1
|
Bae Y, Baek W, Lim CW, Lee SC. A pepper RING-finger E3 ligase, CaFIRF1, negatively regulates the high-salt stress response by modulating the stability of CaFAF1. PLANT, CELL & ENVIRONMENT 2024; 47:1319-1333. [PMID: 38221841 DOI: 10.1111/pce.14818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/11/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024]
Abstract
Controlling protein stability or degradation via the ubiquitin-26S proteasome system is a crucial mechanism in plant cellular responses to stress conditions. Previous studies have revealed that the pepper FANTASTIC FOUR-like gene, CaFAF1, plays a positive role in salt tolerance and that, in this process, CaFAF1 protein degradation is delayed. Here, we sought to isolate the E3 ligases potentially responsible for modulating CaFAF1 protein stability in response to salt stress. The pepper RING-type E3 ligase CaFIRF1 (Capsicum annuum FAF1 Interacting RING Finger protein 1) was found to interact with and ubiquitinate CaFAF1, leading to the degradation of CaFAF1 proteins. In response to high-salt treatments, CaFIRF1-silenced pepper plants exhibited tolerant phenotypes. In contrast, co-silencing of CaFAF1 and CaFIRF1 led to increased sensitivity to high-salt treatments, revealing that CaFIRF1 functions upstream of CaFAF1. A cell-free degradation analysis showed that high-salt treatment suppressed CaFAF1 protein degradation via the 26S proteasome pathway, in which CaFIRF1 is functionally involved. In addition, an in vivo ubiquitination assay revealed that CaFIRF1-mediated ubiquitination of CaFAF1 proteins was reduced by high-salt treatment. Taken together, these findings suggest that the degradation of CaFAF1 mediated by CaFIRF1 has a critical role in pepper plant responses to high salinity.
Collapse
Affiliation(s)
- Yeongil Bae
- Department of Life Science (BK21 Program), Chung-Ang University, Seoul, Korea
| | - Woonhee Baek
- Department of Life Science (BK21 Program), Chung-Ang University, Seoul, Korea
| | - Chae Woo Lim
- Department of Life Science (BK21 Program), Chung-Ang University, Seoul, Korea
| | - Sung Chul Lee
- Department of Life Science (BK21 Program), Chung-Ang University, Seoul, Korea
| |
Collapse
|
2
|
Ebrahimi A, Gharanjik S, Azadvari E, Rashidi-Monfared S. Characterizing reference genes for high-fidelity gene expression analysis under different abiotic stresses and elicitor treatments in fenugreek leaves. PLANT METHODS 2024; 20:40. [PMID: 38491388 PMCID: PMC10943880 DOI: 10.1186/s13007-024-01167-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND Quantifying gene expression is a critical aspect of applied genomics research across all organisms, and real-time PCR has emerged as a powerful tool for this purpose. However, selecting appropriate internal control genes for data normalization presents specific challenges. This study aimed to identify suitable reference genes for gene expression analysis under various conditions, encompassing salinity, low and high-temperature stresses, and different elicitor treatments. These treatments included titanium dioxide, cold plasma, 24-epibrassinolide, and melatonin, resulting in a total of 13 unique treatments and 148 treatment combinations applied to fenugreek plants. RESULTS As per the analysis performed with the BestKeeper tool, EEF-1α, and GAPDH were recognized as the most stable reference genes under the majority of conditions. Furthermore, the GeNorm and NormFinder tools identified β-tubulin and EEF-1α as the most stable reference genes. The findings of this research demonstrated that, although the stability of three reference genes expression was acceptable in almost all evaluated treatments, fluctuations in their expression were observed under the treatments of cold stress with TiO2 NPs application, cold plasma application with salinity stress, and cold plasma application with high-temperature stress compared to others. Simultaneously, the GeNorm analysis results demonstrated that in the mentioned treatments, relying on only one reference gene is inadequate. To corroborate the results, we examined the expression profile of the SSR gene, a pivotal gene in diosgenin biosynthesis, under all investigated treatments and treatment combinations. The outcomes suggested that employing stable reference genes yielded highly consistent results. CONCLUSIONS The varying expression patterns of the target genes emphasize the crucial need for precise optimization of experimental conditions and selecting stable reference genes to achieve accurate results in gene expression studies utilizing real-time PCR. These findings offer valuable insights into the selection of appropriate reference genes for gene expression analysis under diverse conditions using real-time PCR.
Collapse
Affiliation(s)
- Amin Ebrahimi
- Agronomy and Plant Breeding Department, Faculty of Agriculture, Shahrood University of Technology, Semnan, Iran.
| | - Shahrokh Gharanjik
- Department of Plant Breeding and Biotechnology, Faculty of Agricultural Engineering, Shahrood University of Technology, Shahrood, Iran.
| | - Elham Azadvari
- Horticultural Sciences Department, Faculty of Agriculture, Shahrood University of Technology, Shahrood, Iran
| | - Sajad Rashidi-Monfared
- Plant Breeding and Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| |
Collapse
|
3
|
Li X, Zhang T, Jiang L, Fan G. Evaluation of Suitable Reference Genes for Quantitative Real-Time PCR in Various Tissues of Apocynum venetum. Genes (Basel) 2024; 15:231. [PMID: 38397220 PMCID: PMC10888412 DOI: 10.3390/genes15020231] [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: 12/28/2023] [Revised: 01/27/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Apocynum venetum L. is an economically valuable plant with tolerance to drought and salinity. Its leaves are utilized in tea production and pharmaceuticals, while the stem bark serves as a high-quality fiber material. To gain insights into the gene expression patterns of A. venetum using quantitative real-time PCR (qRT-PCR), it is crucial to identify appropriate reference genes. This study selected nine candidate genes, including α-tubulin (TUA), β-tubulin (TUB), actin (ACT), cyclophilin (CYP), elongation factor-1α (EF-1α), the B family of regulatory subunits of protein phosphatase (PPP2R2, PPP2R3, and PPP2R5), and phosphoglycerate kinase (PGK), to determine the most appropriate reference genes in the leaf, stem, and root tissues of A. venetum. A comprehensive ranking by geNorm, NormFinder, BestKeeper, and RefFinder software and Venn diagrams was used to screen more stable reference genes in different tissues. The two most stable reference genes were CYP and TUA in leaves, PGK and PPP2R3 in stems, and TUA and EF-1α in roots, respectively. The relative expression values of the four genes involved in proline metabolism under polyethylene glycol treatment were used to validate the screened reference genes, and they exhibited highly stable expression levels. These findings represent the first set of stable reference genes for future gene expression studies in A. venetum. They significantly contribute to enhancing the accuracy and reliability of gene expression analyses in this economically important plant species.
