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Liu J, Yang C, Bai M, Yan F, Qin H, Wang R, Wan Y, Li G. Selection and validation of reference genes for RT-qPCR analysis of different organs at various development stages in Caragana intermedia. Open Life Sci 2022; 17:1155-1164. [PMID: 36185405 PMCID: PMC9483831 DOI: 10.1515/biol-2022-0463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/28/2022] [Accepted: 06/14/2022] [Indexed: 11/15/2022] Open
Abstract
Reverse transcription quantitative PCR (RT-qPCR) is a technique widely used to investigate the expression of genes. An appropriate reference gene (RG) is essential for RT-qPCR analysis to obtain accurate and reliable results. Caragana intermedia plays an important role in afforestation as a bush. However, due to the lack of appropriate RGs, the research on development-related genes is limited. In this study, the selection for suitable RGs of different organs at various development stages to normalize the results of RT-qPCR about development-related genes was performed. To test the expression stability across all samples, we used the software algorithms such as geNorm, NormFinder, BestKeeper, and RefFinder to evaluate all the candidate RGs. Our results showed that CiEF1α was the most stable RG with little fluctuation among all samples. In addition, CiGAPDH in roots, CiSKIP1 in stems and leaves, and CiEF1α in different organs were selected as the most stable RGs. To confirm the applicability of the most stable RGs, the relative expression of CiWRKY17 was normalized using different candidate RGs. Taken together, our research laid a foundation for the study of development-related genes in C. intermedia.
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Affiliation(s)
- Jinhua Liu
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Chuang Yang
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Mingzhu Bai
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Feng Yan
- Ordos Forestry and Grassland Development Center, Ordos 017010, P.R. China
| | - Haiying Qin
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Ruigang Wang
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China.,Inner Mongolia Enterprise Key Laboratory of Tree Breeding, Mengshu Ecological Construction Group Co., Ltd., Hohhot 011517, P.R. China.,Inner Mongolia Engineering Research Center for Plant Gene Resources Mining and Molecular Breeding, Inner Mongolia Agricultural University, Hohhot 010021, P.R. China
| | - Yongqing Wan
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Guojing Li
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
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Selection and Evaluation of Potential Reference Genes for Quantitative Real-Time PCR in Agaricus blazei Based on Transcriptome Sequencing Data. BIOMED RESEARCH INTERNATIONAL 2021. [DOI: 10.1155/2021/6661842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Quantitative real-time PCR (qRT-PCR) is widely used to detect gene expression due to its high sensitivity, high throughput, and convenience. The accurate choice of reference genes is required for normalization of gene expression in qRT-PCR analysis. In order to identify the optimal candidates for gene expression analysis using qRT-PCR in Agaricus blazei, we studied the potential reference genes in this economically important edible fungus. In this study, transcriptome datasets were used as source for identification of candidate reference genes. And 27 potential reference genes including 21 newly stable genes, three classical housekeeping genes, and homologous genes of three ideal reference genes in Volvariella volvacea, were screened based on transcriptome datasets of A. blazei and previous studies. The expression stability of these genes was investigated by qRT-PCR analysis and further evaluated by four software packages, geNorm, NormFinder, BestKeeper, and RefFinder. Among these candidates, α-TUB (Tubulin alpha) and Cox5a (COX5A subunit VA of cytochrome c oxidase) were revealed as the most stable in fruit body, and suitable for 5 different developmental stages. α-TUB and ATP3 (ATP3 gamma subunit of the F1 sector of mitochondrial F1F0 ATP synthase) showed the most stable expression in stipe tissues and, Uqcrc (core subunit of the ubiquinol-cytochrome c reductase complex) and PUP3 (20S proteasome subunit beta 3) performed well in pileus tissues during the process of A. blazei development, while GAPDH (glyceraldehyde-3-phosphate dehydrogenase) was among the least stable genes in all sample sets. Finally, the Ableln3 (homology of eln3 gene of Coprinus cinereus) was adopted to validate the reliability of these stable and unstable reference genes, indicating that the use of unsuitable reference genes as internal controls could change the target gene’s expression pattern. This study can provide guidance for choosing reference genes for analyzing the expression pattern of target genes and facilitate the functional genomic investigation on fruit body formation and development, as well as stipe elongation and pileus expansion in A. blazei.
