR analysis under drought stress in Lolium multiflorum [45], and it also showed the most stable expression pattern in Linum usitatissimum L. stems [36]. ACT was the most suitable internal control for RT-qPCR analysis in Pinus massoniana L. [11], and it was still the most stably expressed reference gene in Daucus carota L. leaves [7], stem segments of Populus tomentosa [16], and Glycine max L. Merr. [44].…”

Section: Discussionmentioning

confidence: 99%

“…Reference genes usually have basic functions in cells or organisms and are normally expressed at relatively constant rates under different experimental conditions and across different organs [2,6]. Many genes, such as actin, beta-tubulin, elongation factor, polyubiquitin, eukaryotic translation initiation factor, glyceraldehyde-3-phosphate dehydrogenase, histone, ribosomal protein L, cyclophilin, and 18S RNA have been used as reference genes under different experimental conditions and in different species [2,[6][7][8][9][10][11][12][13][14][15] Different statistical algorithms have been developed to assess the expression stability of reference genes under certain experimental conditions for specific species; these algorithms include geNorm, BestKeeper, NormFinder, and RefFinder. These algorithms are widely employed to evaluate the expression stability of reference genes and identify reference genes that are consistent across various species such as Populus tomentosa Carr.…”

Section: Introductionmentioning

confidence: 99%

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Identification of Suitable Reference Genes for RT-qPCR Assays in Liriodendron chinense (Hemsl.) Sarg

Hao

Zhong

et al. 2019

Forests

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The precision and reliability of reverse transcription quantitative polymerase chain reaction (RT-qPCR) depend mainly on suitable reference genes; however, reference genes have not yet been identified for Liriodendron chinense (Hemsl.) Sarg. In this study, the expression stability of 15 candidate reference genes, ACT7, ACT97, UBQ1, eIF2, eIF3, HIS, BIG, AGD11, EFG, GAPDH, CYP, RPL25, UBC, RPB1, and TUB, was tested across multiple organs of L. chinense using four algorithms, geNorm, NormFinder, BestKeeper, and RefFinder. To understand the difference between the selected reference genes and the unsuitable candidate reference genes, the expression level of a target gene, LcPAT7, was normalized across various plant samples. ACT97 and eIF3 represented the best combination across all samples tested, while AGD11 and UBQ1 were unsuitable for normalization in this case. In the vegetative organ subset, ACT97, ACT7, and GAPDH showed the highest expression stability. For floral organs, UBC and eIF3 were the most stable reference genes. Unsuitable reference genes underestimated the expression levels of a target gene, LcPAT7. This study identified two reference genes (ACT97 and eIF3) for the precise and reliable normalization of L. chinense RT-qPCR data across various organs. Our work provides an effective framework for quantifying gene expression in L. chinense.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Identification of Suitable Reference Genes for RT-qPCR Assays in Liriodendron chinense (Hemsl.) Sarg

Hao

Zhong

et al. 2019

Forests

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“…Their amplification efficiency ranged from 1.22 to 2.86, which is higher than in some species like Davidia involucrata [30], Euphorbia esula [31], Phyllostachys edulis [18], but close to more related species such as Pinus pinaster and Picea abies [29]. Furthermore, recent research has reported both low [32] and high [33] amplification efficiencies for P. massoniana genes. What causes this difference is still poorly understood?…”

Section: Discussionmentioning

confidence: 82%

Identification of Reference Genes for Quantitative Gene Expression Studies in Pinus massoniana and Its Introgression Hybrid

Jin

et al. 2019

Forests

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qRT-PCR is a powerful molecular research tool to study the regulation of gene expression. However, to accurately calculate gene expression levels, an experiment should include proper reference genes that show no changes in their expression level. Pinus massoniana, P. hwangshanensis, and their introgression hybrid in Mountain Lushan, China, are an ideal model for studying introgression and speciation. Although some research on reference gene selection for P. massoniana has been reported before, no studies on this subject have been performed where P. massoniana and its introgression hybrid were evaluated simultaneously. Here, we investigated ten genes (upLOC, SDH, ACT, EF, TOC75, DMWD, FBOX, PGK1, UBQ, and CL2417C7) identified from transcriptome data of these two taxa for reference gene potential. These ten genes were then screened across multiple tissues such as cone, young and mature stems, and young needles according to qRT-PCR thermal cycling and dissociation. Correlation coefficient, amplification efficiency, and cycle threshold value (Ct) range were applied to evaluate the reliability of each gene. The stability of candidate reference gene expression was calculated using three algorithms: geNorm, NormFinder, and BestKeeper. Base on the reliability and stability, we then offered a list of genes of recommended and not recommended for seven different tissue type and species. Our results demonstrated that different sample lines require different genes as reference to evaluate.

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Identification of suitable reference genes in Taxodium ‘Zhongshanshan’ under abiotic stresses

Wang

Liu

et al. 2017

Trees

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Reference genes selection for quantitative gene expression studies in Pinus massoniana L.

Cited by 29 publications

References 59 publications

Identification of Suitable Reference Genes for RT-qPCR Assays in Liriodendron chinense (Hemsl.) Sarg

Identification of Suitable Reference Genes for RT-qPCR Assays in Liriodendron chinense (Hemsl.) Sarg

Identification of Reference Genes for Quantitative Gene Expression Studies in Pinus massoniana and Its Introgression Hybrid

Identification of suitable reference genes in Taxodium ‘Zhongshanshan’ under abiotic stresses

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