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Li S, Ge X, Bai G, Chen C. Selection of Reference Genes for Expression Normalization by RT-qPCR in Dracocephalum moldavica L. Curr Issues Mol Biol 2024; 46:6284-6299. [PMID: 38921046 PMCID: PMC11202811 DOI: 10.3390/cimb46060375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
Dracocephalum moldavica is widely used as an ornamental, medicine, and perfume in industry. Real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) is widely and accurately utilized for gene expression evaluations. Selecting optimal reference genes is essential for normalizing RT-qPCR results. However, the identification of suitable reference genes in D. moldavica has not been documented. A total of 12 reference genes in D. moldavica were identified by PEG6000 (15%) treatment under hypertonia conditions in different tissues (roots, stem, leaves, flower, seeds and sepal) and during three stages of flower development, then used to validate the expression stability. There were four algorithms (delta Ct, geNorm, NormFinder, and BestKeeper) used to analyze the stability. Finally, the RefFinder program was employed to evaluate the candidate reference genes' stability. The results showed that ACTIN, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and EF1α (elongation factor-1α) were stable reference genes under the PEG6000 treatment. Heat shock protein 70 (HSP70) was the most stable gene across different flower development stages. ADP-ribosylation factor (ARF) was the most stable gene in different tissues and total samples. This study provides reliable gene expression studies for future research in D. moldavica.
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Affiliation(s)
| | | | | | - Chen Chen
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, Xi’an 710061, China; (S.L.); (X.G.); (G.B.)
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2
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Dhawi F. Abiotic stress tolerance in pearl millet: Unraveling molecular mechanisms via transcriptomics. Sci Prog 2024; 107:368504241237610. [PMID: 38500301 PMCID: PMC10953032 DOI: 10.1177/00368504241237610] [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] [Indexed: 03/20/2024]
Abstract
Pearl millet (Pennisetum glaucum (L.)) is a vital cereal crop renowned for its ability to thrive in challenging environmental conditions; however, the molecular mechanisms governing its salt stress tolerance remain poorly understood. To address this gap, next-generation RNA sequencing was conducted to compare gene expression patterns in pearl millet seedlings exposed to salt stress with those grown under normal conditions. Our RNA sequencing analysis focused on shoots from 13-day-old pearl millet plants subjected to either salinity stress (150 mmol of NaCl for 3 days) or thermal stress (50°C for 60 s). Of 36,041 genes examined, 17,271 genes with fold changes ranging from 2.2 to 19.6 were successfully identified. Specifically, 2388 genes were differentially upregulated in response to heat stress, whereas 4327 genes were downregulated. Under salt stress conditions, 2013 genes were upregulated and 4221 genes were downregulated. Transcriptomic analysis revealed four common abiotic KEGG pathways that play crucial roles in the response of pearl millet to salt and heat stress: phenylpropanoid biosynthesis, photosynthesis-antenna proteins, photosynthesis, and plant hormone signal transduction. These metabolic pathways are necessary for pearl millet to withstand and adapt to abiotic stresses caused by salt and heat. Moreover, the pearl millet shoot heat stress group showed specific transcriptomics related to KEEG metabolic pathways such as cytochrome P450, cutin, suberine, and wax biosynthesis, zeatin biosynthesis, crocin biosynthesis, ginsenoside biosynthesis, saponin biosynthesis, and biosynthesis of various plant secondary metabolites. In contrast, pearl millet shoots exposed to salinity stress exhibited transcriptomic changes associated with KEEG metabolic pathways related to carbon fixation in photosynthetic organisms, mismatch repair, and nitrogen metabolism. Our findings underscore the remarkable cross-tolerance of pearl millet to simultaneous salt and heat stress, elucidated through the activation of shared abiotic KEGG pathways. This study emphasizes the pivotal role of transcriptomics analysis in unraveling the molecular responses of pearl millet under abiotic stress conditions.
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Affiliation(s)
- Faten Dhawi
- Agricultural Biotechnology Department, College of Agricultural and Food Sciences, King Faisal University, Al-Ahsa, Saudi Arabia
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3
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Valenzuela F, D’Afonseca V, Hernández R, Gómez A, Arencibia AD. Validation of Reference Genes in a Population of Blueberry (Vaccinium corymbosum) Plants Regenerated in Colchicine. PLANTS (BASEL, SWITZERLAND) 2022; 11:2645. [PMID: 36235509 PMCID: PMC9573746 DOI: 10.3390/plants11192645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
For the first time we report the validation of reference genes in plants from a population of blueberry (Vaccinium corymbosum) clones cultured in vitro on a colchicine-supplemented medium. Nodal segment explants of the cultivar Duke were regenerated by organogenesis under different periods of colchicine 1 mg/L exposure (1, 2, 3, 5, 30 days). The clones selected for the study showed variability for phenotypic traits after 2 years of adaptation to field conditions, compared to plants of the donor genotype that were regenerated on a medium without colchicine. Vaccinium myrtillus (GAPDH) and Vaccinium macrocarpon (ATP1, NADH, RPOB and COX2) were used as reference genomes for primer design. The results show that colchicine treatments can cause genomic changes in blueberry plants. At the molecular level, exposure of plants to colchicine in early periods could promote an increase in gene expression of specific genes such as ATP1, COX2, GAPDH, MATK, NADH and RPOB. However, prolonged exposure (30 days) could decrease gene expression of the genes studied. For qPCR assays, the primers designed for ATP1, COX2, GAPDH and MATK genes showed high efficiency. In addition, the GAPDH, ATP1, NADH and COX2 genes showed high stability and could be recommended as potential reference genes for gene expression assays in Vaccinium.
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Affiliation(s)
- Francisca Valenzuela
- Centro de Biotecnología en Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
| | - Vivían D’Afonseca
- Departamento de Ciencias Preclínicas, Facultad de Medicina, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
| | - Ricardo Hernández
- Centro de Biotecnología en Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
- Doctorado en Biotecnología Traslacional. Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
| | - Aleydis Gómez
- Centro de Biotecnología en Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
| | - Ariel D. Arencibia
- Centro de Biotecnología en Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
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4
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Systematic screening and validation of reliable reference genes for qRT-PCR analysis in Okra (Abelmoschus esculentus L.). Sci Rep 2022; 12:12913. [PMID: 35902620 PMCID: PMC9334609 DOI: 10.1038/s41598-022-16124-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 07/05/2022] [Indexed: 11/26/2022] Open
Abstract
Quantitative real-time polymerase chain reaction (qRT-PCR) is a sensitive and widely used technique for quantifying gene expression levels, and its accuracy depends on the reference genes used for data normalization. To date, no reference gene has been reported in the nutritious and functional vegetable okra (Abelmoschus esculentus L.). Herein, 11 candidates of reference genes were selected and evaluated for their expression stability in okra in different tissues at different developmental stages by using three software algorithms (geNorm, NormFinder, BestKeeper) and a web-based tool (RefFinder). Among them, eukaryotic initiation factor 4 alpha (eIF4A) and protein phosphatase 2A (PP2A) showed the highest stability, while TUA5 had the lowest stability. The combined usage of these two most stable reference genes was sufficient to normalize gene expression in okra. Then, the above results were further validated by normalizing the expression of the cellulose synthase gene CesA4. This work provides appropriate reference genes for transcript normalization in okra, which will facilitate subsequent functional gene research on this vegetable crop.
