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Ambroise V, Legay S, Jozefczak M, Leclercq CC, Planchon S, Hausman JF, Renaut J, Cuypers A, Sergeant K. Impact of Heavy Metals on Cold Acclimation of Salix viminalis Roots. Int J Mol Sci 2024; 25:1545. [PMID: 38338824 PMCID: PMC10855682 DOI: 10.3390/ijms25031545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
In nature, plants are exposed to a range of climatic conditions. Those negatively impacting plant growth and survival are called abiotic stresses. Although abiotic stresses have been extensively studied separately, little is known about their interactions. Here, we investigate the impact of long-term mild metal exposure on the cold acclimation of Salix viminalis roots using physiological, transcriptomic, and proteomic approaches. We found that, while metal exposure significantly affected plant morphology and physiology, it did not impede cold acclimation. Cold acclimation alone increased glutathione content and glutathione reductase activity. It also resulted in the increase in transcripts and proteins belonging to the heat-shock proteins and related to the energy metabolism. Exposure to metals decreased antioxidant capacity but increased catalase and superoxide dismutase activity. It also resulted in the overexpression of transcripts and proteins related to metal homeostasis, protein folding, and the antioxidant machinery. The simultaneous exposure to both stressors resulted in effects that were not the simple addition of the effects of both stressors taken separately. At the antioxidant level, the response to both stressors was like the response to metals alone. While this should have led to a reduction of frost tolerance, this was not observed. The impact of the simultaneous exposure to metals and cold acclimation on the transcriptome was unique, while at the proteomic level the cold acclimation component seemed to be dominant. Some genes and proteins displayed positive interaction patterns. These genes and proteins were related to the mitigation and reparation of oxidative damage, sugar catabolism, and the production of lignans, trehalose, and raffinose. Interestingly, none of these genes and proteins belonged to the traditional ROS homeostasis system. These results highlight the importance of the under-studied role of lignans and the ROS damage repair and removal system in plants simultaneously exposed to multiple stressors.
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Affiliation(s)
- Valentin Ambroise
- Greentech Innovation Centre (GTIC), Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg; (V.A.); (S.L.); (C.C.L.); (S.P.); (J.-F.H.); (J.R.)
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, B-3590 Diepenbeek, Belgium; (M.J.); (A.C.)
| | - Sylvain Legay
- Greentech Innovation Centre (GTIC), Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg; (V.A.); (S.L.); (C.C.L.); (S.P.); (J.-F.H.); (J.R.)
| | - Marijke Jozefczak
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, B-3590 Diepenbeek, Belgium; (M.J.); (A.C.)
| | - Céline C. Leclercq
- Greentech Innovation Centre (GTIC), Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg; (V.A.); (S.L.); (C.C.L.); (S.P.); (J.-F.H.); (J.R.)
| | - Sebastien Planchon
- Greentech Innovation Centre (GTIC), Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg; (V.A.); (S.L.); (C.C.L.); (S.P.); (J.-F.H.); (J.R.)
| | - Jean-Francois Hausman
- Greentech Innovation Centre (GTIC), Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg; (V.A.); (S.L.); (C.C.L.); (S.P.); (J.-F.H.); (J.R.)
| | - Jenny Renaut
- Greentech Innovation Centre (GTIC), Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg; (V.A.); (S.L.); (C.C.L.); (S.P.); (J.-F.H.); (J.R.)
| | - Ann Cuypers
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, B-3590 Diepenbeek, Belgium; (M.J.); (A.C.)
| | - Kjell Sergeant
- Greentech Innovation Centre (GTIC), Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg; (V.A.); (S.L.); (C.C.L.); (S.P.); (J.-F.H.); (J.R.)
