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Satterlee JW, Alonso D, Gramazio P, Jenike KM, He J, Arrones A, Villanueva G, Plazas M, Ramakrishnan S, Benoit M, Gentile I, Hendelman A, Shohat H, Fitzgerald B, Robitaille GM, Green Y, Swartwood K, Passalacqua MJ, Gagnon E, Hilgenhof R, Huggins TD, Eizenga GC, Gur A, Rutten T, Stein N, Yao S, Poncet A, Bellot C, Frary A, Knapp S, Bendahmane M, Särkinen T, Gillis J, Van Eck J, Schatz MC, Eshed Y, Prohens J, Vilanova S, Lippman ZB. Convergent evolution of plant prickles by repeated gene co-option over deep time. Science 2024; 385:eado1663. [PMID: 39088611 DOI: 10.1126/science.ado1663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/06/2024] [Indexed: 08/03/2024]
Abstract
An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. In this work, we genetically dissected repeated origins and losses of prickles-sharp epidermal projections-that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genus Solanum. Homologs underlie prickle formation across angiosperms that collectively diverged more than 150 million years ago, including rice and roses. By developing new Solanum genetic systems, we leveraged this discovery to eliminate prickles in a wild species and an indigenously foraged berry. Our findings implicate a shared hormone activation genetic program underlying evolutionarily widespread and recurrent instances of plant morphological innovation.
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Affiliation(s)
- James W Satterlee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - David Alonso
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Katharine M Jenike
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jia He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Andrea Arrones
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Gloria Villanueva
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Srividya Ramakrishnan
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Matthias Benoit
- French National Institute for Agriculture, Food, and Environment, Laboratory of Plant-Microbe Interactions, Toulouse, France
| | - Iacopo Gentile
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Hagai Shohat
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Blaine Fitzgerald
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Gina M Robitaille
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yumi Green
- Boyce Thompson Institute, Ithaca, NY, USA
| | | | - Michael J Passalacqua
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Edeline Gagnon
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | | | - Trevis D Huggins
- USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, AR, USA
| | - Georgia C Eizenga
- USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, AR, USA
| | - Amit Gur
- Cucurbits Section, Department of Vegetable Sciences, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishay, Israel
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Crop Plant Genetics, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - Shengrui Yao
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, USA
- Sustainable Agriculture Sciences Center, New Mexico State University, Alcalde, NM, USA
| | - Adrien Poncet
- Laboratoire Reproduction et Developpement des Plantes, INRAE, CNRS, Universite Lyon, Ecole Normale Superieure de Lyon, Lyon, France
| | - Clement Bellot
- Laboratoire Reproduction et Developpement des Plantes, INRAE, CNRS, Universite Lyon, Ecole Normale Superieure de Lyon, Lyon, France
| | - Amy Frary
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | | | - Mohammed Bendahmane
- Laboratoire Reproduction et Developpement des Plantes, INRAE, CNRS, Universite Lyon, Ecole Normale Superieure de Lyon, Lyon, France
| | | | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Yuval Eshed
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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Ghosh R, Metze D, Sant S, Shaikh M, Deshpande A, Firake DM, Pandit S. Chemical ecology of Himalayan eggplant variety's antixenosis: identification of geraniol as an oviposition deterrent against the eggplant shoot and fruit borer. THE NEW PHYTOLOGIST 2023; 240:1259-1274. [PMID: 36918501 DOI: 10.1111/nph.18877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Eggplant (Solanum melongena) suffers severe losses due to a multi-insecticide-resistant lepidopteran pest, shoot and fruit borer (SFB, Leucinodes orbonalis). Heavy and combinatorial application of pesticides for SFB control renders eggplant risky for human consumption. We observed that gravid SFB females do not oviposit on Himalayan eggplant variety RC-RL-22 (RL22). We hypothesized that RL22 contained an antixenosis factor. Females' behavior indicated that the RL22 cue they perceived was olfactory. To identify it, leaf volatile blends of seven eggplant varieties were profiled using solid phase microextraction and gas chromatography mass spectrometry. Seven RL22-specific compounds were detected in the plant headspace. In choice assays, oviposition deterrence efficacies of these candidate compounds were independently tested by their foliar application on SFB-susceptible varieties. Complementation of geraniol, which was exclusively found in RL22, reduced oviposition (> 90%). To validate geraniol's role in RL22's SFB-deterrence, we characterized RL22's geraniol synthase and silenced its gene in planta, using virus-induced gene silencing. Geraniol biosynthesis suppression rendered RL22 SFB-susceptible; foliar geraniol application on the geraniol synthase-silenced plants restored oviposition deterrence. We infer that geraniol is RL22's SFB oviposition deterrent. The use of natural compounds like geraniol, which influence the chemical ecology of oviposition, can reduce the load of hazardous synthetic larvicides.