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Yin X, He T, Yi K, Zhao Y, Hu Y, Liu J, Zhang X, Meng L, Wang L, Liu H, Li Y, Cui G. Comprehensive evaluation of candidate reference genes for quantitative real-time PCR-based analysis in Caucasian clover. Sci Rep 2021; 11:3269. [PMID: 33558610 PMCID: PMC7870939 DOI: 10.1038/s41598-021-82633-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 01/19/2021] [Indexed: 11/08/2022] Open
Abstract
The forage species Caucasian clover (Trifolium ambiguum M. Bieb.), a groundcover plant, is resistant to both cold and drought. However, reference genes for qRT-PCR-based analysis of Caucasian clover are lacking. In this study, 12 reference genes were selected on the basis of transcriptomic data. These genes were used to determine the most stably expressed genes in various organs of Caucasian clover under cold, salt and drought stress for qRT-PCR-based analysis. Reference gene stability was analyzed by geNorm, NormFinder, BestKeeper, the ∆Ct method and RefFinder. Under salt stress, RCD1 and PPIL3 were the most stable reference genes in the leaves, and NLI1 and RCD1 were the most stable references genes in the roots. Under low-temperature stress, APA and EFTu-GTP were the most stable reference genes in the leaves, and the RCD1 and NLI2 genes were highly stable in the roots. Under 10% PEG-6000 stress, NLI1 and NLI2 were highly stable in the leaves, and RCD1 and PPIL3 were the most stable in the roots. Overall, RCD1 and NLI2 were the most stable reference genes in organs under normal conditions and across all samples. The most and least stable reference genes were validated by assessing their appropriateness for normalization via WRKY genes.
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Affiliation(s)
- Xiujie Yin
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Taotao He
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Kun Yi
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Yihang Zhao
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Yao Hu
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Jiaxue Liu
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Xiaomeng Zhang
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Lingdong Meng
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Lina Wang
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Haoyue Liu
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Yonggang Li
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Guowen Cui
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China.
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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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Pinheiro DH, Siegfried BD. Selection of reference genes for normalization of RT-qPCR data in gene expression studies in Anthonomus eugenii Cano (Coleoptera: Curculionidae). Sci Rep 2020; 10:5070. [PMID: 32193506 PMCID: PMC7081190 DOI: 10.1038/s41598-020-61739-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/25/2020] [Indexed: 01/29/2023] Open
Abstract
The pepper weevil, Anthonomus eugenii Cano (Coleoptera: Curculionidae), is the main insect pest of peppers (Capsicum spp.) throughout the southern U.S. and a potential target for novel control methods that may require gene expression analyses. Careful selection of adequate reference genes to normalize RT-qPCR data is an important prerequisite for gene expression studies since the expression stability of reference genes can be affected by the experimental conditions leading to biased or erroneous results. The lack of studies on validation of reference genes for RT-qPCR analysis in A. eugenii limits the investigation of gene expression, therefore it is needed a systematic selection of suitable reference genes for data normalization. In the present study, three programs (BestKeeper, geNorm and NormFinder) were used to analyze the expression stability of candidate reference genes (β-ACT, ArgK, EF1-α, GAPDH, RPL12, RPS23, α-TUB, 18S and 28S) in A. eugenii under different experimental conditions. Our results revealed that the most stably expressed reference genes in A. eugenii varied according to the experimental condition evaluated: developmental stages (EF1-α, 18S and RPL12), sex (RPS23 and RPL12), low temperature (GAPDH and α-TUB), high temperature (α-TUB and RPS23), all temperatures (α-TUB and GAPDH), starvation (RPL12 and α-TUB), and dsRNA exposure (α-TUB and RPL12). Our study provides for the first time valuable information on appropriate reference genes that can be used in the analysis of gene expression by RT-qPCR in biological experiments involving A. eugenii.
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Affiliation(s)
- Daniele H Pinheiro
- University of Florida, Entomology and Nematology Department, Charles Steinmetz Hall, P. O. Box 110620, Gainesville, FL, 32611-0620, United States
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, W5 Norte, P. O. Box 02372, Brasília, DF, 70770-917, Brazil
| | - Blair D Siegfried
- University of Florida, Entomology and Nematology Department, Charles Steinmetz Hall, P. O. Box 110620, Gainesville, FL, 32611-0620, United States.