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Characterization of Siccibacter sp. Strain C2 a Novel Rhizobacterium that Enhances Tolerance of Barley to Salt Stress. Curr Microbiol 2022; 79:239. [PMID: 35794407 DOI: 10.1007/s00284-022-02930-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/09/2022] [Indexed: 11/03/2022]
Abstract
Plant growth promoting rhizobacteria (PGPR) arouse an increasing interest as an eco-friendly solution for improving crop tolerance to environmental stresses. In this study, we report the characterization of a novel halotolerant PGPR strain (named C2) identified in a screen of rhizospheric bacterial isolates from southeast of Tunisia. Phylogenetic analysis showed that strain C2 is most likely affiliated to the genus Siccibacter with Siccibacter turicensis as the closest species (98.19%). This strain was able to perform phosphate solubilization and production of indole acetic acid (IAA), siderophores, hydrogen cyanide (HCN), as well as different hydrolytic enzymes (proteases, amylases, cellulases, and lipases). The potential of strain C2 in enhancing salt stress tolerance of Hordeum vulgare was also investigated. Our greenhouse inoculation assays showed that strain C2 promotes barley growth in the presence of 400 mM NaCl by increasing biomass, root length, and chlorophyll contents. It has a positive effect on the photosynthetic efficiency, concomitantly with lower intercellular CO2 contents, compared to non-inoculated plants. Moreover, barley inoculation with strain C2 under salt stress, resulted in higher accumulation of proline and soluble sugars and alleviate the oxidative stress by decreasing hydrogen peroxide and malondialdehyde contents. Remarkably, this positive effect corroborates with a significant activation in the expression of a subset of barley stress responsive genes, including HVA1, HvDREB1, HvWRKY38 and HvP5CS. In summary, Siccibacter sp. strain C2 is able to enhance barley salt stress tolerance and should be leveraged in developing sustainable practices for cereal crop production.
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Gapdh Shows Altered Gene Expression in Alcohol Models. ACTA MEDICA BULGARICA 2022. [DOI: 10.2478/amb-2022-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Background and objectives. Though glyceraldehyde-3-phosphate dehydrogenase (Gapdh) is one of the most commonly used housekeeping genes for comparison of gene expression data, studies have revealed that Gapdh expression is not constant at different developmental stages, and is modulated by many factors including ethanol. In view of this, in the present study, we investigated the effect of ethanol on Gapdh stability and expression levels in different model systems.
Methods. Evaluation of Gapdh stability was determined by comparison with three commonly used housekeeping genes in alcohol-exposed and control mouse blastocysts, embryos, and placentas (ActB, Hsp90ab1, and Atp5b), and in alcohol-dependent and healthy humans (ACTB, ATP5B, and HSPCB), and was ranked by the software program RefFinder. To detect the Gapdh expression patterns as a target gene, qRT-PCR analysis was applied.
Results. The order of expression stabilities obtained by the RefFinder ranked Gapdh as the most unstable reference gene in studied groups. The study of the expression dynamics of Gapdh showed significant upregulation in ethanol-exposed mouse blastocysts and embryos (FC = 1.56, p = 0.05 and FC = 6.0, p = 0.01) and downregulation in placentas (FC = 0.60, p = 0.01).
Conclusions. Our results revealed that the expression of Gapdh can vary in different model systems under ethanol exposure and imply the need for caution when using it as an internal control. This is the first report for statistically significant change in Gapdh expression after ethanol exposure during preimplantation mouse development.
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7
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Zhang L, Cai Y, Zhang M, Du G, Wang J. Selection and Evaluation of Candidate Reference Genes for Quantitative Real-Time PCR in Aboveground Tissues and Drought Conditions in Rhododendron Delavayi. Front Genet 2022; 13:876482. [PMID: 35495151 PMCID: PMC9046656 DOI: 10.3389/fgene.2022.876482] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/17/2022] [Indexed: 11/18/2022] Open
Abstract
There has been no systematic identification and screening of candidate reference genes for normalization of quantitative real-time PCR (qRT-PCR) results in Rhododendron delavayi to date. Therefore, the present study used GAPDH, Act, EF1, Tub-, Tub-5, UEC1, TATA, TATA-2, UEP, TIP41, and Ubiquitin to predict their stabilities on different aboveground tissues (matured leaves (ML), stem tips (STM), and flower buds (FB)) at different developmental stages (young and adult plants) using five statistical algorithms: Delta Ct method, BestKeeper, geNorm, Normfinder, and RefFinder. The findings were confirmed using ML obtained from plants that had been stressed by drought. By using RefFinder with ML samples collected under drought conditions, it was determined that the top five most stable reference genes were GAPDH > UEC1 > Actin > Tubulin- > Tubulin—5, whereas the least stable reference gene was Ubiquitin. In addition, under control conditions, UEC1, UEC2, Actin, and GAPDH were selected as the highest stable potential reference genes at the juvenile stage of R. delavayi with ML and STM. When ML and STM were combined with drought-stressed samples, TIP41, GAPDH, or their combination proved to be the most effective qRT-PCR primers. The findings will aid in the improvement of the precision and reliability of qRT-PCR data and laying the groundwork for future gene functional studies in R. delavayi.
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Affiliation(s)
- Lu Zhang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, China
- National Engineering Research Center for Ornamental Horticulture, Kunming, China
| | - Yanfei Cai
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, China
- National Engineering Research Center for Ornamental Horticulture, Kunming, China
| | - Mingchao Zhang
- School of Agriculture, Yunnan University, Kunming, China
| | - Guanghui Du
- School of Agriculture, Yunnan University, Kunming, China
- *Correspondence: Guanghui Du, ; Jihua Wang,
| | - Jihua Wang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, China
- National Engineering Research Center for Ornamental Horticulture, Kunming, China
- *Correspondence: Guanghui Du, ; Jihua Wang,
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Tang J, Liang G, Dong S, Shan S, Zhao M, Guo X. Selection and Validation of Reference Genes for Quantitative Real-Time PCR Normalization in Athetis dissimilis (Lepidoptera: Noctuidae) Under Different Conditions. Front Physiol 2022; 13:842195. [PMID: 35273523 PMCID: PMC8902415 DOI: 10.3389/fphys.2022.842195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Reference genes are the key to study gene expression patterns using quantitative real-time PCR (qRT-PCR). No studies on the reference genes of Athetis dissimilis, an important agricultural pest, have been reported. In order to determine the reference genes for qRT-PCR normalization in A. dissimilis under different conditions, 10 candidate genes [18S ribosomal protein (18S), 28S ribosomal protein (28S), arginine kinase (AK), elongation factor 1 alpha (EF1-α), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ribosomal protein L32 (RPL32), ribosomal protein L40 (RPL40), alpha-tubulin (α-TUB), beta-actin (β-ACT), and beta-tubulin (β-TUB)] of A. dissimilis were selected to evaluate their stability as reference genes under different biotic and abiotic conditions by using five tools, geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder. Furthermore, CSP1 and superoxide dismutase (SOD) were used as target genes to validate the candidate reference genes. The results showed that different reference genes were needed under different experimental conditions, among which, EF-1α, RPL40, and 18S are most suitable reference genes for studying genes related development stages of A. dissimilis, RPL40 and α-TUB for larval tissues, α-TUB and 28S for adult tissues, EF-1α and β-ACT for insecticidal treatments, β-ACT and 28S for temperature treatments, EF-1α and β-ACT for starvation treatments, RPL40 and 18S for dietary treatments, and 18S, 28S, and α-TUB for all the samples. These results provide suitable reference genes for studying gene expression in A. dissimilis under different experimental conditions, and also lay the foundation for further research into the function of related genes in A. dissimilis.