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Zhan H, Liu H, Wang T, Liu L, Ai W, Lu X. Selection and validation of reference genes for quantitative real-time PCR of Quercus mongolica Fisch. ex Ledeb under abiotic stresses. PLoS One 2022; 17:e0267126. [PMID: 35482686 PMCID: PMC9049516 DOI: 10.1371/journal.pone.0267126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 04/02/2022] [Indexed: 11/18/2022] Open
Abstract
Quercus mongolica Fisch. ex Ledeb is the main species of coniferous and broadleaved mixed forests in northeast and north China, which has high ornamental, economic, and ecological value. The appropriate reference genes must be selected for quantitative real-time PCR to reveal the molecular mechanisms of stress responses and their contribution to breeding of Q. mongolica. In the present study, we chose 11 candidate reference genes (TUA, CYP18, HIS4, RPS13, ACT97, TUB1, UBQ10, UBC5, SAND, PP2A, and SAMDC) and used four programs (GeNorm, NormFinder, BestKeeper, and RefFinder) to assess the expression stability of the above genes in roots, stems, and leaves under five abiotic stress factors (cold, salt, drought, weak light, and heavy metal). The findings revealed that under various experimental environments, the most stable genes were different; CYP18, ACT97, and RPS13 ranked the highest under most experimental environments. Moreover, two genes induced by stress, CMO and P5CS2, were chosen to demonstrate the reliability of the selected reference genes in various tissues under various stress conditions. Our research provides a significant basis for subsequent gene function studies of Q. mongolica.
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Affiliation(s)
- Hao Zhan
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hanzhang Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Tianchong Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Lin Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Wanfeng Ai
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xiujun Lu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang, China
- * E-mail:
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Zhou F, Chen Y, Wu H, Yin T. A Selection of Reliable Reference Genes for Gene Expression Analysis in the Female and Male Flowers of Salix suchowensis. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050647. [PMID: 35270117 PMCID: PMC8912643 DOI: 10.3390/plants11050647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 05/03/2023]
Abstract
Salix is a dioecious plant. Research on the molecular regulation mechanism of male and female inflorescence differentiation and development is necessary to analyze sex differentiation in the willow and the underlying mechanisms of unisexual flower development. However, at present, there are no reference genes suitable for stable expression in the process of willow inflorescence development. In this study, Salix suchowensis was used as the research material, nine candidate reference genes (α-TUB1, α-TUB2, ACT, H2A, DnaJ, CDC2, GAPDH, TIP41, β-TUB) were selected, and qRT-PCR technology was used to detect the expression of each candidate reference gene in female and male flowers at different developmental stages and using five algorithms (geNorm, Normfinder, Delta Ct, BestKeeper, and RefFinder) to comprehensively evaluate the stability of candidate reference genes. The results showed that ACT and DnaJ were stably expressed in all samples and could be used as reference genes. In addition, the reliability of the screening results was further verified via an expression pattern analysis of the CFS gene that encodes flower specific transcription factor in different samples. The stable reference genes selected in this study provide the basis for future research on the expression analysis of functional genes related to the development of male and female flowers of S. suchowensis.
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Selection and validation of reference genes for normalization of qRT-PCR data to study the cannabinoid pathway genes in industrial hemp. PLoS One 2021; 16:e0260660. [PMID: 34928958 PMCID: PMC8687539 DOI: 10.1371/journal.pone.0260660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/13/2021] [Indexed: 11/19/2022] Open
Abstract
There has been significant interest in researching the pharmaceutical applications of Industrial hemp since its legalization three years ago. The crop is mostly dioecious and known for its production of phytocannabinoids, flavonoids, and terpenes. Although many scientific reports have showed gene expression analysis of hemp through OMICs approaches, unreliable reference genes for normalization of qRT-PCR data make it difficult to validate the OMICs data. Four software packages: geNorm, NormFinder, BestKeeper, and RefFinder were used to evaluate the differential gene expression patterns of 13 candidate reference genes under osmotic, heavy metal, hormonal, and UV stresses. EF-1α ranked as the most stable reference gene across all stresses, TUB was the most stable under osmotic stress, and TATA was the most stable under both heavy metal stress and hormonal stimuli. The expression patterns of two cannabinoid pathway genes, AAE1 and CBDAS, were used to validate the reliability of the selected reference genes. This work provides useful information for gene expression characterization in hemp and future research in the synthesis, transport, and accumulation of secondary metabolites.