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Sarwar MB, Ahmad Z, Anicet BA, Sajid M, Rashid B, Hassan S, Ahmed M, Husnain T. Identification and validation of superior housekeeping gene(s) for qRT-PCR data normalization in Agave sisalana (a CAM-plant) under abiotic stresses. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:567-584. [PMID: 32205931 PMCID: PMC7078421 DOI: 10.1007/s12298-020-00760-y] [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: 10/23/2019] [Revised: 12/26/2019] [Accepted: 01/08/2020] [Indexed: 05/24/2023]
Abstract
The adaptive mechanisms in Agave species enable them to survive and exhibit remarkable tolerance to abiotic stresses. Quantitative real-time PCR is a highly reliable approach for validation of targeted differential gene expression. However, stable housekeeping gene(s) is prerequisite for accurate normalization of expression data by qRT-PCR. Till date, no systematic validation study for candidate housekeeping gene identification or evaluation has been carried-out in Agave species. A total of 17 candidate housekeeping genes were identified from the de novo assembled transcriptomic data of A. sisalana and rigorously analyzed for expression stability assessment under drought, heat, cold and NaCl stress. Different statistical algorithms like geNorm, BestKeeper, NormFinder, and RefFinder on expression data determined the superior housekeeping gene(s) for accurate normalization of the gene of interest (GOI). The comprehensive evaluation revealed the β-Tub 4, WIN-1 and CYC-A as the most stable, while EEF1α, GAPDH, and UBE2 were ranked as the least stable genes in pooled samples. Pairwise combination by geNorm showed that up to two housekeeping genes would be adequate to normalize the GOI expression data precisely. Validation of identified most and least stable housekeeping genes was carried-out by normalizing the expression data of AsHSP20 under abiotic stress conditions. Copy number of AsHSP20 gene supports the reliability of the genes used for normalization. This is the first report on the screening and validation of the housekeeping genes under abiotic stress condition in A. sisalana that would assist to understand the stress tolerance mechanisms by novel gene identification and accurate validation.
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Affiliation(s)
- Muhammad Bilal Sarwar
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Zarnab Ahmad
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Batcho Agossa Anicet
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Moon Sajid
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Bushra Rashid
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Sameera Hassan
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Mukhtar Ahmed
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- National Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
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Selection and Validation of Appropriate Reference Genes for Quantitative RT-PCR Analysis in Rubia yunnanensis Diels Based on Transcriptome Data. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5824841. [PMID: 31998793 PMCID: PMC6973195 DOI: 10.1155/2020/5824841] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/06/2019] [Accepted: 09/28/2019] [Indexed: 12/17/2022]
Abstract
Real-time quantitative polymerase chain reaction (RT-qPCR) has been widely applied in gene expression and transcription abundance analysis because of its high sensitivity, good repeatability, and strong specificity. Selection of relatively stable reference genes is a precondition in order to obtain the reliable analysis results. However, little is known about evaluation of a set of reference genes through scientific experiments in Rubia plants. Here, 15 candidate reference genes were selected from R. yunnanensis transcriptome database and analyzed under abiotic stresses, hormone treatments, and different tissues. Among these 15 candidate reference genes, heterogeneous nuclear ribonucleoprotein (hnRNP), TATA binding protein (TBP), ribosomal protein L5 (RPL5), malate dehydrogenase (MDH), and elongation factor 1-alpha (EF-1α) were indicated as the five most stable reference genes by four statistical programs (geNorm, NormFinder, BestKeeper, and RefFinder). Ultimately, the validity of reference genes was confirmed by normalizing the expression of o-succinylbenzoate-CoA ligase (OSBL) and isochorismate synthase (ICS) involved in the anthraquinone biosynthesis pathway in different tissues and hormone treatments. Meanwhile, four other putative genes involved in the anthraquinone biosynthesis pathway were also normalized with the selected reference genes, which showed similar expression levels with those given by transcriptome data. This work is the first research that aims at a systematic validation on the stability of reference genes selected from R. yunnanensis transcriptome data and will be conducive to analyze gene expression in R. yunnanensis or other Rubia species.
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Shen J, Wu Y, Jiang Z, Xu Y, Zheng T, Wang J, Cheng T, Zhang Q, Pan H. Selection and validation of appropriate reference genes for gene expression studies in Forsythia. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:173-188. [PMID: 32158128 PMCID: PMC7036397 DOI: 10.1007/s12298-019-00731-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/08/2019] [Accepted: 11/04/2019] [Indexed: 05/30/2023]
Abstract
The qRT-PCR method has been widely used to detect gene expression level in plants, helping to understand the molecular mechanisms. However, there are few researches which focus on the selection of the internal reference genes in Forsythia. To select the appropriate reference genes of Forsythia aimed at qRT-PCR normalization, twelve candidate reference genes were selected from our transcriptome data. Their expression was assessed by RT-PCR analysis in 47 Forsythia samples, including 12 species cultivars, different organs and tissues. GeNorm, NormFinder, and BestKeeper software were used to select the appropriate reference genes, AG and PSY were used to verify the accuracy of the outcome. The results showed that UKN1 was a stable reference gene in leaves of twelve Forsythia germplasms and in different developmental stages of fruits. MTP, ABCT + MTP, and ABCT + MTP + TIP were stable reference genes in different organs. ACT and SDH were stable reference genes in different flower tissues and different developmental stages of the flower buds. When Forsythia plants were stressed with PEG or ABA, SDH + UKN1 + G6PD was the stable reference gene group for qRT-PCR. The results provided the basis for investigating the physiological and biochemical processes of Forsythia related to medicinal and ornamental properties, and drought-resistance in the level of gene expression.