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Affiliation(s)
- Jinrong Tang
- Henan International Laboratory for Green Pest Control/College of Plant Protection, Henan Agricultural University, Zhengzhou, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gemei Liang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoqi Dong
- Henan International Laboratory for Green Pest Control/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Shuang Shan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Man Zhao
- Henan International Laboratory for Green Pest Control/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xianru Guo
- Henan International Laboratory for Green Pest Control/College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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Škiljaica A, Jagić M, Vuk T, Leljak Levanić D, Bauer N, Markulin L. Evaluation of reference genes for RT-qPCR gene expression analysis in Arabidopsis thaliana exposed to elevated temperatures. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:367-379. [PMID: 34990067 DOI: 10.1111/plb.13382] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Increases in environmental temperature are directly linked to the issue of climate change and are known to significantly disrupt plant growth and development. Studies of gene expression in plants commonly include RT-qPCR but the reliability of the method depends on the use of suitable reference genes for data normalization. Despite this, no reference genes have been validated specifically for experiments in Arabidopsis thaliana employing treatments with elevated temperature. Here, ten genes were selected for expression stability analysis based on the screening of available literature and microarray data from temperature-treated A. thaliana. Expression levels of candidate reference genes were measured in 12-day-old seedlings, rosette leaves and flower buds of 5-week-old A. thaliana plants exposed to five different temperatures (22°C, 27°C, 32°C, 37°C and 42°C) and their expression stabilities were assessed using four statistical algorithms (BestKeeper, geNorm, NormFinder and comparative ΔCq method). This study provides reliable reference genes for use in A. thaliana RT-qPCR expression analyses employing elevated temperature treatments, namely OGIO and PUX7 in seedlings, UBC21 and PUX7 in leaves, TIP41 and UBC21 in buds, and TIP41 and UBC21 in all three tissues combined. Orthologues of these genes can be of potential use in less studied plants, especially agricultural species heavily affected by climate change.
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Affiliation(s)
- A Škiljaica
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - M Jagić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - T Vuk
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - D Leljak Levanić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - N Bauer
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - L Markulin
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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10
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Duo J, Xiong H, Wu X, Li Y, Si J, Zhang C, Duan R. Genome-wide identification and expression profile under abiotic stress of the barley non-specific lipid transfer protein gene family and its Qingke Orthologues. BMC Genomics 2021; 22:674. [PMID: 34544387 PMCID: PMC8451110 DOI: 10.1186/s12864-021-07958-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plant non-specific lipid transfer proteins (nsLTPs), a group of small, basic ubiquitous proteins to participate in lipid transfer, cuticle formation and stress response, are involved in the regulation of plant growth and development. To date, although the nsLTP gene family of barley (Hordeum vulgare L.) has been preliminarily identified, it is still unclear in the recently completed genome database of barley and Qingke, and its transcriptional profiling under abiotic stress has not been elucidated as well. RESULTS We identified 40 barley nsLTP (HvLTP) genes through a strict screening strategy based on the latest barley genome and 35 Qingke nsLTP (HtLTP) orthologues using blastp, and these LTP genes were divided into four types (1, 2, D and G). At the same time, a comprehensive analysis of the physical and chemical characteristics, homology alignment, conserved motifs, gene structure and evolution of HvLTPs and HtLTPs further supported their similar nsLTP characteristics and classification. The genomic location of HvLTPs and HtLTPs showed that these genes were unevenly distributed, and obvious HvLTP and HtLTP gene clusters were found on the 7 chromosomes including six pairs of tandem repeats and one pair of segment repeats in the barley genome, indicating that these genes may be co-evolutionary and co-regulated. A spatial expression analysis showed that most HvLTPs and HtLTPs had different tissue-specific expression patterns. Moreover, the upstream cis-element analysis of HvLTPs and HtLTPs showed that there were many different stress-related transcriptional regulatory elements, and the expression pattern of HvLTPs and HtLTPs under abiotic stress also indicated that numerous HvLTP and HtLTP genes were related to the abiotic stress response. Taken together, these results may be due to the differences in promoters rather than by genes themselves resulting in different expression patterns under abiotic stress. CONCLUSION Due to a stringent screening and comprehensive analysis of the nsLTP gene family in barley and Qingke and its expression profile under abiotic stress, this study can be considered a useful source for the future studies of nsLTP genes in either barley or Qingke or for comparisons of different plant species.
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Affiliation(s)
- Jiecuo Duo
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, Qinghai Province, China.,Qinghai Qaidam Vocational & Technical College, Delingha, 817000, Qinghai Province, China
| | - Huiyan Xiong
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, 810016, Qinghai Province, China
| | - Xiongxiong Wu
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, Qinghai Province, China
| | - Yuan Li
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, Qinghai Province, China
| | - Jianping Si
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, Qinghai Province, China
| | - Chao Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, Qinghai Province, China
| | - Ruijun Duan
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, Qinghai Province, China.
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11
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Validation of Reference Genes for Studying Different Abiotic Stresses in Oat ( Avena sativa L.) by RT-qPCR. PLANTS 2021; 10:plants10071272. [PMID: 34206660 PMCID: PMC8309034 DOI: 10.3390/plants10071272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 12/27/2022]
Abstract
Oat (Avena sativa L.) is a widely cultivated cereal with high nutritional value and it is grown mainly in temperate regions. The number of studies dealing with gene expression changes in oat continues to increase, and to obtain reliable RT-qPCR results it is essential to establish and use reference genes with the least possible influence caused by experimental conditions. However, no detailed study has been conducted on reference genes in different tissues of oat under diverse abiotic stress conditions. In our work, nine candidate reference genes (ACT, TUB, CYP, GAPD, UBC, EF1, TBP, ADPR, PGD) were chosen and analysed by four statistical methods (GeNorm, Normfinder, BestKeeper, RefFinder). Samples were taken from two tissues (leaves and roots) of 13-day-old oat plants exposed to five abiotic stresses (drought, salt, heavy metal, low and high temperatures). ADPR was the top-rated reference gene for all samples, while different genes proved to be the most stable depending on tissue type and treatment combinations. TUB and EF1 were most affected by the treatments in general. Validation of reference genes was carried out by PAL expression analysis, which further confirmed their reliability. These results can contribute to reliable gene expression studies for future research in cultivated oat.
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12
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Xie J, Liu T, Khashaveh A, Yi C, Liu X, Zhang Y. Identification and Evaluation of Suitable Reference Genes for RT-qPCR Analysis in Hippodamia variegata (Coleoptera: Coccinellidae) Under Different Biotic and Abiotic Conditions. Front Physiol 2021; 12:669510. [PMID: 34079474 PMCID: PMC8165390 DOI: 10.3389/fphys.2021.669510] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/06/2021] [Indexed: 12/18/2022] Open
Abstract
Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) is an accurate and convenient technique for quantifying expression levels of the target genes. Selection of the appropriate reference gene is of the vital importance for RT-qPCR analysis. Hippodamia variegata is one of the most important predatory natural enemies of aphids. Recently, transcriptome and genome sequencings of H. variegata facilitate the gene functional studies. However, there has been rare investigation on the detection of stably expressed reference genes in H. variegata. In the current study, by using five analytical tools (Delta Ct, geNorm, NormFinder, BestKeeper, and RefFinder), eight candidate reference genes, namely, Actin, EF1α, RPL7, RPL18, RPS23, Tubulin-α, Tubulin-β, and TufA, were evaluated under four experimental conditions including developmental stages, tissues, temperatures, and diets. As a result, a specific set of reference genes were recommended for each experimental condition. These findings will help to improve the accuracy and reliability of RT-qPCR data, and lay a foundation for further exploration on the gene function of H. variegata.