Collapse
Affiliation(s)
- Xiaoshuang Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China (T.Z.)
| | - Tingting Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China (T.Z.)
| | - Li Jiang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Guizhi Fan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China (T.Z.)
| |
Collapse
|
4
|
Yu M, Xiong J, Dong K, Quan X, Guo H, Huo J, Qin D, Wang Y, Lu X, Zhu C. AcMYB10 Involved in Anthocyanin Regulation of 'Hongyang' Kiwifruit Induced via Fruit Bagging and High-Postharvest-Temperature Treatments. Genes (Basel) 2024; 15:97. [PMID: 38254986 PMCID: PMC10815172 DOI: 10.3390/genes15010097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Light and temperature are key factors influencing the accumulation of anthocyanin in fruit crops. To assess the effects of fruit bagging during development and high post-ripening temperature on 'Hongyang' kiwifruit, we compared the pigmentation phenotypes and expression levels of anthocyanin-related genes between bagged and unbagged treatments, and between 25 °C and 37 °C postharvest storage temperatures. Both the bagging and 25 °C treatments showed better pigmentation phenotypes with higher anthocyanin concentrations. The results of the qRT-PCR analysis revealed that the gene expression levels of LDOX (leucoanthocyanidin dioxygenase), F3GT (UDP-flavonoid 3-O-glycosyltransferase ), AcMYB10, and AcbHLH42 were strongly correlated and upregulated by both the bagging treatment and 25 °C storage. The results of bimolecular fluorescence complementation and luciferase complementation imaging assays indicated an interaction between AcMYB10 and AcbHLH42 in plant cells, whereas the results of a yeast one-hybrid assay further demonstrated that AcMYB10 activated the promoters of AcLODX and AcF3GT. These results strongly suggest that enhanced anthocyanin synthesis is caused by the promoted expression of AcLODX and AcF3GT, regulated by the complex formed by AcMYB10-AcbHLH42.
Collapse
Affiliation(s)
- Min Yu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jinyu Xiong
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Kun Dong
- Horticulture Branch, Heilongjiang Academy of Agricultural Sciences, Harbin 150040, China
| | - Xin Quan
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Hao Guo
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Junwei Huo
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Dong Qin
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Yanchang Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xuemei Lu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Chenqiao Zhu
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| |
Collapse
|
5
|
Reglinski T, Wurms KV, Vanneste JL, Ah Chee A, Schipper M, Cornish D, Yu J, McAlinden J, Hedderley D. Kiwifruit Resistance to Sclerotinia sclerotiorum and Pseudomonas syringae pv. actinidiae and Defence Induction by Acibenzolar-S-methyl and Methyl Jasmonate Are Cultivar Dependent. Int J Mol Sci 2023; 24:15952. [PMID: 37958935 PMCID: PMC10647243 DOI: 10.3390/ijms242115952] [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: 09/29/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Pathogen susceptibility and defence gene inducibility were compared between the Actinidia arguta cultivar 'Hortgem Tahi' and the two cultivars of A. chinensis 'Hayward' and 'Zesy002'. Plants were treated with acibenzolar-s-methyl (ASM) or methyl jasmonate (MeJA) one week before inoculation with Pseudomonas syringae pv. actinidiae (Psa biovar3) or Sclerotinia sclerotiorum, or secondary induction with chitosan+glucan (Ch-Glu) as a potential pathogen proxy. Defence expression was evaluated by measuring the expression of 18 putative defence genes. 'Hortgem Tahi' was highly susceptible to sclerotinia and very resistant to Psa, whereas 'Zesy002' was highly resistant to both, and 'Hayward' was moderately susceptible to both. Gene expression in 'Hayward' and 'Zesy002' was alike but differed significantly from 'Hortgem Tahi' which had higher basal levels of PR1-i, PR5-i, JIH1, NPR3 and WRKY70 but lower expression of RD22 and PR2-i. Treatment with ASM caused upregulation of NIMIN2, PR1-i, WRKY70, DMR6 and PR5-i in all cultivars and induced resistance to Psa in 'Zesy002' and 'Hayward' but decreased resistance to sclerotinia in 'Zesy002'. MeJA application caused upregulation of LOX2 and downregulation of NIMIN2, DMR6 and PR2-i but did not affect disease susceptibility. The Ch-Glu inducer induced PR-gene families in each cultivar, highlighting its possible effectiveness as an alternative to actual pathogen inoculation. The significance of variations in fundamental and inducible gene expression among the cultivars is explored.
Collapse
Affiliation(s)
- Tony Reglinski
- Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand; (K.V.W.); (J.L.V.); (A.A.C.); (M.S.); (D.C.); (J.Y.); (J.M.)
| | - Kirstin V. Wurms
- Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand; (K.V.W.); (J.L.V.); (A.A.C.); (M.S.); (D.C.); (J.Y.); (J.M.)
| | - Joel L. Vanneste
- Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand; (K.V.W.); (J.L.V.); (A.A.C.); (M.S.); (D.C.); (J.Y.); (J.M.)
| | - Annette Ah Chee
- Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand; (K.V.W.); (J.L.V.); (A.A.C.); (M.S.); (D.C.); (J.Y.); (J.M.)
| | - Magan Schipper
- Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand; (K.V.W.); (J.L.V.); (A.A.C.); (M.S.); (D.C.); (J.Y.); (J.M.)
| | - Deirdre Cornish
- Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand; (K.V.W.); (J.L.V.); (A.A.C.); (M.S.); (D.C.); (J.Y.); (J.M.)