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Affiliation(s)
- Jianshuang Shen
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, China
- National Engineering Research Center for Floriculture, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment of Beijing Municipal Education Commission, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Tsinghua East Road No. 35, Beijing, 100083 China
| | - Yutong Wu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, China
- National Engineering Research Center for Floriculture, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment of Beijing Municipal Education Commission, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Tsinghua East Road No. 35, Beijing, 100083 China
| | - Zhiyi Jiang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, China
- National Engineering Research Center for Floriculture, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment of Beijing Municipal Education Commission, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Tsinghua East Road No. 35, Beijing, 100083 China
| | - Yang Xu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, China
- National Engineering Research Center for Floriculture, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment of Beijing Municipal Education Commission, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Tsinghua East Road No. 35, Beijing, 100083 China
| | - Tangchun Zheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, China
- National Engineering Research Center for Floriculture, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment of Beijing Municipal Education Commission, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Tsinghua East Road No. 35, Beijing, 100083 China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, China
- National Engineering Research Center for Floriculture, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment of Beijing Municipal Education Commission, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Tsinghua East Road No. 35, Beijing, 100083 China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, China
- National Engineering Research Center for Floriculture, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment of Beijing Municipal Education Commission, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Tsinghua East Road No. 35, Beijing, 100083 China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, China
- National Engineering Research Center for Floriculture, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment of Beijing Municipal Education Commission, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Tsinghua East Road No. 35, Beijing, 100083 China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, China
- National Engineering Research Center for Floriculture, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment of Beijing Municipal Education Commission, Beijing, China
- College of Landscape Architecture, Beijing Forestry University, Tsinghua East Road No. 35, Beijing, 100083 China
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Wan Y, Hong A, Zhang Y, Liu Y. Selection and validation of reference genes of Paeonia lactiflora in growth development and light stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:1097-1105. [PMID: 31404229 PMCID: PMC6656899 DOI: 10.1007/s12298-019-00684-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/03/2019] [Accepted: 06/06/2019] [Indexed: 05/14/2023]
Abstract
The stem of Paeonia lactiflora will bend when it grows in greenhouse at a low light intensity. It is important to explore causes of morphological changes of peony to improve its quality. Gene expression can be evaluated by quantitative real-time PCR, based on reference gene. However, systematic selection of reference genes under weak lighting for herbaceous peony is lacking. To address this problem, we first selected 10 candidate reference genes based on a coefficient of variation of gene expression from peony stem transcriptome data. Then, geNorm, NormFinder and BestKeeper were applied to assess the stability of the genes, and RankAggreg was used to give a comprehensive ranking. The results show that there are some differences in optimal reference genes among samples from different organs and under the two lighting conditions, and the optimal number of suitable reference genes is distinct. Two selected suitable reference genes were then used to normalize target genes, and the results were compared with transcriptome data. Consistent gene expression trends were obtained, indicating the reliability of the method. To the best of our knowledge, this is the first time reference genes for herbaceous peony were selected in different organs, developmental stages and under two kinds of lighting conditions. The findings can provide a practical method for selecting reference genes for peony under these conditions and demonstrate a useful combination of reference genes.