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Affiliation(s)
- Jiaoxin Xie
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tinghui Liu
- College of Plant Protections, Agricultural University of Hebei, Baoding, China
| | - Adel Khashaveh
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaoqun Yi
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Plant Protections, Agricultural University of Hebei, Baoding, China
| | - Xiaoxu Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Plant Protections, Agricultural University of Hebei, Baoding, China
| | - Yongjun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Liu W, Feng X, Cao F, Wu D, Zhang G, Vincze E, Wang Y, Chen ZH, Wu F. An ATP binding cassette transporter HvABCB25 confers aluminum detoxification in wild barley. JOURNAL OF HAZARDOUS MATERIALS 2021; 401:123371. [PMID: 32763683 DOI: 10.1016/j.jhazmat.2020.123371] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/18/2020] [Accepted: 06/30/2020] [Indexed: 06/11/2023]
Abstract
Aluminum (Al) stress in acid soils is one of the major factors limiting crop productivity. ATP binding cassette (ABC) transporters have numerous roles in plants, but the link between ABCB protein subfamily and plant Al tolerance is still elusive. Here, we identified and characterized a novel tonoplast HvABCB25 in barley root cells. HvABCB25 was up-regulated in the transcriptome of Al-tolerant wild barley XZ16 under Al treatment and was highly Al-inducible in root tips. ABCB25 is originated from Streptophyte algae and evolutionarily conserved in land plants. Moreover, silencing HvABCB25 in Al-tolerant XZ16 led to significant suppression of Al tolerance as indicated by significantly reduced root growth and enhanced Al accumulation in root cells. Conversely, HvABCB25-overexpressed plants and Golden Promise showed similar Al content in whole roots and in cell sap, but the overexpression lines exhibited significantly higher Al-induced relative root growth and dry weight. Al florescence in cytosol of root cells were significantly less in overexpression lines than that in GP. These results indicated that overexpressing HvABCB25 may be responsible for Al detoxification via vacuolar Al sequestration in barley roots, providing useful insight into the genetic basis for a new Al detoxification mechanism towards plant Al tolerance in acid soils.
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Affiliation(s)
- Wenxing Liu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Xue Feng
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Fangbin Cao
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Dezhi Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Eva Vincze
- Department of Molecular Biology and Genetics, University of Aarhus, Fosøgsvej 1, DK-4200 Slagelse, Denmark
| | - Yizhou Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia.
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
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Fiust A, Rapacz M. Downregulation of three novel candidate genes is important for freezing tolerance of field and laboratory cold acclimated barley. JOURNAL OF PLANT PHYSIOLOGY 2020; 244:153049. [PMID: 31760347 DOI: 10.1016/j.jplph.2019.153049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/25/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
Diversity arrays technology (DArT) marker sequences for barley were used for identifying new potential candidate genes for freezing tolerance (FT). We used quantitative trait loci (QTL) genetic linkage maps for FT and photosynthetic acclimation to cold for six- and two-row barley populations, and a set of 20 DArT markers obtained using the association mapping of parameters for photosynthetic acclimation to low temperatures in barley for the bioinformatics analyses. Several nucleotide and amino acid sequence, annotation databases and associated algorithms were used to identify the similarities of six of the marker sequences to potential genes involved in plant low temperature response. Gene ontology (GO) annotations based on similarities to database sequences were assigned to these marker sequences, and indicated potential involvement in signal transduction pathways in response to stress factors and epigenetic processes, as well as auxin transport mechanisms. Furthermore, relative gene expressions for three of six of new identified genes (Hv.ATPase, Hv.DDM1, and Hv.BIG) were assessed within four barley genotypes of different FT. A physiological assessment of FT was conducted based on plant survival rates in two field-laboratory and one laboratory experiments. The results suggested that plant survival rate after freezing but not the degree of freezing-induced leaf damage between the tested accessions can be correlated with the degree of low-temperature downregulation of the studied candidate genes, which encoded proteins involved in the control of plant growth and development. Additionally, candidate genes for qRT-PCR suitable for the analysis of cold acclimation response in barley were suggested after validation.
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Affiliation(s)
- Anna Fiust
- Department of Plant Physiology, University of Agriculture, Podłużna 3, 30-239, Krakow, Poland.
| | - Marcin Rapacz
- Department of Plant Physiology, University of Agriculture, Podłużna 3, 30-239, Krakow, Poland.
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15
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Mareri L, Milc J, Laviano L, Buti M, Vautrin S, Cauet S, Mascagni F, Natali L, Cavallini A, Bergès H, Pecchioni N, Francia E. Influence of CNV on transcript levels of HvCBF genes at Fr-H2 locus revealed by resequencing in resistant barley cv. 'Nure' and expression analysis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110305. [PMID: 31779917 DOI: 10.1016/j.plantsci.2019.110305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/18/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Resequencing in resistant cultivar 'Nure' and structural comparison with the same region of susceptible 'Morex' was performed in order to gain a better insight into barley Frost-resistance-H2 locus. Accurate annotation showed copy number variation (CNV) in the proximal part of the locus. In 'Nure', two exact copies of the HvCBF4-HvCBF2A region and one of the HvCBF4-HvCBF2B segment were observed, while in 'Morex' the corresponding region harboured a single HvCBF4-HvCBF2A (22 kb) segment. Abundance and diversity of repetitive element classes, gene function gain/losses, regulatory motifs and SNPs in gene sequences were identified. An expression study of key HvCBFs with/without CNV on selected genotypes contrasting for frost resistance and estimated HvCBF4-HvCBF2B copy number (2-10 copies) was also performed. Under light stimulus at warm temperature (23 °C), CNV of HvCBF2A and HvCBF4 correlated with their expression levels and reported frost resistance of genotypes; moreover, expression levels of HvCBF2A and HvCBF14 were strongly correlated (r = 0.908, p < 0.01). On the other hand, frost resistance correlated to HvCBF14 expression (r = 0.871, p < 0.01) only after cold induction (6°C) in the dark. A complex interplay of HvCBFs expression levels under different light/temperature stimuli is discussed in light of CNV and presence/number of regulatory elements that integrate different signal transduction pathways.
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Affiliation(s)
- Lavinia Mareri
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy
| | - Justyna Milc
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy
| | - Luca Laviano
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy
| | - Matteo Buti
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy
| | - Sonia Vautrin
- Centre National de Ressources Génomiques Végétales (CNRGV), Chemin de Borde Rouge 24-Auzeville CS 52627, Castanet Tolosan Cedex, F-31326, France
| | - Stéphane Cauet
- Centre National de Ressources Génomiques Végétales (CNRGV), Chemin de Borde Rouge 24-Auzeville CS 52627, Castanet Tolosan Cedex, F-31326, France
| | - Flavia Mascagni
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, via del Borghetto 80, Pisa, I-56124, Italy
| | - Lucia Natali
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, via del Borghetto 80, Pisa, I-56124, Italy
| | - Andrea Cavallini
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, via del Borghetto 80, Pisa, I-56124, Italy
| | - Hélène Bergès
- Centre National de Ressources Génomiques Végétales (CNRGV), Chemin de Borde Rouge 24-Auzeville CS 52627, Castanet Tolosan Cedex, F-31326, France
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops (CREA-CI), S.S. 673, Km 25,200, Foggia, I-71122, Italy; Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy
| | - Enrico Francia
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy.
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Li Y, Xiong H, Cuo D, Wu X, Duan R. Genome-wide characterization and expression profiling of the relation of the HD-Zip gene family to abiotic stress in barley (Hordeum vulgare L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 141:250-258. [PMID: 31195255 DOI: 10.1016/j.plaphy.2019.05.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 05/16/2023]
Abstract
The homeodomain-leucine zipper (HD-Zip) gene family plays an important role in plant growth and environmental responses. At present, research on the HD-Zip gene family of barley is incomplete. In this study, 32 HD-Zip genes (HvHD-Zip 1-32) were identified from the barley genome and were subsequently divided into four subfamilies according to conserved structure and motif analysis. Whole genome replication events in barley and Arabidopsis, rice, and wheat HD-Zip gene families were analyzed, yielding 3, 14 and 25 gene pairs, respectively, but no segmental or tandem duplication events were identified in the barley HD-Zip gene family. Subsequently, quantitative real-time PCR (qRT-PCR) analysis revealed that the HvHD-Zip gene is sensitive to drought stress and that members of the HD-Zip I and HD-Zip IV subfamilies are generally more sensitive to abiotic stresses. Our results suggest a relationship between barley resistance and the potential key HvHD-Zip gene, which lay the foundation for further functional studies.