| | - Janet Yu
- Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand; (K.V.W.); (J.L.V.); (A.A.C.); (M.S.); (D.C.); (J.Y.); (J.M.)
| | - Jordan McAlinden
- Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand; (K.V.W.); (J.L.V.); (A.A.C.); (M.S.); (D.C.); (J.Y.); (J.M.)
| | - Duncan Hedderley
- Palmerston North Research Centre, The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand;
| |
Collapse
|
6
|
Tian Y, Li L, Wang R, Ji N, Ma C, Lei J, Guan W, Zhang X. Pullulan-Based Active Coating Incorporating Potassium Metabisulfite Maintains Postharvest Quality and Induces Disease Resistance to Soft Rot in Kiwifruit. Foods 2023; 12:3197. [PMID: 37685129 PMCID: PMC10487164 DOI: 10.3390/foods12173197] [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: 07/24/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Soft rot is a severe postharvest disease of kiwifruit that causes enormous economic losses annually. In this study, we aimed to explore an effective pullulan-based active coating, incorporating food additives to reduce soft rot and extend the shelf life of cold-stored kiwifruit. The results showed that 1 g/L potassium metabisulfite could completely inhibit the mycelial growth of Diaporthe sp., Botryosphaeria dothidea, Phomopsis sp. and Alternaria sp., which were the primary pathogens of kiwifruit soft rot. Furthermore, the pullulan coating, combined with a 10 g/L potassium metabisulfite group, had a decay rate 46% lower than the control (CK) group and maintained fruit quality at the end of shelf life. The retention of physicochemical properties such as soluble solid content (SSC), firmness, weight loss and respiration rate also confirmed the efficacy of the treatment. In addition, at the end of shelf life, pullulan coating, combined with potassium metabisulfite, increased the accumulation of total phenolic content (37.59%) and flavonoid content (9.28%), maintained a high energy charge (51.36%), and enhanced superoxide dismutase (SOD) (6.27%), peroxidase (POD) (62.50%), catalase (CAT) (84.62%) and phenylalanine ammonia lyase (PAL) (24.61%) enzyme activities as well as initiating the upregulation of their gene expression levels. As a result, the disease resistance of fruit was improved, and the occurrence of soft rot was delayed. Overall, this study demonstrated that using the pullulan-based active coating incorporating potassium metabisulfite treatment effectively controlled soft rot and retarded the senescence of postharvest kiwifruit.
Collapse
Affiliation(s)
- Yiming Tian
- College of Food and Pharmaceutical Engineering, Guiyang University, Guiyang 550005, China; (Y.T.); (L.L.); (N.J.); (C.M.); (J.L.); (X.Z.)
| | - Lamei Li
- College of Food and Pharmaceutical Engineering, Guiyang University, Guiyang 550005, China; (Y.T.); (L.L.); (N.J.); (C.M.); (J.L.); (X.Z.)
| | - Rui Wang
- College of Food and Pharmaceutical Engineering, Guiyang University, Guiyang 550005, China; (Y.T.); (L.L.); (N.J.); (C.M.); (J.L.); (X.Z.)
| | - Ning Ji
- College of Food and Pharmaceutical Engineering, Guiyang University, Guiyang 550005, China; (Y.T.); (L.L.); (N.J.); (C.M.); (J.L.); (X.Z.)
| | - Chao Ma
- College of Food and Pharmaceutical Engineering, Guiyang University, Guiyang 550005, China; (Y.T.); (L.L.); (N.J.); (C.M.); (J.L.); (X.Z.)
| | - Jiqing Lei
- College of Food and Pharmaceutical Engineering, Guiyang University, Guiyang 550005, China; (Y.T.); (L.L.); (N.J.); (C.M.); (J.L.); (X.Z.)
| | - Wenqiang Guan
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Xu Zhang
- College of Food and Pharmaceutical Engineering, Guiyang University, Guiyang 550005, China; (Y.T.); (L.L.); (N.J.); (C.M.); (J.L.); (X.Z.)
| |
Collapse
|
7
|
Wurms KV, Reglinski T, Buissink P, Ah Chee A, Fehlmann C, McDonald S, Cooney J, Jensen D, Hedderley D, McKenzie C, Rikkerink EHA. Effects of Drought and Flooding on Phytohormones and Abscisic Acid Gene Expression in Kiwifruit. Int J Mol Sci 2023; 24:ijms24087580. [PMID: 37108744 PMCID: PMC10143653 DOI: 10.3390/ijms24087580] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Environmental extremes, such as drought and flooding, are becoming more common with global warming, resulting in significant crop losses. Understanding the mechanisms underlying the plant water stress response, regulated by the abscisic acid (ABA) pathway, is crucial to building resilience to climate change. Potted kiwifruit plants (two cultivars) were exposed to contrasting watering regimes (water logging and no water). Root and leaf tissues were sampled during the experiments to measure phytohormone levels and expression of ABA pathway genes. ABA increased significantly under drought conditions compared with the control and waterlogged plants. ABA-related gene responses were significantly greater in roots than leaves. ABA responsive genes, DREB2 and WRKY40, showed the greatest upregulation in roots with flooding, and the ABA biosynthesis gene, NCED3, with drought. Two ABA-catabolic genes, CYP707A i and ii were able to differentiate the water stress responses, with upregulation in flooding and downregulation in drought. This study has identified molecular markers and shown that water stress extremes induced strong phytohormone/ABA gene responses in the roots, which are the key site of water stress perception, supporting the theory kiwifruit plants regulate ABA to combat water stress.