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Affiliation(s)
- Yingling Wan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Aiying Hong
- Management Office of Caozhou Peony Garden, Heze, 274000 Shandong People’s Republic of China
| | - Yixuan Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Yan Liu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 People’s Republic of China
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Sun H, Jiang X, Sun M, Cong H, Qiao F. Evaluation of reference genes for normalizing RT-qPCR in leaves and suspension cells of Cephalotaxus hainanensis under various stimuli. PLANT METHODS 2019; 15:31. [PMID: 30962812 PMCID: PMC6434779 DOI: 10.1186/s13007-019-0415-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Reverse transcription quantitative real-time PCR (RT-qPCR) is a widely used approach for investigating gene expression levels in plants because of its high reproducibility, sensitivity, accuracy and rapidness. Evaluation of reference genes for normalizing RT-qPCR data is a necessary step, especially in new plant varieties. Cephalotaxus hainanensis is a precious medicinal plant belonging to the family of Cephalotaxaceae and no RT-qPCR studies have been reported on it. RESULTS In this study, 9 candidate reference genes were selected from the transcriptome data of C. hainanensis; 3 statistical algorithms (geNorm, NormFinder, BestKeeper) were applied to evaluate their expression stabilities through 180 samples under 6 stimuli treatments in leaves and leaf-derived suspension cultured cells; a comprehensive stabilities ranking was also performed by RefFinder. The results showed that suitable reference genes in C. hainanensis should be selected for normalization relative to different experimental sets. 18S showed a higher stability than other candidate reference genes which ranked at the top two suitable genes under all experimental setups in this study. CONCLUSION This study is the first to evaluate the stability of reference genes in C. hainanensis and supply an important foundation to use the RT-qPCR for an accurate and far-reaching gene expression analysis in C. hainanensis.
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Affiliation(s)
- Huapeng Sun
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture/Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan People’s Republic of China
| | - Xuefei Jiang
- Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources/Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228 Hainan People’s Republic of China
| | - Mengli Sun
- Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources/Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228 Hainan People’s Republic of China
| | - Hanqing Cong
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture/Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan People’s Republic of China
| | - Fei Qiao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture/Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan People’s Republic of China
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11
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Qu R, Miao Y, Cui Y, Cao Y, Zhou Y, Tang X, Yang J, Wang F. Selection of reference genes for the quantitative real-time PCR normalization of gene expression in Isatis indigotica fortune. BMC Mol Biol 2019; 20:9. [PMID: 30909859 PMCID: PMC6434783 DOI: 10.1186/s12867-019-0126-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/16/2019] [Indexed: 01/08/2023] Open
Abstract
Background Isatis indigotica, a traditional Chinese medicine, produces a variety of active ingredients. However, little is known about the key genes and corresponding expression profiling involved in the biosynthesis pathways of these ingredients. Quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful, commonly-used method for gene expression analysis, but the accuracy of the quantitative data produced depends on the appropriate selection of reference genes. Results In this study, the systematic analysis of the reference genes was performed for quantitative real-Time PCR normalization in I. indigotica. We selected nine candidate reference genes, including six traditional housekeeping genes (ACT, α-TUB, β-TUB, UBC, CYP, and EF1-α), and three newly stable internal control genes (MUB, TIP41, and RPL) from a transcriptome dataset of I. indigotica, and evaluated their expression stabilities in different tissues (root, stem, leaf, and petiole) and leaves exposed to three abiotic treatments (low-nitrogen, ABA, and MeJA) using geNorm, NormFinder, BestKeeper, and comprehensive RefFind algorithms. The results demonstrated that MUB and EF1-α were the two most stable reference genes for all samples. TIP41 as the optimal reference gene for low-nitrogen stress and MeJA treatment, while ACT had the highest ranking for ABA treatment and CYP was the most suitable for different tissues. Conclusions The results revealed that the selection and validation of appropriate reference genes for normalizing data is mandatory to acquire accurate quantification results. The necessity of specific internal control for specific conditions was also emphasized. Furthermore, this work will provide valuable information to enhance further research in gene function and molecular biology on I. indigotica and other related species. Electronic supplementary material The online version of this article (10.1186/s12867-019-0126-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Renjun Qu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yujing Miao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yingjing Cui
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yiwen Cao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoqing Tang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jie Yang
- Institute of Food Crops, Jiangsu Academy Agriculture Sciences, Nanjing, 210014, China
| | - Fangquan Wang
- Institute of Food Crops, Jiangsu Academy Agriculture Sciences, Nanjing, 210014, China