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Affiliation(s)
- Rituparna Ghosh
- Agricultural Biotechnology and Chemical Ecology (ABCE) Lab, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | - Dennis Metze
- Agricultural Biotechnology and Chemical Ecology (ABCE) Lab, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | - Surhud Sant
- Agricultural Biotechnology and Chemical Ecology (ABCE) Lab, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | - Maroof Shaikh
- Agricultural Biotechnology and Chemical Ecology (ABCE) Lab, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | - Ashish Deshpande
- Agricultural Biotechnology and Chemical Ecology (ABCE) Lab, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | - Dnyaneshwar M Firake
- Division of Crop Protection, ICAR Research Complex for NEH Region, Umiam, Meghalaya, 793103, India
- ICAR-Directorate of Floricultural Research, Pune, Maharashtra, 411036, India
| | - Sagar Pandit
- Agricultural Biotechnology and Chemical Ecology (ABCE) Lab, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
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Wang Y, Zhang YQ, Wu ZW, Fang T, Wang F, Zhao H, Du ZQ, Yang CX. Selection of reference genes for RT-qPCR analysis in developing chicken embryonic ovary. Mol Biol Rep 2023; 50:3379-3387. [PMID: 36729208 DOI: 10.1007/s11033-023-08280-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/12/2023] [Indexed: 02/03/2023]
Abstract
BACKGROUND Normalization of the expression profiling of target genes, in a tissue-specific manner and under different experimental conditions, requires stably expressed gene(s) to be used as internal reference(s). However, to study the molecular regulation of oocyte meiosis initiation during ovary development in chicken embryos, stable reference gene(s) still need to be compared and confirmed. METHODS AND RESULTS Six candidate genes previously used as internal references for the chicken embryo (Actb, Cvh, Dazl, Eef1a, Gapdh and Rpl15) were chosen, and their expression profiles in left ovaries dissected at five chicken embryonic days (E12.5, E15.5, E17.5, E18.5 and E20.5) were evaluated, respectively. Separately, GeNorm, NormFinder, BestKeeper and Comparative ΔCt methods were used to assess the stability of candidate reference genes, and all results were combined to give the final rank by RefFinder. All methods identified that Eef1a and Rpl15 were the two most stable internal reference genes, whereas Cvh is the most unstable one. Moreover, expression levels of three marker genes for chicken oocyte meiosis entry (Stra8, Scp3 and Dmc1) were normalized, based on Eef1a, Rpl15, or their combinations, respectively. CONCLUSION Our findings provide the most suitable internal reference genes (Eef1a and Rpl15), to investigate further molecular regulation of ovary development and oocyte meiosis initiation in chicken embryos.
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Affiliation(s)
- Yi Wang
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China
| | - Yu-Qing Zhang
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China
| | - Zi-Wei Wu
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China
| | - Ting Fang
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China
| | - Fang Wang
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China
| | - Han Zhao
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China
| | - Zhi-Qiang Du
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China.
| | - Cai-Xia Yang
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China.
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Hu A, Yang X, Zhu J, Wang X, Liu J, Wang J, Wu H, Zhang H, Zhang H. Selection and validation of appropriate reference genes for RT-qPCR analysis of Nitraria sibirica under various abiotic stresses. BMC PLANT BIOLOGY 2022; 22:592. [PMID: 36526980 PMCID: PMC9758788 DOI: 10.1186/s12870-022-03988-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Nitraria sibirica Pall. is a halophytic shrub with strong environmental adaptability that can survive in extremely saline-alkali and drought-impacted environments. Gene expression analysis aids in the exploration of the molecular mechanisms of plant responses to abiotic stresses. RT-qPCR is the most common technique for studying gene expression. Stable reference genes are a prerequisite for obtaining accurate target gene expression results in RT-qPCR analysis. RESULTS In this study, a total of 10 candidate reference genes were selected from the transcriptome of N. sibirica, and their expression stability in leaves and roots under different treatment conditions (salt, alkali, drought, cold, heat and ABA) was evaluated with the geNorm, NormFinder, BestKeeper, comparative ΔCt and RefFinder programs. The results showed that the expression stability of the candidate reference genes was dependent on the tissue and experimental conditions tested. ACT7 combined with R3H, GAPDH, TUB or His were the most stable reference genes in the salt- or alkali-treated leaves, salt-treated roots and drought-treated roots, respectively; R3H and GAPDH were the most suitable combination for drought-treated leaves, heat-treated root samples and ABA-treated leaves; DIM1 and His maintained stable expression in roots under alkali stress; and TUB combined with R3H was stable in ABA-treated roots. TBCB and GAPDH exhibited stable expression in heat-treated leaves; TBCB, R3H, and ERF3A were stable in cold-treated leaves; and the three most stable reference genes for cold-treated roots were TBCB, ACT11 and DIM1. The reliability of the selected reference genes was further confirmed by evaluating the expression patterns of the NsP5CS gene under the six treatment conditions. CONCLUSION This study provides a theoretical reference for N. sibirica gene expression standardization and quantification under various abiotic stress conditions and will help to reveal the molecular mechanisms that confer stress tolerance to N. sibirica.
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Affiliation(s)
- Aishuang Hu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, 063299, Tangshan, China
- Hebei saline-alkali Land Greening Technology Innovation Center, 063299, Tangshan, China
| | - Xiuyan Yang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Jianfeng Zhu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Xiuping Wang
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, 063299, Tangshan, China
- Hebei saline-alkali Land Greening Technology Innovation Center, 063299, Tangshan, China
| | - Jiaxin Liu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Jiping Wang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Haiwen Wu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Huilong Zhang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China.
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China.
| | - Huaxin Zhang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China.
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China.
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Evaluation and validation of reference genes in Cymbidium faberi for real-time quantitative PCR. Biotechniques 2022; 73:171-181. [PMID: 36178123 DOI: 10.2144/btn-2022-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
For all organs at all Cymbidium faberi stages, ACT, UBQ3 and GAPDH can be selected as reference genes. For organs of the vegetative stage, UBQ2 and UBQ3 can be chosen for analysis of normalized gene expression. For the bud stage, ACT and UBQ3 can be used for analysis of gene expression. For the full blossom stage, ACT, UBQ3 and UBQ2 can be introduced into relative gene expression analysis. For vegetative organs, UBQ2 and ACT can be used as reference genes. For reproductive organs, ACT, UBQ3 and UBQ2 can be used as a reference for data processing. CfAG1 gene expression is more consistent when UBQ3, GAPDH and ACT are used as reference genes.