Collapse
Affiliation(s)
- Kirstin V Wurms
- Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand
| | - Tony Reglinski
- Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand
| | - Poppy Buissink
- Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand
| | - Annette Ah Chee
- Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand
| | - Christina Fehlmann
- Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand
| | - Stella McDonald
- Mount Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
| | - Janine Cooney
- Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand
| | - Dwayne Jensen
- Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand
| | - Duncan Hedderley
- Palmerston North Research Centre, The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand
| | - Catherine McKenzie
- Te Puke Research Centre, The New Zealand Institute for Plant and Food Research Limited, Te Puke 3182, New Zealand
| | - Erik H A Rikkerink
- Mount Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
| |
Collapse
|
8
|
Ferreira MJ, Silva J, Pinto SC, Coimbra S. I Choose You: Selecting Accurate Reference Genes for qPCR Expression Analysis in Reproductive Tissues in Arabidopsis thaliana. Biomolecules 2023; 13:biom13030463. [PMID: 36979397 PMCID: PMC10046263 DOI: 10.3390/biom13030463] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Quantitative real-time polymerase chain reaction (qPCR) is a widely used method to analyse the gene expression pattern in the reproductive tissues along with detecting gene levels in mutant backgrounds. This technique requires stable reference genes to normalise the expression level of target genes. Nonetheless, a considerable number of publications continue to present qPCR results normalised to a single reference gene and, to our knowledge, no comparative evaluation of multiple reference genes has been carried out in specific reproductive tissues of Arabidopsis thaliana. Herein, we assessed the expression stability levels of ten candidate reference genes (UBC9, ACT7, GAPC-2, RCE1, PP2AA3, TUA2, SAC52, YLS8, SAMDC and HIS3.3) in two conditional sets: one across flower development and the other using inflorescences from different genotypes. The stability analysis was performed using the RefFinder tool, which combines four statistical algorithms (geNorm, NormFinder, BestKeeper and the comparative ΔCt method). Our results showed that RCE1, SAC52 and TUA2 had the most stable expression in different flower developmental stages while YLS8, HIS3.3 and ACT7 were the top-ranking reference genes for normalisation in mutant studies. Furthermore, we validated our results by analysing the expression pattern of genes involved in reproduction and examining the expression of these genes in published mutant backgrounds. Overall, we provided a pool of appropriate reference genes for expression studies in reproductive tissues of A. thaliana, which will facilitate further gene expression studies in this context. More importantly, we presented a framework that will promote a consistent and accurate analysis of gene expression in any scientific field. Simultaneously, we highlighted the relevance of clearly defining and describing the experimental conditions associated with qPCR to improve scientific reproducibility.
Collapse
Affiliation(s)
- Maria João Ferreira
- LAQV/REQUIMTE, Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Jessy Silva
- LAQV/REQUIMTE, Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
- School of Sciences, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Sara Cristina Pinto
- LAQV/REQUIMTE, Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Sílvia Coimbra
- LAQV/REQUIMTE, Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
- Correspondence:
| |
Collapse
|
9
|
Wang Y, Tan Z, Zhen X, Liang Y, Gao J, Zhao Y, Liu S, Zha M. Contribution of Sucrose Metabolism in Phloem to Kiwifruit Bacterial Canker Resistance. PLANTS (BASEL, SWITZERLAND) 2023; 12:918. [PMID: 36840266 PMCID: PMC9962870 DOI: 10.3390/plants12040918] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/31/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Kiwifruit bacterial canker, caused by Pseudomonas syringae pv. actinidiae (Psa), is a catastrophic disease affecting kiwifruit worldwide. As no effective cure has been developed, planting Psa-resistant cultivars is the best way to avoid bacterial canker in kiwifruit cultivation. However, the differences in the mechanism of resistance between cultivars is poorly understood. In the present study, five local kiwifruit cultivars were used for Psa resistance evaluation and classified into different resistance categories, tolerant (T), susceptible (S), and highly susceptible (HS), based on their various symptoms of lesions on the cane. Susceptible and highly susceptible varieties had a higher sucrose concentration, and a greater decrease in sucrose content was observed after Psa inoculation in phloem than in tolerant varieties. Three invertase activities and their corresponding gene expressions were detected in the phloem with lesions and showed the same trends as the variations in sucrose concentration. Meanwhile, after Psa inoculation, enzyme activities involved in antioxidant defense responses, such as PAL, POD, and CAT, were also altered in the phloem of the lesion position. With no differences among cultivars, PAL and POD activities in phloem first increased and then decreased after Psa inoculation. However, great differences in CAT activities were observed between T and S/HS categories. Our results demonstrate that sucrose content was negatively correlated with the disease resistance of different cultivars and that the increase in immune response enzymes is likely caused by increased sucrose metabolism in the phloem.
Collapse
Affiliation(s)
- Yan Wang
- College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, China
- Key Laboratory of Plant Resources Conservation and Utilization, College of Hunan Province, Jishou 416000, China
| | - Zecheng Tan
- College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, China
| | - Xi Zhen
- College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, China
| | - Yuanyuan Liang
- College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, China
| | - Jianyou Gao
- College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, China
| | - Yanhui Zhao
- College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, China
| | - Shibiao Liu
- College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, China
- Key Laboratory of Plant Resources Conservation and Utilization, College of Hunan Province, Jishou 416000, China
| | - Manrong Zha
- College of Biology Resources and Environmental Sciences, Jishou University, Jishou 416000, China
- Key Laboratory of Plant Resources Conservation and Utilization, College of Hunan Province, Jishou 416000, China
| |
Collapse
|
10
|
Wang Q, Guo C, Yang S, Zhong Q, Tian J. Screening and Verification of Reference Genes for Analysis of Gene Expression in Garlic ( Allium sativum L.) under Cold and Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:763. [PMID: 36840111 PMCID: PMC9963267 DOI: 10.3390/plants12040763] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The principal objective of this study was to screen and verify reference genes appropriate for gene expression evaluation during plant growth and development under distinct growth conditions. Nine candidate reference genes were screened based on garlic transcriptome sequence data. RT-qPCR was used to detect the expression levels of the aforementioned reference genes in specific tissues under drought and cold stress. Then, geNorm, NormFinder, BestKeeper, and ReFinder were used to consider the consistency of the expression levels of candidate reference genes. Finally, the stress-responsive gene expression of ascorbate peroxidase (APX) was quantitatively evaluated to confirm the chosen reference genes. Our results indicated that there were variations in the abundance and stability of nine reference gene transcripts underneath cold and drought stress, among which ACT and UBC-E2 had the highest transcript abundance, and 18S rRNA and HIS3 had the lowest transcript abundance. UBC and UBC-E2 were the most stably expressed genes throughout all samples; UBC and UBC-E2 were the most stably expressed genes during cold stress, and ACT and UBC were the most stably expressed genes under drought stress. The most stably expressed genes in roots, pseudostems, leaves, and cloves were EF1, ACT, HIS3, UBC, and UBC-E2, respectively, while GAPDH was the most unstable gene during drought and cold stress conditions and in exclusive tissues. Taking the steady reference genes UBC-E2, UBC, and ACT as references during drought and cold stress, the reliability of the expression levels was further demonstrated by detecting the expression of AsAPX. Our work thereby offers a theoretical reference for the evaluation of gene expression in garlic in various tissues and under stress conditions.