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Su W, Yuan Y, Zhang L, Jiang Y, Gan X, Bai Y, Peng J, Wu J, Liu Y, Lin S. Selection of the optimal reference genes for expression analyses in different materials of Eriobotrya japonica. PLANT METHODS 2019; 15:7. [PMID: 30705689 PMCID: PMC6348664 DOI: 10.1186/s13007-019-0391-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 01/19/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Loquat (Eriobotrya japonica) is a subtropical tree bearing fruit that ripens during late spring and early summer, which is the off-season for fruit production. The specific flowering habit of loquat, which starts in fall and ends in winter, has attracted an increasing number of researchers who believe that it may represent an ideal model for studying flowering shift adaptations to climate change in Rosaceae. These studies require an understanding of gene expression patterns within the fruit and other tissues of this plant. Although ACTINs (ACTs) have previously been used as reference genes (RGs) for gene expression studies in loquats, a comprehensive analysis of whether these RGs are optimal for normalizing RT-qPCR data has not been performed. RESULTS In this study, 11 candidate RGs (RIBOSOMAL-LIKE PROTEIN4 (RPL4), RIBOSOMAL-LIKE PROTEIN18 (RPL18), Histone H3.3 (HIS3), Alpha-tubulin-3 (TUA3), S-Adenosyl Methionine Decarboxylase (SAMDC), TIP41-like Family Protein (TIP41), (UDP)-glucose Pyrophosphorylase (UGPase), 18S ribosomal RNA (18S), Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH), Plasma Intrinsic Protein 2 (PIP2) and ACTIN(ACT)) were assessed to determine their expression stability in 23 samples from different tissues or organs of loquat. Integrated expression stability evaluations using five computational statistical methods (GeNorm, NormFinder, ΔCt, BestKeeper, and RefFinder) suggested that a RG set, including RPL4, RPL18, HIS3 and TUA3, was the most stable one across all of the tested loquat samples. The expression pattern of EjCDKB1;2 in the tested loquat tissues normalized to the selected RG set demonstrated its reliability. CONCLUSIONS This study reveals the reliable RGs for accurate normalization of gene expression in loquat. In addition, our findings demonstrate an efficient system for identifying the most effective RGs for different organs, which may be applied to related rosaceous crops.
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Affiliation(s)
- Wenbing Su
- Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture), College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
- Key Laboratory of Loquat Germplasm Innovation and Utilization, Putian University, Putian, 351100 China
| | - Yuan Yuan
- Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture), College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
- Guangzhou Institute of Agricultural Sciences, Guangzhou, 510308 China
| | - Ling Zhang
- Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture), College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Yuanyuan Jiang
- Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture), College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Xiaoqing Gan
- Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture), College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Yunlu Bai
- Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture), College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Jiangrong Peng
- Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture), College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Jincheng Wu
- Key Laboratory of Loquat Germplasm Innovation and Utilization, Putian University, Putian, 351100 China
| | - Yuexue Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 China
- Key Laboratory of Loquat Germplasm Innovation and Utilization, Putian University, Putian, 351100 China
| | - Shunquan Lin
- Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture), College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
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Selection and Validation of Novel RT-qPCR Reference Genes under Hormonal Stimuli and in Different Tissues of Santalum album. Sci Rep 2018; 8:17511. [PMID: 30504917 PMCID: PMC6269485 DOI: 10.1038/s41598-018-35883-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 11/07/2018] [Indexed: 02/04/2023] Open
Abstract
Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a widely used technique to investigate gene expression levels due to its high throughput, specificity, and sensitivity. An appropriate reference gene is essential for RT-qPCR analysis to obtain accurate and reliable results. To date, no reliable reference gene has been validated for the economically tropical tree, sandalwood (Santalum album L.). In this study, 13 candidate reference genes, including 12 novel putative reference genes selected from a large set of S. album transcriptome data, as well as the currently used β-actin gene (ACT), were validated in different tissues (stem, leaf, root and callus), as well as callus tissue under salicylic acid (SA), jasmonic acid methyl ester (MeJA), and gibberellin (GA) treatments using geNorm, NormFinder, BestKeeper, Delta Ct and comprehensive RefFinder algorithms. Several novel candidate reference genes were much more stable than the currently used traditional gene ACT. ODD paired with Fbp1 for SA treatment, CSA and Fbp3 for MeJA treatment, PP2C and Fbp2 for GA treatment, as well as Fbp1 combined with Fbp2 for the total of three hormone treatments were the most accurate reference genes, respectively. FAB1A, when combined with PP2C, was identified as the most suitable reference gene combination for the four tissues tested, while the combination of HLMt, PPR and FAB1A were the most optimal reference genes for all of the experimental samples. In addition, to verify our results, the relative expression level of the SaSSy gene was evaluated by the validated reference genes and their combinations in the three S. album tissues and under MeJA treatment. The evaluated reference genes in this study will improve the accuracy of RT-qPCR analysis and will benefit S. album functional genomics studies in different tissues and under hormone stimuli in the future.