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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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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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Li T, Yuan W, Qiu S, Shi J. Selection of reference genes for gene expression analysis in Liriodendron hybrids' somatic embryogenesis and germinative tissues. Sci Rep 2021; 11:4957. [PMID: 33654231 PMCID: PMC7925589 DOI: 10.1038/s41598-021-84518-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/15/2021] [Indexed: 01/29/2023] Open
Abstract
The differential expression of genes is crucial for plant somatic embryogenesis (SE), and the accurate quantification of gene expression levels relies on choosing appropriate reference genes. To select the most suitable reference genes for SE studies, 10 commonly used reference genes were examined in synchronized somatic embryogenic and subsequent germinative cultures of Liriodendron hybrids by using quantitative real-time reverse transcription PCR. Four popular normalization algorithms: geNorm, NormFinder, Bestkeeper and Delta-Ct were used to select and validate the suitable reference genes. The results showed that elongation factor 1-gamma, histone H1 linker protein, glyceraldehyde-3-phosphate dehydrogenase and α-tubulin were suitable for SE tissues, while elongation factor 1-gamma and actin were best for the germinative organ tissues. Our work will benefit future studies of gene expression and functional analyses of SE in Liriodendron hybrids. It is also serves as a guide of reference gene selection in early embryonic gene expression analyses for other woody plant species.
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Affiliation(s)
- Tingting Li
- Zhejiang Academy of Forestry, Hangzhou, 310023, China.
| | - Weigao Yuan
- Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | - Shuai Qiu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.,Research and Development Center, Hangzhou Landscaping Incorporated, Hangzhou, 310020, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
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Zhang K, Fan W, Chen D, Jiang L, Li Y, Yao Z, Yang Y, Qiu D. Selection and validation of reference genes for quantitative gene expression normalization in Taxus spp. Sci Rep 2020; 10:22205. [PMID: 33335184 PMCID: PMC7747704 DOI: 10.1038/s41598-020-79213-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 12/04/2020] [Indexed: 11/09/2022] Open
Abstract
Quantitative real-time PCR (qRT-PCR) is commonly used to measure gene expression to further explore gene function, while suitable reference genes must be stably expressed under different experimental conditions to obtain accurate and reproducible data for relative quantification. Taxol or paclitaxel is an important anticancer compound mainly identified in Taxus spp. The molecular mechanism of the regulation of taxol biosynthesis is current research goal. However, in the case of Taxus spp., few reports were published on screening suitable reference genes as internal controls for qRT-PCR. Here, eight reference genes were selected as candidate reference genes for further study. Common statistical algorithms geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder were used to analyze the data from samples collected from a cell line of Taxus × media under various experimental conditions and from tissues of Taxus chinensis var. mairei. The expression patterns of TcMYC under salicylic acid treatment differed significantly, with the best and worst reference genes in the cell line. This study screened out suitable reference genes (GAPDH1 and SAND) under different treatments and tissues for the accurate and reliable normalization of the qRT-PCR expression data of Taxus spp. At the same time, this study will aid future research on taxol biosynthesis-related genes expression in Taxus spp., and can also be directly used to other related species.
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Affiliation(s)
- Kaikai Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.,College of Horticulture, Agricultural University of Hebei, Baoding, 071001, China
| | - Wei Fan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Duanfen Chen
- College of Horticulture, Agricultural University of Hebei, Baoding, 071001, China
| | - Luyuan Jiang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.,College of Horticulture, Agricultural University of Hebei, Baoding, 071001, China
| | - Yunfeng Li
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiwang Yao
- College of Horticulture, Agricultural University of Hebei, Baoding, 071001, China
| | - Yanfang Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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Systematic selection and validation of suitable reference genes for quantitative real-time PCR normalization studies of gene expression in Nitraria tangutorum. Sci Rep 2020; 10:15891. [PMID: 32985612 PMCID: PMC7522712 DOI: 10.1038/s41598-020-73059-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/10/2020] [Indexed: 12/11/2022] Open
Abstract
Suitable reference genes can be used to calibrate the error in quantitative real-time PCR (qPCR) experiments, making the results more credible. However, there are no reference genes suitable for multiple species and under different experimental conditions. Nitraria tangutorum Bobr. is a typical plant native to desert areas. It is drought-resistant, saline-alkali resistant, extreme temperatures-resistant, and has strong adaptability. To date, the importance of this germplasm has not been sufficiently understood; therefore, it is still unclear which genes can be used as reference genes to calibrate qPCR data of N. tangutorum. In this study we analyzed the expression levels of 10 candidate reference genes (ACT, GAPDH, TUA, TUB, CYP, UBC, His, PP2A, HSP, and EF1-α) in N. tangutorum seedlings under a series of experimental conditions, including in different organs (root, stem, and leaf) and under abiotic stresses (salt, drought, heat, and cold) and hormone stimuli (abscisic acid) by qPCR. Three software programs (geNorm, NormFinder, and BestKeeper) were used to evaluate the expression stability of the ten genes. Comprehensive analysis showed that EF1-α and His had the best expression stability, whereas HSP was the least suitable as a reference gene. The expression profile of NtCER7, a gene related to the regulation of cuticular wax biosynthesis in N. tangutorum, verified the accuracy of the experimental results. Based on this study, we recommend EF1-α and His as suitable reference genes for N. tangutorum. This paper provides the first data on stable reference genes in N. tangutorum, which will be beneficial to studying the gene expression of N. tangutorum and other Nitraria species in the future.