Collapse
Affiliation(s)
- Qizhang Wang
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Chunqian Guo
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Shipeng Yang
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Qiwen Zhong
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Jie Tian
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China
| |
Collapse
|
11
|
Chen Y, Bao W, Hong W, Dong X, Gong M, Cheng Q, Mao K, Yao C, Liu Z, Wang N. Evaluation of eleven kiwifruit genotypes for bicarbonate tolerance and characterization of two tolerance-contrasting genotypes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:202-213. [PMID: 36427382 DOI: 10.1016/j.plaphy.2022.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Screening bicarbonate-tolerant genotypes is an environmentally-friendly and long-term effective strategy to cope with bicarbonate-induced chlorosis in fruit crops grown on calcareous soils. We investigated eleven genotypes from four kiwifruit species (Actinidia chinensis, A. macrosperma, A. polygama, and A. valvata) for differences in bicarbonate tolerance. We also characterized the physiological and molecular differences in two contrasting genotypes of this group. In the first experiment, bicarbonate-treated plantlets were irrigated with 3.0 g L-1 CaCO3 and 5.04 g L-1 NaHCO3 in peat and perlite medium culture. Based on principal component analysis, weight-based membership function method and cluster analysis, the tested genotypes were classified into three groups: (1) tolerant, including YX, Av-1, Acd, Ap, Av-2, and QM; (2) moderately tolerant, including Av-3, Am, Av-4, and HWD; and (3) sensitive, including only QH. In the second experiment, QH (bicarbonate-sensitive) and YX (bicarbonate-tolerant) were grown in sand culture with 4.0 g L-1 CaCO3 and 0.84 g L-1 or 1.26 g L-1 NaHCO3. Compared with QH, YX showed a better ability to take up iron (Fe) by roots and to transport Fe from roots to shoots in the bicarbonate treatments, probably due to a better capacity to protect from oxidative damage and to excrete protons, and a differential expression of genes associated with Fe uptake and translocation, including HA8, IRT1, YSL3 and NRAMP3. The results can facilitate identifying potential resources for bicarbonate tolerance and breeding new rootstocks, and contribute to the elucidation of the bicarbonate tolerance mechanisms in the genus Actinidia.
Collapse
Affiliation(s)
- Yuanlei Chen
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wenwu Bao
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Weijin Hong
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaoke Dong
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Manyu Gong
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Quanqi Cheng
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ke Mao
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chunchao Yao
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhande Liu
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Nannan Wang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
12
|
Ji T, Ma S, Liang M, Wang X, Gao L, Tian Y. Reference genes identification for qRT-PCR normalization of gene expression analysis in Cucumis sativus under Meloidogyne incognita infection and Pseudomonas treatment. FRONTIERS IN PLANT SCIENCE 2022; 13:1061921. [PMID: 36589116 PMCID: PMC9799720 DOI: 10.3389/fpls.2022.1061921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
qRT-PCR is a common and key technical means to study gene expression in biological research. However, reliability and accuracy of quantification by qRT-PCR is entirely dependent on the identification of appropriate reference genes. Cucumber as an economical vegetable is widely cultivated worldwide and is subject to serious nematode infection, especially from M. incognita. Plant could employ beneficial soil bacteria in the rhizosphere to enhance plant adaptability to various stresses. In this study, the optimal reference genes in cucumber under M. incognita stress and Pseudomonas treatment were calculated and confirmed. A total of thirteen candidate reference genes were identified across three different treatments. Of these, geNorm, NormFinder and BestKeeper programs combined RefFinder software identified EF1 and UBI are the most suitable reference gene in the root knot and whole root of cucumber infected M. incognita, respectively, and CACS is the most suitable reference gene in the whole root of cucumber treated by Pseudomonas. The work first validated the most suitable reference genes for the normalization gene expression in cucumber by nematode infected or Pseudomonas inoculated, and these results would facilitate the further research on M. incognita or Pseudomonas soil rhizosphere microbe interaction with cucumber.
Collapse
Affiliation(s)
| | | | | | | | - Lihong Gao
- *Correspondence: Yongqiang Tian, ; Lihong Gao,
| | | |
Collapse
|
13
|
Correia C, Magnani F, Pastore C, Cellini A, Donati I, Pennisi G, Paucek I, Orsini F, Vandelle E, Santos C, Spinelli F. Red and Blue Light Differently Influence Actinidia chinensis Performance and Its Interaction with Pseudomonas syringae pv. Actinidiae. Int J Mol Sci 2022; 23:13145. [PMID: 36361938 PMCID: PMC9658526 DOI: 10.3390/ijms232113145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 03/08/2024] Open
Abstract
Light composition modulates plant growth and defenses, thus influencing plant-pathogen interactions. We investigated the effects of different light-emitting diode (LED) red (R) (665 nm) and blue (B) (470 nm) light combinations on Actinidia chinensis performance by evaluating biometric parameters, chlorophyll a fluorescence, gas exchange and photosynthesis-related gene expression. Moreover, the influence of light on the infection by Pseudomonas syringae pv. actinidiae (Psa), the etiological agent of bacterial canker of kiwifruit, was investigated. Our study shows that 50%R-50%B (50R) and 25%R-75%B (25R) lead to the highest PSII efficiency and photosynthetic rate, but are the least effective in controlling the endophytic colonization of the host by Psa. Monochromatic red light severely reduced ΦPSII, ETR, Pn, TSS and photosynthesis-related genes expression, and both monochromatic lights lead to a reduction of DW and pigments content. Monochromatic blue light was the only treatment significantly reducing disease symptoms but did not reduce bacterial endophytic population. Our results suggest that monochromatic blue light reduces infection primarily by modulating Psa virulence more than host plant defenses.