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Affiliation(s)
- Yuan Li
- College of Eco-environmental Engineering, Qinghai University, Qinghai, 810016, China
| | - Huiyan Xiong
- College of Agriculture and Animal Husbandry, Qinghai University, Qinghai, 810016, China
| | - Duojie Cuo
- College of Eco-environmental Engineering, Qinghai University, Qinghai, 810016, China
| | - Xiongxiong Wu
- College of Eco-environmental Engineering, Qinghai University, Qinghai, 810016, China
| | - Ruijun Duan
- College of Eco-environmental Engineering, Qinghai University, Qinghai, 810016, China; Qinghai Provincial Key Laboratory of Hulless Barley Genetics and Breeding, Qinghai University, Qinghai, 810016, China.
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17
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In silico analysis and gene expression of heat stress responses genes in Hordeum vulgare L. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Mitrová K, Svoboda P, Milella L, Ovesná J. Alliinase and cysteine synthase transcription in developing garlic ( Allium sativum L.) over time. Food Chem 2018; 251:103-109. [DOI: 10.1016/j.foodchem.2017.12.090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/11/2017] [Accepted: 12/31/2017] [Indexed: 12/19/2022]
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19
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Liang C, Hao J, Meng Y, Luo L, Li J. Identifying optimal reference genes for the normalization of microRNA expression in cucumber under viral stress. PLoS One 2018; 13:e0194436. [PMID: 29543906 PMCID: PMC5854380 DOI: 10.1371/journal.pone.0194436] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/02/2018] [Indexed: 11/28/2022] Open
Abstract
Cucumber green mottle mosaic virus (CGMMV) is an economically important pathogen and causes significant reduction of both yield and quality of cucumber (Cucumis sativus). Currently, there were no satisfied strategies for controlling the disease. A better understanding of microRNA (miRNA) expression related to the regulation of plant-virus interactions and virus resistance would be of great assistance when developing control strategies for CGMMV. However, accurate expression analysis is highly dependent on robust and reliable reference gene used as an internal control for normalization of miRNA expression. Most commonly used reference genes involved in CGMMV-infected cucumber are not universally expressed depending on tissue types and stages of plant development. It is therefore crucial to identify suitable reference genes in investigating the role of miRNA expression. In this study, seven reference genes, including Actin, Tubulin, EF-1α, 18S rRNA, Ubiquitin, GAPDH and Cyclophilin, were evaluated for the most accurate results in analyses using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Gene expression was assayed on cucumber leaves, stems and roots that were collected at different days post inoculation with CGMMV. The expression data were analyzed using algorithms including delta-Ct, geNorm, NormFinder, and BestKeeper as well as the comparative tool RefFinder. The reference genes were subsequently validated using miR159. The results showed that EF-1α and GAPDH were the most reliable reference genes for normalizing miRNA expression in leaf, root and stem samples, while Ubiquitin and EF-1α were the most suitable combination overall.
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Affiliation(s)
- Chaoqiong Liang
- Department of Plant Pathology, China Agricultural University/Key Laboratory of Plant Pathology, Ministry of Agriculture, Beijing, China
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
- Plant Gene Expression Center, United States Department of Agriculture, Agricultural Research Service, Albany, California, United States of America
| | - Jianjun Hao
- School of Food and Agriculture, The University of Maine, Orono, Maine, United States of America
| | - Yan Meng
- Department of Plant Pathology, China Agricultural University/Key Laboratory of Plant Pathology, Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, China
| | - Laixin Luo
- Department of Plant Pathology, China Agricultural University/Key Laboratory of Plant Pathology, Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, China
| | - Jianqiang Li
- Department of Plant Pathology, China Agricultural University/Key Laboratory of Plant Pathology, Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, China
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20
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Liu J, Huang S, Niu X, Chen D, Chen Q, Tian L, Xiao F, Liu Y. Genome-wide identification and validation of new reference genes for transcript normalization in developmental and post-harvested fruits of Actinidia chinensis. Gene 2017; 645:1-6. [PMID: 29242074 DOI: 10.1016/j.gene.2017.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/16/2017] [Accepted: 12/09/2017] [Indexed: 01/28/2023]
Abstract
The appropriate reference genes are important and essential for reliable results of transcript normalization in real-time qRT-PCR. In the current study, we identified 1203 stably expressed genes from 35,286 genes' expression profiles in developmental fruits of Actinidia chinensis. We manually selected six candidate genes and assessed their expression levels, using two sets of fruit samples of A. chinensis: flesh fruits at four developmental stages and post-harvested fruits. The expression stability of these six genes was assessed by three independent algorithms: geNorm, NormFinder, and BestKeeper. Statistical results indicated these six genes can serve as internal control in both developmental and post-harvested fruits. Among these genes, UBQ_CONJ_E2 (Ubiquitin-conjugating enzyme E2 36) and TUB_FCB (Tubulin folding cofactor B) were the two best reference genes identified in this study. The identification and validation of these reference genes can be helpful for elucidating the studies of fruit development and post-harvested fruits' storage in A. chinensis and other fruit crops of Actinidiaceae.
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Affiliation(s)
- Jian Liu
- School of Food Science and Engineering, Hefei University of Technology, Hefei 230009, China
| | - Shengxiong Huang
- School of Food Science and Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Xiangli Niu
- School of Food Science and Engineering, Hefei University of Technology, Hefei 230009, China
| | - Danyang Chen
- School of Food Science and Engineering, Hefei University of Technology, Hefei 230009, China
| | - Qiang Chen
- School of Food Science and Engineering, Hefei University of Technology, Hefei 230009, China
| | - Li Tian
- School of Food Science and Engineering, Hefei University of Technology, Hefei 230009, China
| | - FangMing Xiao
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844-2339, USA
| | - Yongsheng Liu
- School of Food Science and Engineering, Hefei University of Technology, Hefei 230009, China; Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China.
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21
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Wang ML, Li QH, Xin HH, Chen X, Zhu XJ, Li XH. Reliable reference genes for normalization of gene expression data in tea plants (Camellia sinensis) exposed to metal stresses. PLoS One 2017; 12:e0175863. [PMID: 28453515 PMCID: PMC5409199 DOI: 10.1371/journal.pone.0175863] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 03/31/2017] [Indexed: 02/01/2023] Open
Abstract
Tea plants [Camellia sinensis (L.) O. Kuntze] are an important leaf-type crop that are widely used for the production of non-alcoholic beverages in the world. Exposure to excessive amounts of heavy metals adversely affects the quality and yield of tea leaves. To analyze the molecular responses of tea plants to heavy metals, a reliable quantification of gene expression is important and of major importance herein is the normalization of the measured expression levels for the target genes. Ideally, stably expressed reference genes should be evaluated in all experimental systems. In this study, 12 candidate reference genes (i.e., 18S rRNA, Actin, CYP, EF-1α, eIF-4α, GAPDH, MON1, PP2AA3, TBP, TIP41, TUA, and UBC) were cloned from tea plants, and the stability of their expression was examined systematically in 60 samples exposed to diverse heavy metals (i.e., manganese, aluminum, copper, iron, and zinc). Three Excel-based algorithms (geNorm, NormFinder, and BestKeeper) were used to evaluate the expression stability of these genes. PP2AA3 and 18S rRNA were the most stably expressed genes, even though their expression profiles exhibited some variability. Moreover, commonly used reference genes (i.e., GAPDH and TBP) were the least appropriate reference genes for most samples. To further validate the suitability of the analyzed reference genes, the expression level of a phytochelatin synthase gene (i.e., CsPCS1) was determined using the putative reference genes for data normalizations. Our results may be beneficial for future studies involving the quantification of relative gene expression levels in tea plants.