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Screening and verification of reference genes for analysis of gene expression in winter rapeseed (Brassica rapa L.) under abiotic stress. PLoS One 2020; 15:e0236577. [PMID: 32941459 PMCID: PMC7498103 DOI: 10.1371/journal.pone.0236577] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 07/08/2020] [Indexed: 02/04/2023] Open
Abstract
Winter rapeseed (Brassica rapa L.) is the main oilseed crop in northern China and can safely overwinter at 35 (i.e., Tianshui, China) to 48 degrees north latitude (i.e., Altai, Heilongjiang, Raohe, and Xinjiang, China). In order to identify stable reference genes to understand the molecular mechanisms of stress tolerance in winter rapeseed, internal reference genes of winter rapeseed under four abiotic stresses were analyzed using GeNorm, NormFinder, BestKeeper, and RefFinder software. The most stable combinations of internal reference genes were β-actin and SAND in cold-stressed leaves, β-actin and EF1a in cold-stressed roots, F-box and SAND in high temperature-stressed leaves, and PP2A and RPL in high temperature-stressed roots, SAND and PP2A in NaCl-stressed leaves, RPL and UBC in NaCl-stressed roots, RPL and PP2A in PEG-stressed leaves, and PP2A and RPL in PEG-stressed roots. Expression profiles of PXG3 were used to verify these results. The stable reference genes identified in this study are useful tools for identifying stress-responsive genes to understand the molecular mechanisms of stress tolerance in winter rapeseed.
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Long X, Lu J, Kav NNV, Qin Y, Fang Y. Identification and evaluation of suitable reference genes for gene expression analysis in rubber tree leaf. Mol Biol Rep 2020; 47:1921-1933. [PMID: 32020426 DOI: 10.1007/s11033-020-05288-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/28/2020] [Indexed: 10/25/2022]
Abstract
Gene expression profiles are increasingly applied to investigate molecular mechanism for which, normalization with suitable reference genes is critical. Previously we have reported several suitable reference genes for laticifer samples from rubber tree, however, little is known in leaf. The main objective of this current study was to identify some stable expression reference genes at various developmental stages of leaf, as well as during abiotic (high and low temperature extremes) and biotic stresses (pathogen stress). Gene expression profilings identified the ubiquitin-proteasome system as excellent potential as reference genes for rubber tree leaf. Among a total of 30 tested genes investigated, 24 new candidate (including 11 genes involved in the ubiquitin-proteasome system), 4 previously identified and 2 specific genes, were further evaluated using quantitative real-time PCR. Our results indicated that the new candidate genes had better expression stability comparing with others. For instance, an ubiquitin conjugating enzyme (RG0099) and three ubiquitin-protein ligases (RG0928, RG2190 and RG0118) expressed stably in all samples, and were confirmed to be suitable reference genes for rubber tree leaf under four different conditions. Finally, we suggest that using more than one reference gene may be appropriate in gene expression studies when employing different software to normalize gene expression data. Our findings have significant implications for the reliability of data obtained from genomics studies in rubber tree and perhaps in other species.
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Affiliation(s)
- Xiangyu Long
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
| | - Jilai Lu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.,College of Forestry, Hainan University, Haikou, 570228, Hainan, China
| | - Nat N V Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, T6G 2P5, Canada
| | - Yunxia Qin
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Yongjun Fang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
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Selection of reliable reference genes for gene expression analysis in seeds at different developmental stages and across various tissues in Paeonia ostii. Mol Biol Rep 2019; 46:6003-6011. [PMID: 31446531 DOI: 10.1007/s11033-019-05036-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/14/2019] [Indexed: 12/31/2022]
Abstract
Paeonia ostii seeds have recently been identified as a new source of α-linolenic acid in China. Studying the gene expression patterns of unsaturated fatty acid-related genes would be helpful for understanding the mechanism of α-linolenic acid accumulation. Quantitative real-time polymerase chain reaction (qRT-PCR) is a useful method for reliably evaluating gene expression, and it is necessary to select reliable reference genes for data normalization in qRT-PCR analysis. In this study, we evaluated the expression stability of 12 candidate reference genes using four mathematical algorithms (∆Ct, BestKeeper, NormFinder, and geNorm). The web-based tool RefFinder was used to integrate the results and to provide a comprehensive ranking order. The expression stability ranking orders of reference genes were different caculated by these four algorithms, and the ranking order analyzed by the RefFinder was UBQ > Tip41 > UCE > EF-1α > α-TUB > PP2A > ACT > GAPDH > SAM > CYP > β-TUB > 18S at the different seed development stages, and UBQ > Tip41 > EF-1α > α-TUB > PP2A > UCE > GAPDH > SAM > ACT > CYP > 18S > β-TUB in P. ostii tissues. UBQ and Tip41 are the two most stable whereas 18S and β-TUB are the two least stable reference genes for gene expression in various tissues and seeds at different developmental stages in P. ostii.