Collapse
Affiliation(s)
- Cristiana Correia
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
- IB2Lab, LAQV-Requimte, Department of Biology, Faculty of Sciences, University of Porto, Rua Campo Alegre, 4169-007 Porto, Portugal
| | - Federico Magnani
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Chiara Pastore
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Antonio Cellini
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Irene Donati
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Giuseppina Pennisi
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Ivan Paucek
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Francesco Orsini
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Elodie Vandelle
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Conceição Santos
- IB2Lab, LAQV-Requimte, Department of Biology, Faculty of Sciences, University of Porto, Rua Campo Alegre, 4169-007 Porto, Portugal
| | - Francesco Spinelli
- Department of Agricultural Sciences, Alma Mater Studiorum University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| |
Collapse
|
14
|
García JA, Garrido I, Ortega A, del Moral J, Llerena JL, Espinosa F. Physiological and Molecular Responses of Vitis vinifera cv. Tempranillo Affected by Esca Disease. Antioxidants (Basel) 2022; 11:antiox11091720. [PMID: 36139794 PMCID: PMC9495647 DOI: 10.3390/antiox11091720] [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: 07/21/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Esca is a multi-fungal disease affecting grapevines. The objective of the study was to evaluate the physiological and molecular response of the grapevine cv. Tempranillo to esca disease, carried out in a vineyard under Mediterranean climatic conditions in western Spain. The photosynthetic pigments in the leaves decreased, with a strong decrease in the photosynthetic efficiency. The proline content increased significantly in the early stages of affected leaves, being possibly involved in the maintenance of lipid peroxidation levels in leaves, which do not increase. The phenol, flavonoid, and phenylpropanoid content decreased in esca-affected leaves, as does the total antioxidant capacity (FRAP), while the polyphenol oxidase (PPO) activity suffers a strong increase with the development of the disease. In affected grapes, the lipid peroxidation and the total phenol content decrease, but not the anthocyanin content. The ascorbate pool decreases with the disease and with time. On the other hand, pool GSH + GSSG is lower in affected leaves, but increases with time. These alterations show a clear change in the redox homeostasis. The expression of genes phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO), superoxide dismutase (SOD), and chalcone synthase (ChaS1 and ChaS3) become considerably higher in response to esca, being even higher when the infection time increases. The alteration of AsA and GSH levels, phenolic compounds, PPO activity, proline content, and FRAP, together with the increase of the PAL, PPO, SOD,ChaS1, and ChaS3 gene expression, are clearly implicated in the esca response in plants. The expression of these genes, similar to the PPO activity, can be used as markers of state in the development of the disease.
Collapse
Affiliation(s)
- José Antonio García
- Centro Tecnológico Nacional Agroalimentario “Extremadura” (CTAEX), Ctra. Villafranco-Balboa 1.2, 06195 Badajoz, Spain
| | - Inmaculada Garrido
- Grupo Investigación Fisiología y Biología Celular y Molecular de Plantas (BBB015), Facultad de Ciencias, Campus Avenida de Elvas s/n, Universidad de Extremadura, 06071 Badajoz, Spain
| | - Alfonso Ortega
- Grupo Investigación Fisiología y Biología Celular y Molecular de Plantas (BBB015), Facultad de Ciencias, Campus Avenida de Elvas s/n, Universidad de Extremadura, 06071 Badajoz, Spain
| | - Jerónimo del Moral
- Grupo Investigación Calidad y Microbiología de los Alimentos (AGAO17), Instituto Universitario de Investigación de Recursos Agrarios (INURA), 06071 Badajoz, Spain
| | - José Luis Llerena
- Centro Tecnológico Nacional Agroalimentario “Extremadura” (CTAEX), Ctra. Villafranco-Balboa 1.2, 06195 Badajoz, Spain
- Grupo Investigación Fisiología y Biología Celular y Molecular de Plantas (BBB015), Facultad de Ciencias, Campus Avenida de Elvas s/n, Universidad de Extremadura, 06071 Badajoz, Spain
| | - Francisco Espinosa
- Grupo Investigación Fisiología y Biología Celular y Molecular de Plantas (BBB015), Facultad de Ciencias, Campus Avenida de Elvas s/n, Universidad de Extremadura, 06071 Badajoz, Spain
- Correspondence:
| |
Collapse
|
15
|
TBP, PPIA, YWHAZ and EF1A1 Are the Most Stably Expressed Genes during Osteogenic Differentiation. Int J Mol Sci 2022; 23:ijms23084257. [PMID: 35457075 PMCID: PMC9025278 DOI: 10.3390/ijms23084257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
RT-qPCR is the gold standard and the most commonly used method for measuring gene expression. Selection of appropriate reference gene(s) for normalization is a crucial part of RT-qPCR experimental design, which allows accurate quantification and reliability of the results. Because there is no universal reference gene and even commonly used housekeeping genes’ expression can vary under certain conditions, careful selection of an appropriate internal control must be performed for each cell type or tissue and experimental design. The aim of this study was to identify the most stable reference genes during osteogenic differentiation of the human osteosarcoma cell lines MG-63, HOS, and SaOS-2 using the geNorm, NormFinder, and BestKeeper statistical algorithms. Our results show that TBP, PPIA, YWHAZ, and EF1A1 are the most stably expressed genes, while ACTB, and 18S rRNA expressions are most variable. These data provide a basis for future RT-qPCR normalizations when studying gene expression during osteogenic differentiation, for example, in studies of osteoporosis and other bone diseases.