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Affiliation(s)
- Ming-Le Wang
- Tea Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Qing-Hui Li
- Tea Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Hua-Hong Xin
- Tea Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Xuan Chen
- Tea Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Xu-Jun Zhu
- Tea Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Xing-Hui Li
- Tea Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
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22
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Zhang Y, Han X, Chen S, Zheng L, He X, Liu M, Qiao G, Wang Y, Zhuo R. Selection of suitable reference genes for quantitative real-time PCR gene expression analysis in Salix matsudana under different abiotic stresses. Sci Rep 2017; 7:40290. [PMID: 28120870 PMCID: PMC5264508 DOI: 10.1038/srep40290] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/05/2016] [Indexed: 12/22/2022] Open
Abstract
Salix matsudana is a deciduous, rapidly growing willow species commonly cultivated in China, which can tolerate drought, salt, and heavy metal stress conditions. Selection of suitable reference genes for quantitative real-time PCR is important for normalizing the expression of the key genes associated with various stresses. To validate suitable reference genes, we selected 11 candidate reference genes (five traditional housekeeping genes and six novel genes) and analyzed their expression stability in various samples, including different tissues and under different abiotic stress treatments. The expression of these genes was determined using five programs-geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder. The results showed that α-TUB2 (alpha-tubulin 2) and DnaJ (chaperone protein DnaJ 49) were the most stable reference genes across all the tested samples. We measured the expression profiles of the defense response gene SmCAT (catalase) using the two most stable and one least stable reference genes in all samples of S. matsudana. The relative quantification of SmCAT varied greatly according to the different reference genes. We propose that α-TUB2 and DnaJ should be the preferred reference genes for normalization and quantification of transcript levels in future gene expression studies in willow species under various abiotic stress conditions.
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Affiliation(s)
- Yunxing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- School of Architectural and Artistic Design, Henan Polytechnic University, Jiaozuo, Henan 454000, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Shuangshuang Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Liu Zheng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Xuelian He
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Mingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Guirong Qiao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yang Wang
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
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23
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Tang X, Zhang N, Si H, Calderón-Urrea A. Selection and validation of reference genes for RT-qPCR analysis in potato under abiotic stress. PLANT METHODS 2017; 13:85. [PMID: 29075311 PMCID: PMC5644265 DOI: 10.1186/s13007-017-0238-7] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/10/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Real-time quantitative PCR (RT-qPCR) is the most commonly used method for accurately detecting gene expression patterns. As part of RT-qPCR analysis, normalization of the data requires internal control gene(s) that display uniform expression under different biological conditions. However, no invariable internal control gene exists, and therefore more than one reference gene is needed to normalize RT-qPCR results. Identification of stable reference genes in potato will improve assay accuracy for selecting stress-tolerance genes and identifying molecular mechanisms conferring stress tolerance in this species. RESULTS In the experiment, we assessed the expression of eight candidate internal control genes, namely elongation factor-1alpha (EF1α), actin, tubulin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), adenine phosphoribosyl transferase (APRT), 60S ribosomal protein L8 (L8), Cullin 3A (CUL3A), and exocyst complex component sec3 (sec3), in a diverse set of potato samples representing drought stress and osmotic stress challenges, and using geNorm, NormFinder, BestKeeper and RefFinder softwares. CONCLUSIONS The results indicated that EF1α and sec3 were the most stably expressed genes in the potato under drought and osmotic stress conditions. This work will facilitate future work on gene expression studies in potato and also benefit other species of the Solanaceae, such as tomato.
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Affiliation(s)
- Xun Tang
- Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Ning Zhang
- Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Huaijun Si
- Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Alejandro Calderón-Urrea
- Department of Biology, California State University, 2555 East San Ramon Avenue, Fresno, CA 93740 USA
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de Andrade LM, dos Santos Brito M, Fávero Peixoto Junior R, Marchiori PER, Nóbile PM, Martins APB, Ribeiro RV, Creste S. Reference genes for normalization of qPCR assays in sugarcane plants under water deficit. PLANT METHODS 2017; 13:28. [PMID: 28428808 PMCID: PMC5392966 DOI: 10.1186/s13007-017-0178-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/02/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Sugarcane (Saccharum spp.) is the main raw material for sugar and ethanol production. Among the abiotic stress, drought is the main one that negatively impact sugarcane yield. Although gene expression analysis through quantitative PCR (qPCR) has increased our knowledge about biological processes related to drought, gene network that mediates sugarcane responses to water deficit remains elusive. In such scenario, validation of reference gene is a major requirement for successful analyzes involving qPCR. RESULTS In this study, candidate genes were tested for their suitable as reference genes for qPCR analyses in two sugarcane cultivars with varying drought tolerance. Eight candidate reference genes were evaluated in leaves sampled in plants subjected to water deficit in both field and greenhouse conditions. In addition, five genes were evaluated in shoot roots of plants subjected to water deficit by adding PEG8000 to the nutrient solution. NormFinder and RefFinder algorithms were used to identify the most stable gene(s) among genotypes and under different experimental conditions. Both algorithms revealed that in leaf samples, UBQ1 and GAPDH genes were more suitable as reference genes, whereas GAPDH was the best reference one in shoot roots. CONCLUSION Reference genes suitable for sugarcane under water deficit were identified, which would lead to a more accurate and reliable analysis of qPCR. Thus, results obtained in this study may guide future research on gene expression in sugarcane under varying water conditions.
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Affiliation(s)
- Larissa Mara de Andrade
- Centro de Cana, Instituto Agronômico (IAC), P.O. Box 206, Ribeirão Preto, SP 14001-970 Brazil
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14049-900 Brazil
| | | | - Rafael Fávero Peixoto Junior
- Centro de Cana, Instituto Agronômico (IAC), P.O. Box 206, Ribeirão Preto, SP 14001-970 Brazil
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14049-900 Brazil
| | | | - Paula Macedo Nóbile
- Centro de Cana, Instituto Agronômico (IAC), P.O. Box 206, Ribeirão Preto, SP 14001-970 Brazil
| | - Alexandre Palma Boer Martins
- Centro de Cana, Instituto Agronômico (IAC), P.O. Box 206, Ribeirão Preto, SP 14001-970 Brazil
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14049-900 Brazil
| | - Rafael Vasconcelos Ribeiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, P.O. Box 6109, Campinas, SP 13083-970 Brazil
| | - Silvana Creste
- Centro de Cana, Instituto Agronômico (IAC), P.O. Box 206, Ribeirão Preto, SP 14001-970 Brazil
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Cao J, Wang L, Lan H. Validation of reference genes for quantitative RT-PCR normalization in Suaeda aralocaspica, an annual halophyte with heteromorphism and C4 pathway without Kranz anatomy. PeerJ 2016; 4:e1697. [PMID: 26893974 PMCID: PMC4756755 DOI: 10.7717/peerj.1697] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/26/2016] [Indexed: 01/08/2023] Open
Abstract
Reverse transcription quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful analytical technique for the measurement of gene expression, which depends on the stability of the reference gene used for data normalization. Suaeda aralocaspica, an annual halophyte with heteromorphic seeds and possessing C4 photosynthesis pathway without Kranz anatomy, is an ideal plant species to identify stress tolerance-related genes and compare relative expression at transcriptional level. So far, no molecular information is available for this species. In the present study, six traditionally used reference genes were selected and their expression stability in two types of seeds of S. aralocaspica under different experimental conditions was evaluated. Three analytical programs, geNorm, NormFinder and BestKeeper, were used to assess and rank the stability of reference gene expression. Results revealed that although some reference genes may display different transcriptional profiles between the two types of seeds, β-TUB and GAPDH appeared to be the most suitable references under different developmental stages and tissues. GAPDH was the appropriate reference gene under different germination time points and salt stress conditions, and ACTIN was suitable for various abiotic stress treatments for the two types of seeds. For all the sample pools, β-TUB served as the most stable reference gene, whereas 18S rRNA and 28S rRNA performed poorly and presented as the least stable genes in our study. UBQ seemed to be unsuitable as internal control under different salt treatments. In addition, the expression of a photosynthesis-related gene (PPDK) of C4 pathway and a salt tolerance-related gene (SAT) of S. aralocaspica were used to validate the best performance reference genes. This is the first systematic comparison of reference gene selection for qRT-PCR work in S. aralocaspica and these data will facilitate further studies on gene expression in this species and other euhalophytes.