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Wang G, Tian C, Wang Y, Wan F, Hu L, Xiong A, Tian J. Selection of reliable reference genes for quantitative RT-PCR in garlic under salt stress. PeerJ 2019; 7:e7319. [PMID: 31341748 PMCID: PMC6640627 DOI: 10.7717/peerj.7319] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/18/2019] [Indexed: 12/21/2022] Open
Abstract
Quantitative real-time reverse-transcriptase PCR (qRT-PCR) has been frequently used for detecting gene expression. To obtain reliable results, selection of suitable reference genes is a fundamental and necessary step. Garlic (Allium sativum), a member from Alliaceae family, has been used both as a food flavoring and as a traditional medicine. In the present study, garlic plants were exposed to salt stress (200 mM NaCl) for 0, 1, 4 and 12 h, and garlic roots, bulbs, and leaves were harvested for subsequent analysis. The expression stability of eight candidate reference genes, eukaryotic translation initiation factor 4α (eIF-4α), actin (ACTIN), tubulin β-7 (TUB7), TAP42-interacting protein of 41 kDa (TIP41), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), SAND family protein (SAND), elongation factor 1 alpha (EF-1α), and protein phosphatase 2A (PP2A) were evaluated by geNorm, NormFinder, and BestKeeper. All genes tested displayed variable expression profiles under salt stress. In the leaf and root group, ACTIN was the best reference gene for normalizing gene expression. In garlic clove, ACTIN and SAND were the least variable, and were suitable for gene expression studies under salt stress; these two genes also performed well in all samples tested. Based on our results, we recommend that it is essential to use specific reference genes in different situations to obtain accurate results. Using a combination of multiple stable reference genes, such as ACTIN and SAND, to normalize gene expression is encouraged. The results from the study will be beneficial for accurate determination of gene expression in garlic and other plants.
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Affiliation(s)
- Guanglong Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Chang Tian
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yunpeng Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Faxiang Wan
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Laibao Hu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Aisheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jie Tian
- Academy of Agriculture and Forestry Sciences of Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Qinghai Key Laboratory of Vegetable Genetics and Physiology, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai, China
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Coêlho MRV, Rivas R, Ferreira-Neto JRC, Pandolfi V, Bezerra-Neto JP, Benko-Iseppon AM, Santos MG. Reference genes selection for Calotropis procera under different salt stress conditions. PLoS One 2019; 14:e0215729. [PMID: 30998798 PMCID: PMC6472812 DOI: 10.1371/journal.pone.0215729] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 04/08/2019] [Indexed: 02/04/2023] Open
Abstract
Calotropis procera is a perennial Asian shrub with significant adaptation to adverse climate conditions and poor soils. Given its increased salt and drought stress tolerance, C. procera stands out as a powerful candidate to provide alternative genetic resources for biotechnological approaches. The qPCR (real-time quantitative polymerase chain reaction), widely recognized among the most accurate methods for quantifying gene expression, demands suitable reference genes (RGs) to avoid over- or underestimations of the relative expression and incorrect interpretation. This study aimed at evaluating the stability of ten RGs for normalization of gene expression of root and leaf of C. procera under different salt stress conditions and different collection times. The selected RGs were used on expression analysis of three target genes. Three independent experiments were carried out in greenhouse with young plants: i) Leaf100 = leaf samples collected 30 min, 2 h, 8 h and 45 days after NaCl-stress (100 mM NaCl); ii) Root50 and iii) Root200 = root samples collected 30 min, 2 h, 8 h and 1day after NaCl-stress (50 and 200 mM NaCl, respectively). Stability rank among the three algorithms used showed high agreement for the four most stable RGs. The four most stable RGs showed high congruence among all combination of collection time, for each software studied, with minor disagreements. CYP23 was the best RG (rank of top four) for all experimental conditions (Leaf100, Root50, and Root200). Using appropriated RGs, we validated the relative expression level of three differentially expressed target genes (NAC78, CNBL4, and ND1) in Leaf100 and Root200 samples. This study provides the first selection of stable reference genes for C. procera under salinity. Our results emphasize the need for caution when evaluating the stability RGs under different amplitude of variable factors.
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Affiliation(s)
- Maria R. V. Coêlho
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Fisiologia Vegetal, Recife, PE, Brazil
| | - Rebeca Rivas
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Fisiologia Vegetal, Recife, PE, Brazil
| | - José Ribamar C. Ferreira-Neto
- Universidade Federal de Pernambuco, Departamento de Genética, Laboratório Genética e Biotecnologia Vegetal, Recife, PE, Brazil
| | - Valesca Pandolfi
- Universidade Federal de Pernambuco, Departamento de Genética, Laboratório Genética e Biotecnologia Vegetal, Recife, PE, Brazil
| | - João P. Bezerra-Neto
- Universidade Federal de Pernambuco, Departamento de Genética, Laboratório Genética e Biotecnologia Vegetal, Recife, PE, Brazil
| | - Ana Maria Benko-Iseppon
- Universidade Federal de Pernambuco, Departamento de Genética, Laboratório Genética e Biotecnologia Vegetal, Recife, PE, Brazil
| | - Mauro G. Santos
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Fisiologia Vegetal, Recife, PE, Brazil
- * E-mail:
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Moreira VS, Soares VLF, Silva RJS, Sousa AO, Otoni WC, Costa MGC. Selection and validation of reference genes for quantitative gene expression analyses in various tissues and seeds at different developmental stages in Bixa orellana L. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:369-378. [PMID: 29692545 PMCID: PMC5911269 DOI: 10.1007/s12298-018-0528-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 02/16/2018] [Accepted: 03/26/2018] [Indexed: 06/07/2023]
Abstract
Bixa orellana L., popularly known as annatto, produces several secondary metabolites of pharmaceutical and industrial interest, including bixin, whose molecular basis of biosynthesis remain to be determined. Gene expression analysis by quantitative real-time PCR (qPCR) is an important tool to advance such knowledge. However, correct interpretation of qPCR data requires the use of suitable reference genes in order to reduce experimental variations. In the present study, we have selected four different candidates for reference genes in B. orellana, coding for 40S ribosomal protein S9 (RPS9), histone H4 (H4), 60S ribosomal protein L38 (RPL38) and 18S ribosomal RNA (18SrRNA). Their expression stabilities in different tissues (e.g. flower buds, flowers, leaves and seeds at different developmental stages) were analyzed using five statistical tools (NormFinder, geNorm, BestKeeper, ΔCt method and RefFinder). The results indicated that RPL38 is the most stable gene in different tissues and stages of seed development and 18SrRNA is the most unstable among the analyzed genes. In order to validate the candidate reference genes, we have analyzed the relative expression of a target gene coding for carotenoid cleavage dioxygenase 1 (CCD1) using the stable RPL38 and the least stable gene, 18SrRNA, for normalization of the qPCR data. The results demonstrated significant differences in the interpretation of the CCD1 gene expression data, depending on the reference gene used, reinforcing the importance of the correct selection of reference genes for normalization.