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Song Q, Dou L, Zhang W, Peng Y, Huang M, Wang M. Public transcriptome database-based selection and validation of reliable reference genes for breast cancer research. Biomed Eng Online 2021; 20:124. [PMID: 34895237 PMCID: PMC8665499 DOI: 10.1186/s12938-021-00963-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/21/2021] [Indexed: 11/21/2022] Open
Abstract
Background Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is the most sensitive technique for evaluating gene expression levels. Choosing appropriate reference genes (RGs) is critical for normalizing and evaluating changes in the expression of target genes. However, uniform and reliable RGs for breast cancer research have not been identified, limiting the value of target gene expression studies. Here, we aimed to identify reliable and accurate RGs for breast cancer tissues and cell lines using the RNA-seq dataset. Methods First, we compiled the transcriptome profiling data from the TCGA database involving 1217 samples to identify novel RGs. Next, ten genes with relatively stable expression levels were chosen as novel candidate RGs, together with six conventional RGs. To determine and validate the optimal RGs we performed qRT-PCR experiments on 87 samples from 11 types of surgically excised breast tumor specimens (n = 66) and seven breast cancer cell lines (n = 21). Five publicly available algorithms (geNorm, NormFinder, ΔCt method, BestKeeper, and ComprFinder) were used to assess the expression stability of each RG across all breast cancer tissues and cell lines. Results Our results show that RG combinations SF1 + TRA2B + THRAP3 and THRAP3 + RHOA + QRICH1 showed stable expression in breast cancer tissues and cell lines, respectively, and that they displayed good interchangeability. We propose that these combinations are optimal triplet RGs for breast cancer research. Conclusions In summary, we identified novel and reliable RG combinations for breast cancer research based on a public RNA-seq dataset. Our results lay a solid foundation for the accurate normalization of qRT-PCR results across different breast cancer tissues and cells. Supplementary Information The online version contains supplementary material available at 10.1186/s12938-021-00963-8.
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Affiliation(s)
- Qiang Song
- Department of Central Laboratory, Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Chongqing, 404000, China
| | - Lu Dou
- Department of Central Laboratory, Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Chongqing, 404000, China
| | - Wenjin Zhang
- Department of Central Laboratory, Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Chongqing, 404000, China
| | - Yang Peng
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Man Huang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, No.165, Xin Cheng Lu, Wanzhou, Chongqing, 404000, China.
| | - Mengyuan Wang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, No.165, Xin Cheng Lu, Wanzhou, Chongqing, 404000, China.
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Chen Y, Luo B, Liu C, Zhang Z, Zhou C, Zhou T, Peng G, Wang X, Li W, Wu C, Rao L, Wang Q. Identification of reliable reference genes for quantitative real-time PCR analysis of the Rhus chinensis Mill. leaf response to temperature changes. FEBS Open Bio 2021; 11:2763-2773. [PMID: 34403204 PMCID: PMC8487043 DOI: 10.1002/2211-5463.13275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/25/2021] [Accepted: 08/16/2021] [Indexed: 11/24/2022] Open
Abstract
Rhus chinensis Mill. (RCM) is the host plant of Galla chinensis, which is valued in traditional medicine. Environmental temperature directly determines the probability of gallnut formation and RCM growth. At present, there is no experiment to systematically analyse the stability of internal reference gene (RG) expression in RCM. In this experiment, leaves that did not form gallnuts were used as the control group, while leaves that formed gallnuts were used as the experimental group. First, we conducted transcriptome experiments on RCM leaves to obtain 45 103 differential genes and functional enrichment annotations between the two groups. On this basis, this experiment established a transcriptional gene change model of leaves in the process of gallnut formation after being bitten by aphids, and RCM reference candidate genes were screened from RNA sequencing (RNA‐seq) data. This study is based on RCM transcriptome data and evaluates the stability of 11 potential reference genes under cold stress (4 °C) and heat stress (34 °C), using three statistical algorithms (geNorm, NormFinder, and BestKeeper). The results show that GAPDH1 + PP2A2/UBQ are stable reference genes under heat stress, while GAPDH1 + ACT are the most stable under cold stress. This study is the first to screen candidate reference genes in RCM and could help guide future molecular studies in this genus.