Collapse
|
16
|
Yuan L, Zhao Y, Xie H, Shi Y, Xie X, Chai A, Li L, Li B. Selection and evaluation of suitable reference genes for quantitative gene expression analysis during infection of Cucumis sativus with Pectobacterium brasiliense. J Appl Microbiol 2022; 132:3717-3734. [PMID: 35138009 DOI: 10.1111/jam.15481] [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: 09/23/2021] [Revised: 01/17/2022] [Accepted: 02/04/2022] [Indexed: 11/27/2022]
Abstract
AIMS Bacterial soft rot caused by Pectobacterium brasiliense (Pbr) has resulted in severe economic losses of cucumber production in northern China. Quantitative reverse transcription PCR (RT-qPCR) is widely used to determine the fold change in the expression of genes of interest, and an appropriate reference gene played a critical role in the evaluation of genes expression. However, the suitable reference genes for transcript normalization during the interaction between cucumber and Pbr have not yet been systematically validated. In this study, we aimed to identify the suitable reference genes for accurate and reliable normalization of cucumber and Pbr RT-qPCR data. METHODS AND RESULTS We selected fourteen candidate reference genes for cucumber and ten candidate reference genes for Pbr were analyzed by using four algorithms (the deltaCt method, BestKeeper, NormFinder and geNorm). Furthermore, five genes in cucumber involved in plant resistance and five genes in Pbr related to the virulence were selected to confirm the reliability of the reference genes by RT-qPCR. CsARF (ADP-ribosylation factor 1) and pgi (glucose-6-phosphate isomerase) were suggested as the most suitable reference genes for cucumber and Pbr, respectively. CONCLUSION Our results suggested that CsARF (ADP-ribosylation factor 1) and pgi (glucose-6-phosphate isomerase) could be as the reference genes to normalize expression data for cucumber and Pbr during the process of pathogen-host interaction, respectively. SIGNIFICANCE AND IMPACT OF THE STUDY To our knowledge, this is the first systematic study of the optimal reference genes specific to cucumber and Pbr, which could help advance the molecular interactions research in Cucurbitaceae vegetables and Pectobacterium species pathosystems.
Collapse
Affiliation(s)
- Lifang Yuan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.,Shandong Academy of Grapes, Shandong Academy of Agricultural Sciences, Shandong, China
| | - Yurong Zhao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hua Xie
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, Beijing, China
| | - Yanxia Shi
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuewen Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ali Chai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Baoju Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
17
|
Nunes da Silva M, Carvalho SMP, Rodrigues AM, Gómez-Cadenas A, António C, Vasconcelos MW. Defence-related pathways, phytohormones and primary metabolism are key players in kiwifruit plant tolerance to Pseudomonas syringae pv. actinidiae. PLANT, CELL & ENVIRONMENT 2022; 45:528-541. [PMID: 34773419 DOI: 10.1111/pce.14224] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 05/07/2023]
Abstract
The reasons underlying the differential tolerance of Actinidia spp. to the pandemic pathogen Pseudomonas syringae pv. actinidiae (Psa) have not yet been elucidated. We hypothesized that differential plant-defence strategies linked to transcriptome regulation, phytohormones and primary metabolism might be key and that Actinidia chinensis susceptibility results from an inefficient activation of defensive mechanisms and metabolic impairments shortly following infection. Here, 48 h postinoculation bacterial density was 10-fold higher in A. chinensis var. deliciosa than in Actinidia arguta, accompanied by significant increases in glutamine, ornithine, jasmonic acid (JA) and salicylic acid (SA) (up to 3.2-fold). Actinidia arguta showed decreased abscisic acid (ABA) (0.7-fold), no changes in primary metabolites, and 20 defence-related genes that were only differentially expressed in this species. These include GLOX1, FOX1, SN2 and RBOHA, which may contribute to its higher tolerance. Results suggest that A. chinensis' higher susceptibility to Psa is due to an inefficient activation of plant defences, with the involvement of ABA, JA and SA, leading to impairments in primary metabolism, particularly the ammonia assimilation cycle. A schematic overview on the interaction between Psa and genotypes with distinct tolerance is provided, highlighting the key transcriptomic and metabolomic aspects contributing to the different plant phenotypes after infection.
Collapse
Affiliation(s)
- Marta Nunes da Silva
- Centro de Biotecnologia e Química Fina (CBQF), Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Porto, Portugal
- GreenUPorto - Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences of University of Porto, Vairão, Portugal
| | - Susana M P Carvalho
- GreenUPorto - Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences of University of Porto, Vairão, Portugal
| | - Ana M Rodrigues
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Oeiras, Portugal
| | - Aurelio Gómez-Cadenas
- Departamento de Ciencias Agrarias y del Medio Natural, Universitat Jaume I, Castelló de la Plana, Spain
| | - Carla António
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Oeiras, Portugal
| | - Marta W Vasconcelos
- Centro de Biotecnologia e Química Fina (CBQF), Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Porto, Portugal
| |
Collapse
|
18
|
Wurms K, Ah Chee A, Stannard K, Anderson R, Jensen D, Cooney J, Hedderley D. Defence Responses Associated with Elicitor-Induced, Cultivar-Associated Resistance to Latania Scale in Kiwifruit. PLANTS (BASEL, SWITZERLAND) 2021; 11:10. [PMID: 35009014 PMCID: PMC8747134 DOI: 10.3390/plants11010010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Latania scale insect is a pest of global significance affecting kiwifruit. The sessile insect (life stage: settled crawler-mature adult) is covered with a waxy cap that protects it from topical pesticides, so increasingly, a selection of resistant cultivars and application of elicitors are being used in pest control. Thus far, the application of a salicylic acid (SA) phytohormone pathway elicitor, acibenzolar-S-methyl (ASM), has been shown to reduce insect development (as indicated by cap size) on one kiwifruit cultivar ('Hayward'). To investigate how cultivar-associated resistance is affected by the ability to respond to different elicitors, we measured phytohormones (by LCMS) and gene expression (by qPCR and NanoString) on latania scale-tolerant 'Hort16A' and susceptible 'Hayward' kiwifruit over two seasons. Potted plants in the presence/absence of settled latania scales were treated with ASM (0.2 g/L) or methyl jasmonate (MeJA, 0.05% v/v), representing elicitors of the SA and JA signalling pathways, respectively. 'Hort16A' cultivar resistance to latania scale was associated with elevated expression of SA and SA-related defence genes (PR1 and two PR2 family genes) in the ASM treatment. MeJA treatments did not significantly affect insect development in 'Hayward' (latania scale did not survive on 'Hort16A') and did not correlate with phytohormone and gene expression measurements in either cultivar. 'Hayward' had greater concentrations than 'Hort16A' of inert storage forms of both SA and JA across all treatments. This information contributes to the selection of tolerant cultivars and the effective use of elicitors for control of latania scale in kiwifruit.