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Affiliation(s)
- Viviane S. Moreira
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia 45662-900 Brazil
| | - Virgínia L. F. Soares
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia 45662-900 Brazil
| | - Raner J. S. Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia 45662-900 Brazil
| | - Aurizangela O. Sousa
- Departamento de Tecnologia e Ciências Sociais, Universidade do Estado da Bahia, Juazeiro, Bahia 48905-680 Brazil
| | - Wagner C. Otoni
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900 Brazil
| | - Marcio G. C. Costa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia 45662-900 Brazil
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Zheng T, Chen Z, Ju Y, Zhang H, Cai M, Pan H, Zhang Q. Reference gene selection for qRT-PCR analysis of flower development in Lagerstroemia indica and L. speciosa. PLoS One 2018; 13:e0195004. [PMID: 29579116 PMCID: PMC5868847 DOI: 10.1371/journal.pone.0195004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 03/14/2018] [Indexed: 11/19/2022] Open
Abstract
Quantitative real-time polymerase chain reaction (qRT-PCR) is a prevalent method for gene expression analysis, depending on the stability of the reference genes for data normalization. Lagerstroemia indica and L. speciosa are popular ornamental plants which are famous for the long flowering period. However, no systematic studies on reference genes in Lagerstroemia have yet been conducted. In the present study, we selected nine candidate reference genes (GAPDH, TUA, TUB, 18S, RPII, EF-1α, ATC, EIF5A and CYP) and evaluated their expression stability in different tissues during floral development of L. indica and L. speciosa using four algorithms (geNorm, NormFinder, BestKeeper and, RefFinder). Results showed that RPII and EF-1α were the most stably expressed and suitable reference genes for both of Lagerstroemia species. Moreover, ACT exhibited high expression stability in L. indica and GAPDH was a suitable reference gene for L. speciosa in different flower development stages. TUB was an unsuitable reference gene for gene expression normalization due to significant variations in expression across all samples. Finally, we verified the reliability of the selected candidate reference genes by amplifying an AGAMOUS homolog (LsAG1) of Arabidopsis thaliana. This study provides a list of suitable reference genes, thereby broadening the genetic basis of the gene expression patterns in Lagerstroemia species.
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Affiliation(s)
- Tangchun Zheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Zhilin Chen
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
- School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Yiqian Ju
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
- School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Han Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
- School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Ming Cai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
- School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
- School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
- School of Landscape Architecture, Beijing Forestry University, Beijing, China
- * E-mail:
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Isolation and expression analysis of EcbZIP17 from different finger millet genotypes shows conserved nature of the gene. 3 Biotech 2017; 7:342. [PMID: 28955639 DOI: 10.1007/s13205-017-0984-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/16/2017] [Indexed: 10/18/2022] Open
Abstract
Basic leucine zipper (bZIP) transcription factors comprise one of the largest gene families in plants. They play a key role in almost every aspect of plant growth and development and also in biotic and abiotic stress tolerance. In this study, we report isolation and characterization of EcbZIP17, a group B bZIP transcription factor from a climate smart cereal, finger millet (Eleusine coracana L.). The genomic sequence of EcbZIP17 is 2662 bp long encompassing two exons and one intron with ORF of 1722 bp and peptide length of 573 aa. This gene is homologous to AtbZIP17 (Arabidopsis), ZmbZIP17 (maize) and OsbZIP60 (rice) which play a key role in endoplasmic reticulum (ER) stress pathway. In silico analysis confirmed the presence of basic leucine zipper (bZIP) and transmembrane (TM) domains in the EcbZIP17 protein. Allele mining of this gene in 16 different genotypes by Sanger sequencing revealed no variation in nucleotide sequence, including the 618 bp long intron. Expression analysis of EcbZIP17 under heat stress exhibited similar pattern of expression in all the genotypes across time intervals with highest upregulation after 4 h. The present study established the conserved nature of EcbZIP17 at nucleotide and expression level.