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Affiliation(s)
- Jing Cao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University , Urumqi , China
| | - Lu Wang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University , Urumqi , China
| | - Haiyan Lan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University , Urumqi , China
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Yang Y, Zhang X, Chen Y, Guo J, Ling H, Gao S, Su Y, Que Y, Xu L. Selection of Reference Genes for Normalization of MicroRNA Expression by RT-qPCR in Sugarcane Buds under Cold Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:86. [PMID: 26904058 PMCID: PMC4742636 DOI: 10.3389/fpls.2016.00086] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/17/2016] [Indexed: 05/15/2023]
Abstract
Sugarcane, accounting for 80% of world's sugar, originates in the tropics but is cultivated mainly in the subtropics. Therefore, chilling injury frequently occurs and results in serious losses. Recent studies in various plant species have established microRNAs as key elements in the post-transcriptional regulation of response to biotic and abiotic stresses including cold stress. Though, its accuracy is largely influenced by the use of reference gene for normalization, quantitative PCR is undoubtedly a popular method used for identification of microRNAs. For identifying the most suitable reference genes for normalizing miRNAs expression in sugarcane under cold stress, 13 candidates among 17 were investigated using four algorithms: geNorm, NormFinder, deltaCt, and Bestkeeper, and four candidates were excluded because of unsatisfactory efficiency and specificity. Verification was carried out using cold-related genes miR319 and miR393 in cold-tolerant and sensitive cultivars. The results suggested that miR171/18S rRNA and miR171/miR5059 were the best reference gene sets for normalization for miRNA RT-qPCR, followed by the single miR171 and 18S rRNA. These results can aid research on miRNA responses during sugarcane stress, and the development of sugarcane tolerant to cold stress. This study is the first report concerning the reference gene selection of miRNA RT-qPCR in sugarcane.
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Huang X, Gao Y, Jiang B, Zhou Z, Zhan A. Reference gene selection for quantitative gene expression studies during biological invasions: A test on multiple genes and tissues in a model ascidian Ciona savignyi. Gene 2015; 576:79-87. [PMID: 26428313 DOI: 10.1016/j.gene.2015.09.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/16/2015] [Accepted: 09/25/2015] [Indexed: 12/20/2022]
Abstract
As invasive species have successfully colonized a wide range of dramatically different local environments, they offer a good opportunity to study interactions between species and rapidly changing environments. Gene expression represents one of the primary and crucial mechanisms for rapid adaptation to local environments. Here, we aim to select reference genes for quantitative gene expression analysis based on quantitative Real-Time PCR (qRT-PCR) for a model invasive ascidian, Ciona savignyi. We analyzed the stability of ten candidate reference genes in three tissues (siphon, pharynx and intestine) under two key environmental stresses (temperature and salinity) in the marine realm based on three programs (geNorm, NormFinder and delta Ct method). Our results demonstrated only minor difference for stability rankings among the three methods. The use of different single reference gene might influence the data interpretation, while multiple reference genes could minimize possible errors. Therefore, reference gene combinations were recommended for different tissues - the optimal reference gene combination for siphon was RPS15 and RPL17 under temperature stress, and RPL17, UBQ and TubA under salinity treatment; for pharynx, TubB, TubA and RPL17 were the most stable genes under temperature stress, while TubB, TubA and UBQ were the best under salinity stress; for intestine, UBQ, RPS15 and RPL17 were the most reliable reference genes under both treatments. Our results suggest that the necessity of selection and test of reference genes for different tissues under varying environmental stresses. The results obtained here are expected to reveal mechanisms of gene expression-mediated invasion success using C. savignyi as a model species.
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Affiliation(s)
- Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yangchun Gao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Bei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fishery Science Research Institute, Dalian, Liaoning, China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fishery Science Research Institute, Dalian, Liaoning, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
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Larriba E, Jaime MDLA, Nislow C, Martín-Nieto J, Lopez-Llorca LV. Endophytic colonization of barley (Hordeum vulgare) roots by the nematophagous fungus Pochonia chlamydosporia reveals plant growth promotion and a general defense and stress transcriptomic response. JOURNAL OF PLANT RESEARCH 2015; 128:665-78. [PMID: 25982739 DOI: 10.1007/s10265-015-0731-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 03/05/2015] [Indexed: 05/06/2023]
Abstract
Plant crop yields are negatively conditioned by a large set of biotic and abiotic factors. An alternative to mitigate these adverse effects is the use of fungal biological control agents and endophytes. The egg-parasitic fungus Pochonia chlamydosporia has been traditionally studied because of its potential as a biological control agent of plant-parasitic nematodes. This fungus can also act as an endophyte in monocot and dicot plants, and has been shown to promote plant growth in different agronomic crops. An Affymetrix 22K Barley GeneChip was used in this work to analyze the barley root transcriptomic response to P. chlamydosporia root colonization. Functional gene ontology (GO) and gene set enrichment analyses showed that genes involved in stress response were enriched in the barley transcriptome under endophytism. An 87.5% of the probesets identified within the abiotic stress response group encoded heat shock proteins. Additionally, we found in our transcriptomic analysis an up-regulation of genes implicated in the biosynthesis of plant hormones, such as auxin, ethylene and jasmonic acid. Along with these, we detected induction of brassinosteroid insensitive 1-associated receptor kinase 1 (BR1) and other genes related to effector-triggered immunity (ETI) and pattern-triggered immunity (PTI). Our study supports at the molecular level the growth-promoting effect observed in plants endophytically colonized by P. chlamydosporia, which opens the door to further studies addressing the capacity of this fungus to mitigate the negative effects of biotic and abiotic factors on plant crops.
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Affiliation(s)
- Eduardo Larriba
- Department of Marine Sciences and Applied Biology, University of Alicante, 03080, Alicante, Spain
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Choudhary M, Jayanand, Padaria JC. Transcriptional profiling in pearl millet (Pennisetum glaucum L.R. Br.) for identification of differentially expressed drought responsive genes. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2015; 21:187-96. [PMID: 25964713 PMCID: PMC4411378 DOI: 10.1007/s12298-015-0287-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/23/2015] [Accepted: 03/03/2015] [Indexed: 05/04/2023]
Abstract
Pearl millet (Pennisetum glaucum) is an important cereal of traditional farming systems that has the natural ability to withstand various abiotic stresses. The present study aims at the identification and validation of major differentially expressed genes in response to drought stress in P. glaucum by Suppression Subtractive Hybridization (SSH) analysis. Twenty-two days old seedlings of P. glaucum cultivar PPMI741 were subjected to drought stress by treatment of 30 % Polyethylene glycol for different time periods 30 min (T1), 2 h (T2), 4 h (T3), 8 h (T4), 16 h (T5), 24 h (T6) and 48 h (T7) respectively, monitored by examining the RWC of seedlings. Total RNA was isolated to construct drought responsive subtractive cDNA library through SSH, sequenced to identify the differentially expressed genes in response to drought stress and validated by qRT-PCR.745 ESTs were assembled into a collection of 299 unigenes having 52 contigs and 247 singletons. All 745 ESTs were submitted to ENA-EMBL databases (Accession no. HG516611- HG517355). After analysis, 10 differentially expressed genes were validated namely Abscisic stress ripening protein, Ascorbate peroxidase, Inosine-5'-monophosphate dehydrogenase, Putative beta-1, 3-glucanase, Glyoxalase, Rab7, Aspartic proteinase Oryzasin, DnaJ-like protein and Calmodulin-like protein by qRT-PCR. The identified ESTs reveal a major portion of the stress responsive transcriptome that may prove to be a vent to unravel molecular basis underlying tolerance of pearl millet (Pennisetum glaucum) to drought stress. These genes could be utilized for transgenic breeding or transferred to crop plants through marker assisted selection for the development of better drought resistant cultivars having enhanced adaptability to survive harsh environmental conditions.