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Yan X, Qian C, Yin X, Fan X, Zhao X, Gu M, Wang T, Ma XF. A whole-transcriptome approach to evaluate reference genes for quantitative diurnal gene expression studies under natural field conditions in Tamarix ramosissima leaves. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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15
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Park M, Hong SG, Park H, Lee BH, Lee H. Identification of reference genes for RT-qPCR in the Antarctic moss Sanionia uncinata under abiotic stress conditions. PLoS One 2018; 13:e0199356. [PMID: 29920565 PMCID: PMC6007896 DOI: 10.1371/journal.pone.0199356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/06/2018] [Indexed: 12/31/2022] Open
Abstract
Sanionia uncinata is a dominant moss species in the maritime Antarctic. Due to its high adaptability to harsh environments, this extremophile plant has been considered a good target for studying the molecular adaptation mechanisms of plants to a variety of environmental stresses. Despite the importance of S. uncinata as a representative Antarctic plant species for the identification and characterization of genes associated with abiotic stress tolerance, suitable reference genes, which are critical for RT-qPCR analyses, have not yet been identified. In this report, 11 traditionally used and 6 novel candidate reference genes were selected from transcriptome data of S. uncinata and the expression stability of these genes was evaluated under various abiotic stress conditions using three statistical algorithms; geNorm, NormFinder, and BestKeeper. The stability ranking analysis selected the best reference genes depending on the stress conditions. Among the 17 candidates, the most stable references were POB1 and UFD2 for cold stress, POB1 and AKB for drought treatment, and UFD2 and AKB for the field samples from a different water contents in Antarctica. Overall, novel genes POB1 and AKB were the most reliable references across all samples, irrespective of experimental conditions. In addition, 6 novel candidate genes including AKB, POB1 and UFD2, were more stable than the housekeeping genes traditionally used for internal controls, indicating that transcriptome data can be useful for identifying novel robust normalizers. The reference genes validated in this study will be useful for improving the accuracy of RT-qPCR analysis for gene expression studies of S. uncinata in Antarctica and for further functional genomic analysis of bryophytes.
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Affiliation(s)
- Mira Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
- Department of Life Sciences, Sogang University, Seoul, South Korea
| | - Soon Gyu Hong
- Division of Life Sciences, Korea Polar Research Institute, Incheon, South Korea
- Polar Science, University of Science & Technology, Daejeon, South Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
- Polar Science, University of Science & Technology, Daejeon, South Korea
| | - Byeong-ha Lee
- Department of Life Sciences, Sogang University, Seoul, South Korea
- * E-mail: (HL); (B-hL)
| | - Hyoungseok Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
- Polar Science, University of Science & Technology, Daejeon, South Korea
- * E-mail: (HL); (B-hL)
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16
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Wang B, Du H, Yao Z, Ren C, Ma L, Wang J, Zhang H, Ma H. Validation of reference genes for accurate normalization of gene expression with quantitative real-time PCR in Haloxylon ammodendron under different abiotic stresses. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:455-463. [PMID: 29692553 PMCID: PMC5911265 DOI: 10.1007/s12298-018-0520-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/20/2017] [Accepted: 02/08/2018] [Indexed: 05/27/2023]
Abstract
Haloxylon ammodendron plays an important role in maintaining the structure and function of the entire ecosystem where it grows. No suitable reference genes have been reported in H. ammodendron plants to date. In this study, a total of 8 reference genes (18S, ACT1, ACT7, UBC18, TUA5, GAPDH, EF-1α and UBQ10) were selected from the available trancriptome database, and the expression stability of these 8 candidate genes was validated under different abiotic stress with three different statistical algorithms (geNorm, NormFinder and BestKeeper). The results produced from different models were in agreement with each other essentially: 18S and TUA5 were the most stable genes under drought stress, 18S, the most stable gene under heat stress and mechanical damage, ACT7 and UBC18, stable under salt stress while TUA5 and GAPDH expressed constantly under mechanical damage, and ACT1 expressed steadily under cold conditions. Expression profiles of several stress response genes, including FT-5, FT-9, DREB2A and DREB2C, were further confirmed with various candidate reference genes. None of the candidate genes showed a constant expression among all tested samples. Hence, it's essential to use more than one reference gene in order to guarantee the accuracy of quantitative real-time PCR. The results of this study will contribute to the accuracy and reliability in transcripts quantification, which is of significance to transcription-based studies and applications in this important shrub H. ammodendron.