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Niu K, Shi Y, Ma H. Selection of Candidate Reference Genes for Gene Expression Analysis in Kentucky Bluegrass ( Poa pratensis L.) under Abiotic Stress. FRONTIERS IN PLANT SCIENCE 2017; 8:193. [PMID: 28261247 PMCID: PMC5306334 DOI: 10.3389/fpls.2017.00193] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/31/2017] [Indexed: 05/20/2023]
Abstract
Kentucky bluegrass (Poa pratensis L.) belong to Gramineae and is widely used in lawns, golf courses, landscapes, and sport fields as a prominent cool-season grass. Gene expression patterns during different stages of plant development can provide clues toward the understanding of its biological functions. The selection and validation of reference genes are the first steps in any real-time quantitative PCR gene expression study. Therefore, suitable reference genes are necessary for obtaining reliable results in real-time quantitative PCR analyses of Kentucky bluegrass. In the present study, 9 candidate reference genes were chosen, and their expression stability in the leaves and roots of Kentucky bluegrass under different stresses (drought, salt, heat, and cold) were evaluated using the GeNorm, NormFinder, BestKeeper, and RefFinder programs. The results showed that the expression stability of the candidate reference genes was dependent on the experimental conditions. The combination of SAM with GAPDH was the most stable in leaves under salt stress and cold stress, while TUB combined with ACT or GAPDH was stable in roots under salt or cold stress, respectively. ACT and SAM maintained stable expression in drought-treated leaves, and GAPDH combined with ACT was stable in drought-treated roots. SAM and TUB exhibited stable expression in heat-treated leaves. ACT and RPL were stable in heat-treated roots. In addition, the expression patterns of PpFEH in response to drought and cold stress were used to confirm the reliability of the selected reference genes, indicating that the use of an inappropriate reference gene as the internal control will cause erroneous results. This work is the first study on the expression stability of reference genes in Kentucky bluegrass and will be particularly useful in the selection of stress-tolerance genes and the identification of the molecular mechanisms conferring stress tolerance in this species.
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Corral-Vazquez C, Blanco J, Salas-Huetos A, Vidal F, Anton E. Normalization matters: tracking the best strategy for sperm miRNA quantification. Mol Hum Reprod 2016; 23:45-53. [DOI: 10.1093/molehr/gaw072] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/11/2016] [Accepted: 11/14/2016] [Indexed: 11/14/2022] Open
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Wang Z, Wang Y, Yang J, Hu K, An B, Deng X, Li Y. Reliable Selection and Holistic Stability Evaluation of Reference Genes for Rice Under 22 Different Experimental Conditions. Appl Biochem Biotechnol 2016; 179:753-75. [PMID: 26940571 DOI: 10.1007/s12010-016-2029-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 02/22/2016] [Indexed: 01/26/2023]
Abstract
Stable and uniform expression of reference genes across samples plays a key role in accurate normalization of gene expression by reverse-transcription quantitative polymerase chain reaction (RT-qPCR). For rice study, there is still a lack of validation and recommendation of appropriate reference genes with high stability depending on experimental conditions. Eleven candidate reference genes potentially owning high stability were evaluated by geNorm and NormFinder for their expression stability in 22 various experimental conditions. Best combinations of multiple reference genes were recommended depending on experimental conditions, and the holistic stability of reference genes was also evaluated. Reference genes would become more variable and thus needed to be critically selected in experimental groups of tissues, heat, 6-benzylamino purine, and drought, but they were comparatively stable under cold, wound, and ultraviolet-B stresses. Triosephosphate isomerase (TI), profilin-2 (Profilin-2), ubiquitin-conjugating enzyme E2 (UBC), endothelial differentiation factor (Edf), and ADP-ribosylation factor (ARF) were stable in most of our experimental conditions. No universal reference gene showed good stability in all experimental conditions. To get accurate expression result, suitable combination of multiple reference genes for a specific experimental condition would be a better choice. This study provided an application guideline to select stable reference genes for rice gene expression study.
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Affiliation(s)
- Zhaohai Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Ya Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Jing Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Keke Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Baoguang An
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Xiaolong Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China. .,State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China.
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22
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Li J, Jia H, Han X, Zhang J, Sun P, Lu M, Hu J. Selection of Reliable Reference Genes for Gene Expression Analysis under Abiotic Stresses in the Desert Biomass Willow, Salix psammophila. FRONTIERS IN PLANT SCIENCE 2016; 7:1505. [PMID: 27761137 PMCID: PMC5050224 DOI: 10.3389/fpls.2016.01505] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/22/2016] [Indexed: 05/11/2023]
Abstract
Salix psammophila is a desert shrub willow that has extraordinary adaptation to abiotic stresses and plays an important role in maintaining local ecosystems. Moreover, S. psammophila is regarded as a promising biomass feedstock because of its high biomass yields and short rotation coppice cycle. However, few suitable reference genes (RGs) for quantitative real-time polymerase chain reaction (qRT-PCR) constrain the study on normalization of gene expression in S. psammophila until now. Here, we investigated the expression stabilities of 14 candidate RGs across tissue types and under four abiotic stress treatments, including heat, cold, salt, and drought treatments. After calculation of PCR efficiencies, three different software, NormFinder, geNorm, and BestKeeper were employed to analyze systematically the qRT-PCR data, and the outputs were merged by RankAggreg software. The optimal RGs selected for gene expression analysis were EF1α (Elongation factor-1 alpha) and OTU (OTU-like cysteine protease family protein) for different tissue types, UBC (Ubiquitin-conjugating enzyme E2) and LTA4H (Leukotriene A-4 hydrolase homolog) for heat treatment, HIS (Histone superfamily protein H3) and ARF2 (ADP-ribosylation factor 2) for cold treatment, OTU and ACT7 (Actin 7) for salt treatment, UBC and LTA4H for drought treatment. The expression of UBC, ARF2, and VHAC (V-type proton ATPase subunit C) varied the least across tissue types and under abiotic stresses. Furthermore, the relative genes expression profiles of one tissue-specific gene WOX1a (WUSCHEL-related homeobox 1a), and four stress-inducible genes, including Hsf-A2 (Heat shock transcription factors A2), CBF3 (C-repeat binding factor 3), HKT1 (High-Affinity K+ Transporter 1), and GST (Glutathione S-transferase), were conducted to confirm the validity of the RGs in this study. These results provided an important RGs application guideline for gene expression characterization in S. psammophila.