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Affiliation(s)
- Yanchao Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China.,Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Changsha, China
| | - Biao Luo
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China.,Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Changsha, China
| | - Chuwei Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China.,Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Changsha, China
| | - Zhengfeng Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Chi Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China.,Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Changsha, China
| | - Ting Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China.,Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Changsha, China
| | - Guoping Peng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China.,Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Changsha, China
| | - Xujun Wang
- Hunan Academy of Forestry, Changsha, China
| | - Waichin Li
- Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, China
| | - Chuan Wu
- Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, China.,School of Metallurgy and Environment, Central South University, Changsha, China
| | - Liqun Rao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China.,Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Changsha, China
| | - Qiming Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China.,Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Changsha, China
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Xie M, Zhong Y, Lin L, Zhang G, Su W, Ni W, Qu M, Chen H. Evaluation of reference genes for quantitative real-time PCR normalization in the scarab beetle Holotrichia oblita. PLoS One 2020; 15:e0240972. [PMID: 33085726 PMCID: PMC7577503 DOI: 10.1371/journal.pone.0240972] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022] Open
Abstract
Quantitative real-time polymerase chain reaction (qPT-PCR) is commonly used to analyze gene expression, however, the accuracy of the normalized results is affected by the expression stability of reference genes. Holotrichia oblita (Coleoptera: Scarabaeidae) causes serious damage to crops. Reliable reference genes in H. oblita are needed for qRT-PCR analysis. Therefore, we evaluated 13 reference genes under biotic and abiotic conditions. RefFinder provided a comprehensive stability ranking, and geNorm suggested the optimal number of reference genes for normalization. RPL13a and RPL18 were the most suitable reference genes for developmental stages, tissues, and temperature treatments; RPL13a and RPS3 were the most suitable for pesticide and photoperiod treatments; RPS18 and RPL18 were the most suitable for the two sexes. We validated the normalized results using odorant-binding protein genes as target genes in different tissues. Compared with the selected suitable reference genes, the expression of OBP1 in antennae, abdomen, and wings, and OBP2 in antennae and wings were overestimated due to the instability of ACTb. These results identified several reliable reference genes in H. oblita for normalization, and are valuable for future molecular studies.
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Affiliation(s)
- Minghui Xie
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Yongzhi Zhong
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Lulu Lin
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Guangling Zhang
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Weihua Su
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Wanli Ni
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Mingjing Qu
- Shandong Peanut Research Institute, Qingdao, Shandong, China
| | - Haoliang Chen
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
- * E-mail:
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Song H, Mao W, Duan Z, Que Q, Zhou W, Chen X, Li P. Selection and validation of reference genes for measuring gene expression in Toona ciliata under different experimental conditions by quantitative real-time PCR analysis. BMC PLANT BIOLOGY 2020; 20:450. [PMID: 33003996 PMCID: PMC7528382 DOI: 10.1186/s12870-020-02670-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Before studying gene expression of different organisms, it is important to determine the best reference gene. At present, the most accurate method of detecting gene expression is quantitative real-time PCR (RT-qPCR). With this method, reference genes that are stable in different biological systems and under different conditions can be obtained. Toona ciliata Roem (T. ciliata). is a valuable and fast-growing timber specie. In this study, 20 reference genes were identified using RT-qPCR, as a primary prerequisite for future gene expression analysis. Four different methods, geNorm, NormFinder, BestKeeper, and RankAggreg were used to evaluate the expression stability of the 20 candidate reference genes in various tissues under different conditions. RESULTS The experimental results showed that TUB-α was the most stably expressed reference gene across all samples and UBC17 was the most stable in leaves and young stems under Hypsipyla robusta (H. robusta) and methyl jasmonate (MeJA) treatments. In addition, PP2C59 and UBC5B were the best-performing genes in leaves under H. robusta treatment, while HIS1 and ACT7 were the best reference genes in young stems. The two best reference genes were 60S-18 and TUB-α after treatment at 4 °C. The expression of HIS6 and MUB1 was the most stable under PEG6000 treatment. The accuracy of the selected reference genes was verified using the transcription factor MYB3 (TcMYB3) gene. CONCLUSIONS This is the first report to verify the best reference genes for normalizing gene expression in T. ciliata under different conditions, which will facilitate future elucidation of gene regulations in this species.