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Affiliation(s)
- Bo Wang
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Huihui Du
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Zhengpei Yao
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Cai Ren
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Li Ma
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Jiao Wang
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Hua Zhang
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Hao Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
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Liang W, Zou X, Carballar-Lejarazú R, Wu L, Sun W, Yuan X, Wu S, Li P, Ding H, Ni L, Huang W, Zou S. Selection and evaluation of reference genes for qRT-PCR analysis in Euscaphis konishii Hayata based on transcriptome data. PLANT METHODS 2018; 14:42. [PMID: 29881443 PMCID: PMC5985561 DOI: 10.1186/s13007-018-0311-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 05/29/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Quantitative real-time reverse transcription-polymerase chain reaction has been widely used in gene expression analysis, however, to have reliable and accurate results, reference genes are necessary to normalize gene expression under different experimental conditions. Several reliable reference genes have been reported in plants of Traditional Chinese Medicine, but none have been identified for Euscaphis konishii Hayata. RESULTS In this study, 12 candidate reference genes, including 3 common housekeeping genes and 9 novel genes based on E. konishii Hayata transcriptome data were selected and analyzed in different tissues (root, branch, leaf, capsule and seed), capsule and seed development stages. Expression stability was calculated using geNorm and NormFinder, the minimal number of reference genes required for accurate normalization was calculated by Vn/Vn + 1 using geNorm. EkEEF-5A-1 and EkADF2 were the two most stable reference genes for all samples, while EkGSTU1 and EkGAPDH were the most stable reference genes for tissue samples. For seed development stages, EkGAPDH and EkEEF-5A-1 were the most stable genes, whereas EkGSTU1 and EkGAPDH were identified as the two most stable genes in the capsule development stages. Two reference genes were sufficient to normalize gene expression across all sample sets. CONCLUSION Results of this study revealed that suitable reference genes should be selected for different experimental samples, and not all the common reference genes are suitable for different tissue samples and/or experimental conditions. In this study, we present the first data of reference genes selection for E. konishii Hayata based on transcriptome data, our data will facilitate further studies in molecular biology and gene function on E. konishii Hayata and other closely related species.
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Affiliation(s)
- Wenxian Liang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoxing Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Lingjiao Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weihong Sun
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xueyuan Yuan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Songqing Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Pengfei Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hui Ding
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin Ni
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Huang
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuangquan Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
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18
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Zhang L, Zhang Q, Jiang Y, Li Y, Zhang H, Li R. Reference genes identification for normalization of qPCR under multiple stresses in Hordeum brevisubulatum. PLANT METHODS 2018; 14:110. [PMID: 30568722 PMCID: PMC6297944 DOI: 10.1186/s13007-018-0379-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/10/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Real-time quantitative PCR has been widely used as the most reliable method to measure gene expression, due to its high accuracy and specificity. Wild barley (Hordeum brevisubulatum (Trin.) Link) is a wild relative species in Triticeae that has strong tolerance to abiotic stresses and extremely wide adaptation. However, suitable references gene have not been documented for standardization of gene expression in wild barley under abiotic stress. RESULTS Here we report the first systematic and comprehensive analysis of reference genes for quantitative real-time PCR standardization in wild barley. We selected 11 genes, including ACT (Actin), ADP (ADP-ribosylation factor 1), CYP2 (Cyclophilin 2), EF-1α (Elongation factor 1-alpha), GAPDH (Glyceraldehyde 3-phosphate dehydrogenase), HSP90 (Heat shock protein 90), TUBα (Alpha-tubulin), TUBβ6 (Beta-tubulin 6), UBI (Ubiquitin), 18SrRNA-1 (guanine1575-N7-methyltransferase) and 18SrRNA-3 (adenine1779-N6-dimethyltransferase) from a wild barley transcriptome database and analyzed their expression stabilities in shoots and roots of wild barley seedling under various stress conditions using comparative ΔCt, BestKeeper, Normfinder and geNorm software. The results demonstrated that ADP was the most suitable reference gene in salt stress while UBI showed peak stability under mannitol and ABA stress; EF-1α was the most appropriate reference gene for PEG, GA3, ethylene and heat stress; 18SrRNA-3 was the best choice for cold stress; and TUBα was the first stable gene across different tissues. CONCLUSIONS Our main contribution was to identify reference genes with suitable and stable expression in wild barley under various stress conditions and in different tissues to provide a useful resource for future studies. The results demonstrate the importance of transcriptome data as a useful resource for the screening of candidate reference genes and highlight the need for specific reference genes for specific conditions. Furthermore, these findings will provide valuable information for wild barley and relative species for future research.
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Affiliation(s)
- Lili Zhang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Qike Zhang
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Ying Jiang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yang Li
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Haiwen Zhang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ruifen Li
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Evaluation of reference genes for reverse transcription quantitative real-time PCR (RT-qPCR) studies in Silene vulgaris considering the method of cDNA preparation. PLoS One 2017; 12:e0183470. [PMID: 28817728 PMCID: PMC5560574 DOI: 10.1371/journal.pone.0183470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 08/04/2017] [Indexed: 01/05/2023] Open
Abstract
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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