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Affiliation(s)
- Jianbo Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Huixia Jia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry UniversityNanjing, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Pei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Mengzhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry UniversityNanjing, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry UniversityNanjing, China
- *Correspondence: Jianjun Hu,
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23
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González-Aguilera KL, Saad CF, Chávez Montes RA, Alves-Ferreira M, de Folter S. Selection of Reference Genes for Quantitative Real-Time RT-PCR Studies in Tomato Fruit of the Genotype MT-Rg1. FRONTIERS IN PLANT SCIENCE 2016; 7:1386. [PMID: 27679646 PMCID: PMC5021083 DOI: 10.3389/fpls.2016.01386] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 08/31/2016] [Indexed: 05/20/2023]
Abstract
Quantitative real-time RT-PCR (qRT-PCR) has become one of the most widely used methods for accurate quantification of gene expression. Since there are no universal reference genes for normalization, the optimal strategy to normalize raw qRT-PCR data is to perform an initial comparison of a set of independent reference genes to assess the most stable ones in each biological model. Normalization of a qRT-PCR experiment helps to ensure that the results are both statistically significant and biologically meaningful. Tomato is the model of choice to study fleshy fruit development. The miniature tomato (Solanum lycopersicum L.) cultivar Micro-Tom (MT) is considered a model system for tomato genetics and functional genomics. A new genotype, containing the Rg1 allele, improves tomato in vitro regeneration. In this work, we evaluated the expression stability of four tomato reference genes, namely CAC, SAND, Expressed, and ACTIN2. We showed that the genes CAC and Exp are the best reference genes of the four we tested during fruit development in the MT-Rg1 genotype. Furthermore, we validated the reference genes by showing that the expression profiles of the transcription factors FRUITFULL1 and APETALA2c during fruit development are comparable to previous reports using other tomato cultivars.
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Affiliation(s)
- Karla L. González-Aguilera
- Unidad de Genómica Avanzada – Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuato, Mexico
| | - Carolina F. Saad
- Laboratório de Genética Molecular Vegetal, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Ricardo A. Chávez Montes
- Unidad de Genómica Avanzada – Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuato, Mexico
| | - Marcio Alves-Ferreira
- Laboratório de Genética Molecular Vegetal, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Stefan de Folter
- Unidad de Genómica Avanzada – Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuato, Mexico
- *Correspondence: Stefan de Folter,
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24
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Ni MM, Xu T, Wang YR, He YH, Zhou Q, Huang C, Meng XM, Li J. Inhibition of IRF3 expression reduces TGF-β1-induced proliferation of hepatic stellate cells. J Physiol Biochem 2015; 72:9-23. [PMID: 26611114 DOI: 10.1007/s13105-015-0452-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 11/20/2015] [Indexed: 02/07/2023]
Abstract
Therapeutic management of liver fibrosis remains an unresolved clinical problem. Activation of hepatic stellate cell (HSC) is a pivotal event in the progression of liver fibrosis. Recent reports have showed that inhibition of activated HSC proliferation contributes to the reversal of liver fibrosis. Interferon regulatory factor 3 (IRF3), one member of the interferon regulatory factor (IRF) family, is recently proven to be a critical modulator in cardiac fibrosis. And accumulating evidence demonstrated that IRF3 plays a crucial role in liver diseases, such as hepatic steatosis, liver inflammation, and alcoholic liver injury. However, the understanding of the function of IRF3 in liver fibrosis remains limited. Our results identified the role of IRF3 in regulating human HSC (LX-2 cell) cell proliferation and apoptosis. The present study indicated that the expression of IRF3 was significantly increased in HSCs in response to TGF-β1 stimulation. Moreover, a stable and unlimited source of human HSC, the LX-2 cell line, transfected with IRF3-siRNA significantly decreases the expression level of type I collagen (Col1a1) and α-smooth muscle actin (α-SMA) in activated LX-2 cells. On the contrary, overexpression of IRF3 gives rise to an upregulation of Col1a1 and α-SMA in LX-2 cells, and further promoted HSC proliferation. Moreover, the inhibition of IRF3 significantly suppressed TGF-β1-induced HSC proliferation and increased its apoptosis. Of note, the present study indicated IRF3 may regulate LX-2 cell proliferation by via AKT signaling pathway. In summary, these observations suggest IRF3 may function as a novel regulator to modulate TGF-β1-induced LX-2 proliferation, at least in part, via AKT signaling pathway.
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Affiliation(s)
- Ming-ming Ni
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China
| | - Tao Xu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China
| | - Ya-rui Wang
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China
| | - Ying-hua He
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China
| | - Qun Zhou
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China
| | - Cheng Huang
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China
| | - Xiao-ming Meng
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China
| | - Jun Li
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China. .,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China. .,School of Pharmacy, Anhui Medical University, 81 Mei Shan Road, Hefei, Anhui Province, 230032, China.
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