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Affiliation(s)
- Huiyun Song
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou, 510642, China
| | - Wenmai Mao
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou, 510642, China
| | - Zhihao Duan
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou, 510642, China
| | - Qingmin Que
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou, 510642, China
| | - Wei Zhou
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou, 510642, China
| | - Xiaoyang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou, 510642, China
| | - Pei Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China.
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou, 510642, China.
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Yang Z, Wang K, Aziz U, Zhao C, Zhang M. Evaluation of duplicated reference genes for quantitative real-time PCR analysis in genome unknown hexaploid oat ( Avena sativa L.). PLANT METHODS 2020; 16:138. [PMID: 33072174 PMCID: PMC7560290 DOI: 10.1186/s13007-020-00679-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/05/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Oat (Avena sativa L.), a hexaploid crop with unknown genome, has valuable nutritional, medicinal and pharmaceutical uses. However, no suitable RGs (reference genes) for qPCR (quantitative real-time PCR) has been documented for oat yet. Single-copy gene is often selected as RG, which is challengeable or impactable in unexplored polyploids. RESULTS In this study, eleven candidate RGs, including four duplicated genes, were selected from oat transcriptome. The stability and the optimal combination of these candidate RGs were assessed in 18 oat samples by using four statistical algorithms including the ΔCt method, geNorm, NormFinder and BestKeeper. The most stable RGs for "all samples", "shoots and roots of seedlings", "developing seeds" and "developing endosperms" were EIF4A (Eukaryotic initiation factor 4A-3), UBC21 (Ubiquitin-Conjugating Enzyme 21), EP (Expressed protein) and EIF4A respectively. Among these RGs, UBC21 was a four-copy duplicated gene. The reliability was validated by the expression patterns of four various genes normalized to the most and the least stable RGs in different sample sets. CONCLUSIONS Results provide a proof of concept that the duplicated RG is feasible for qPCR in polyploids. To our knowledge, this study is the first systematic research on the optimal RGs for accurate qPCR normalization of gene expression in different organs and tissues of oat.
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Affiliation(s)
- Zheng Yang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Kai Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Usman Aziz
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Cuizhu Zhao
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Meng Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
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Identification of Appropriate Reference Genes for Normalizing miRNA Expression in Citrus Infected by Xanthomonas citri subsp. citri. Genes (Basel) 2019; 11:genes11010017. [PMID: 31877985 PMCID: PMC7017248 DOI: 10.3390/genes11010017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 01/01/2023] Open
Abstract
MicroRNAs (miRNAs) are short noncoding RNA molecules that regulate gene expression at the posttranscriptional level. Reverse transcription-quantitative PCR (RT-qPCR) is one of the most common methods used for quantification of miRNA expression, and the levels of expression are normalized by comparing with reference genes. Thus, the selection of reference genes is critically important for accurate quantification. The present study was intended to identify appropriate miRNA reference genes for normalizing the level of miRNA expression in Citrus sinensis L. Osbeck and Citrus reticulata Blanco infected by Xanthomonas citri subsp. citri, which caused citrus canker disease. Five algorithms (Delta Ct, geNorm, NormFinder, BestKeeper and RefFinder) were used for screening reference genes, and two quantification approaches, poly(A) extension RT-qPCR and stem-loop RT-qPCR, were used to determine the most appropriate method for detecting expression patterns of miRNA. An overall comprehensive ranking output derived from the multi-algorithms showed that poly(A)-tailed miR162-3p/miR472 were the best reference gene combination for miRNA RT-qPCR normalization in citrus canker research. Candidate reference gene expression profiles determined by poly(A) RT-qPCR were more consistent in the two citrus species. To the best of our knowledge, this is the first systematic comparison of two miRNA quantification methods for evaluating reference genes. These results highlight the importance of rigorously assessing candidate reference genes and clarify some contradictory results in miRNA research on citrus.
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