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Affiliation(s)
- Minakshi Choudhary
- />Biotechnology and Climate Change Laboratory, National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Jayanand
- />Shobhit University, NH-58, Modipuram, Meerut, 250110 India
| | - Jasdeep Chatrath Padaria
- />Biotechnology and Climate Change Laboratory, National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
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Castonguay Y, Michaud J, Dubé MP. Reference Genes for RT-qPCR Analysis of Environmentally and Developmentally Regulated Gene Expression in Alfalfa. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/ajps.2015.61015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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The choice of reference genes for assessing gene expression in sugarcane under salinity and drought stresses. Sci Rep 2014; 4:7042. [PMID: 25391499 PMCID: PMC4229666 DOI: 10.1038/srep07042] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/27/2014] [Indexed: 01/18/2023] Open
Abstract
Sugarcane (Saccharum spp. hybrids) is a world-wide cash crop for sugar and biofuel in tropical and subtropical regions and suffers serious losses in cane yield and sugar content under salinity and drought stresses. Although real-time quantitative PCR has a numerous advantage in the expression quantification of stress-related genes for the elaboration of the corresponding molecular mechanism in sugarcane, the variation happened across the process of gene expression quantification should be normalized and monitored by introducing one or several reference genes. To validate suitable reference genes or gene sets for sugarcane gene expression normalization, 13 candidate reference genes have been tested across 12 NaCl- and PEG-treated sugarcane samples for four sugarcane genotypes using four commonly used systematic statistical algorithms termed geNorm, BestKeeper, NormFinder and the deltaCt method. The results demonstrated that glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and eukaryotic elongation factor 1-alpha (eEF-1a) were identified as suitable reference genes for gene expression normalization under salinity/drought-treatment in sugarcane. Moreover, the expression analyses of SuSK and 6PGDH further validated that a combination of clathrin adaptor complex (CAC) and cullin (CUL) as reference should be better for gene expression normalization. These results can facilitate the future research on gene expression in sugarcane under salinity and drought stresses.
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Reference gene selection for quantitative real-time PCR normalization in Reaumuria soongorica. PLoS One 2014; 9:e104124. [PMID: 25117551 PMCID: PMC4130609 DOI: 10.1371/journal.pone.0104124] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 07/10/2014] [Indexed: 11/19/2022] Open
Abstract
Despite its superiority for evaluating gene expression, real-time quantitative polymerase chain reaction (qPCR) results can be significantly biased by the use of inappropriate reference genes under different experimental conditions. Reaumuria soongorica is a dominant species of desert ecosystems in arid central Asia. Given the increasing interest in ecological engineering and potential genetic resources for arid agronomy, it is important to analyze gene function. However, systematic evaluation of stable reference genes should be performed prior to such analyses. In this study, the stabilities of 10 candidate reference genes were analyzed under 4 kinds of abiotic stresses (drought, salt, dark, and heat) within 4 accessions (HG010, HG020, XGG030, and XGG040) from 2 different habitats using 3 algorithms (geNorm, NormFinder, and BestKeeper). After validation of the ribulose-1,5-bisphosphate carboxylase/oxygenase large unite (rbcL) expression pattern, our data suggested that histone H2A (H2A) and eukaryotic initiation factor 4A-2 (EIF4A2) were the most stable reference genes, cyclophilin (CYCL) was moderate, and elongation factor 1α (EF1α) was the worst choice. This first systematic analysis for stably expressed genes will facilitate future functional analyses and deep mining of genetic resources in R. soongorica and other species of the Reaumuria genus.
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Janská A, Aprile A, Cattivelli L, Zámečník J, de Bellis L, Ovesná J. The up-regulation of elongation factors in the barley leaf and the down-regulation of nucleosome assembly genes in the crown are both associated with the expression of frost tolerance. Funct Integr Genomics 2014; 14:493-506. [PMID: 24838952 DOI: 10.1007/s10142-014-0377-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 04/08/2014] [Accepted: 04/25/2014] [Indexed: 12/26/2022]
Abstract
We report a series of microarray-based leaf and crown transcriptome comparisons involving three barley cultivars (cvs. Luxor, Igri and Atlas 68) which express differing degrees of frost tolerance. The transcripts were obtained following the exposure of seedlings to low (above and below zero) temperatures, aiming to identify those genes and signalling/metabolic pathways which are associated with frost tolerance. Both the leaves and the crowns responded to low temperature by the up-regulation of a suite of abscisic acid (ABA)-responsive genes, most of which have already been recognized as components of the plant low temperature response. The inter-cultivar comparison indicated that genes involved in maintaining the leaf's capacity to synthesize protein and to retain chloroplast activity were important for the expression of frost tolerance. In the crown, the repression of genes associated with nucleosome assembly and transposon regulation were the most relevant transcriptional changes associated with frost tolerance, highlighting the role of gene repression in the cold acclimation response.
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Affiliation(s)
- Anna Janská
- Department of Molecular Biology, Crop Research Institute, v.v.i., Drnovská 507, 161 06, Prague 6, Czech Republic,
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Wang Z, Chen Y, Fang H, Shi H, Chen K, Zhang Z, Tan X. Selection of reference genes for quantitative reverse-transcription polymerase chain reaction normalization in Brassica napus under various stress conditions. Mol Genet Genomics 2014; 289:1023-35. [PMID: 24770781 DOI: 10.1007/s00438-014-0853-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 04/07/2014] [Indexed: 12/16/2022]
Abstract
Data normalization is essential for reliable output of quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR) assays, as the unsuitable choice of reference gene(s), whose expression might be influenced by exogenous treatments in plant tissues, could cause misinterpretation of results. To date, no systematic studies on reference genes have been performed in stressed Brassica napus. In this study, we investigated the expression variations of nine candidate reference genes in 40 samples of B. napus leaves subjected to various exogenous treatments. Parallel analyses by geNorm and NormFinder revealed that optimal reference genes differed across the different sets of samples. The best-ranked reference genes were PP2A and TIP41 for salt stress, TIP41 and ACT7 for heavy metal (Cr(6+)) stress, PP2A and UBC21 for drought stress, F-box and SAND for cold stress, F-box and ZNF for salicylic acid stress, TIP41, ACT7, and PP2A for methyl jasmonate stress, TIP41 and ACT7 for abscisic acid stress, and TIP41, UBC21, and PP2A for Sclerotinia sclerotiorum stress. Two newly employed reference genes, TIP41 and PP2A, showed better performances, suggesting their suitability in multiple conditions. To further validate the suitability of the reference genes, the expression patterns of BnWRKY40 and BnMKS1 were studied in parallel. This study is the first systematic analysis of reference gene selection for qRT-PCR normalization in B. napus, an agriculturally important crop, under different stress conditions. The results will contribute toward more accurate and widespread use of qRT-PCR in gene analysis of the genus Brassica.
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Affiliation(s)
- Zheng Wang
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, 212013, People's Republic of China,
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