Collapse
Affiliation(s)
- Kirstin Wurms
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Private Bag 3230, Waikato Mail Centre, Hamilton 3240, New Zealand; (A.A.C.); (D.J.); (J.C.)
| | - Annette Ah Chee
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Private Bag 3230, Waikato Mail Centre, Hamilton 3240, New Zealand; (A.A.C.); (D.J.); (J.C.)
| | - Kate Stannard
- Plant & Food Research, 412 No. 1 Road, RD2, Te Puke 3182, New Zealand; (K.S.); (R.A.)
| | - Rachelle Anderson
- Plant & Food Research, 412 No. 1 Road, RD2, Te Puke 3182, New Zealand; (K.S.); (R.A.)
| | - Dwayne Jensen
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Private Bag 3230, Waikato Mail Centre, Hamilton 3240, New Zealand; (A.A.C.); (D.J.); (J.C.)
| | - Janine Cooney
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Private Bag 3230, Waikato Mail Centre, Hamilton 3240, New Zealand; (A.A.C.); (D.J.); (J.C.)
| | - Duncan Hedderley
- Plant & Food Research, Private Bag 11600, Palmerston North 4442, New Zealand;
| |
Collapse
|
19
|
Mao M, Xue Y, He Y, Zhou X, Hu H, Liu J, Feng L, Yang W, Luo J, Zhang H, Li X, Ma J. Validation of Reference Genes for Quantitative Real-Time PCR Normalization in Ananas comosus var. bracteatus During Chimeric Leaf Development and Response to Hormone Stimuli. Front Genet 2021; 12:716137. [PMID: 34745205 PMCID: PMC8566434 DOI: 10.3389/fgene.2021.716137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/28/2021] [Indexed: 12/05/2022] Open
Abstract
Reverse transcription quantitative real-time PCR (RT-qPCR) is a common way to study gene regulation at the transcriptional level due to its sensibility and specificity, but it needs appropriate reference genes to normalize data. Ananas comosus var. bracteatus, with white-green chimeric leaves, is an important pantropical ornamental plant. Up to date, no reference genes have been evaluated in Ananas comosus var. bracteatus. In this work, we used five common statistics tools (geNorm, NormFinder, BestKeeper, ΔCt method, RefFinder) to evaluate 10 candidate reference genes. The results showed that Unigene.16454 and Unigene.16459 were the optimal reference genes for different tissues, Unigene.16454 and zinc finger ran-binding domain-containing protein 2 (ZRANB2) for chimeric leaf at different developmental stages, isocitrate dehydrogenase [NADP] (IDH) and triacylglycerol lipase SDP1-like (SDP) for seedlings under different hormone treatments. The comprehensive results showed IDH, pentatricopeptide repeat-containing protein (PPRC), Unigene.16454, and caffeoyl-CoA O methyltransferase 5-like (CCOAOMT) are the top-ranked stable genes across all the samples. The stability of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was the least during all experiments. Furthermore, the reliability of recommended reference gene was validated by the detection of porphobilinogen deaminase (HEMC) expression levels in chimeric leaves. Overall, this study provides appropriate reference genes under three specific experimental conditions and will be useful for future research on spatial and temporal regulation of gene expression and multiple hormone regulation pathways in Ananas comosus var. bracteatus.
Collapse
Affiliation(s)
- Meiqin Mao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Yanbin Xue
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Yehua He
- College of Horticultural Biotechnology, South China Agricultural University, Guangzhou, China
| | - Xuzixing Zhou
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Hao Hu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Jiawen Liu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Lijun Feng
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Wei Yang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Jiaheng Luo
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Huiling Zhang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Xi Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Jun Ma
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
20
|
Selection and stability validation of reference gene candidates for transcriptional analysis in Rousettus aegyptiacus. Sci Rep 2021; 11:21662. [PMID: 34737406 PMCID: PMC8568961 DOI: 10.1038/s41598-021-01260-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/18/2021] [Indexed: 11/08/2022] Open
Abstract
Bats are the only mammals capable of powered flight and their body temperature can reach up to 42 °C during flight. Additionally, bats display robust type I IFN interferon (IFN-I) responses and some species constitutively express IFN-α. Reference genes with stable expression under temperature oscillations and IFN-I release are therefore critical for normalization of quantitative reverse-transcription polymerase chain reaction (qRT-PCR) data in bats. The expression stability of reference genes in Rousettus aegyptiacus remains elusive, although this species is frequently used in the infection research. We selected ACTB, EEF1A1, GAPDH and PGK1 as candidate reference genes and evaluated their expression stability in various tissues and cells from this model bat species upon IFN-I treatment at 35 °C, 37 °C and 40 °C by qRT-PCR. We employed two statistical algorithms, BestKeeper and NormFinder, and found that EEF1A1 exhibited the highest expression stability under all tested conditions. ACTB and GAPDH displayed unstable expression upon temperature change and IFN-I treatment, respectively. By normalizing to EEF1A1, we uncovered that GAPDH expression was significantly induced by IFN-I in R. aegyptiacus. Our study identifies EEF1A1 as the most suitable reference gene for qRT-PCR studies upon temperature changes and IFN-I treatment and unveils the induction of GAPDH expression by IFN-I in R. aegyptiacus. These findings are pertinent to other bat species and may be relevant for non-volant mammals that show physiological fluctuations of core body temperature.
Collapse
|
21
|
Zhu X, Wang B, Wang X, Wei X. Screening of stable internal reference gene of Quinoa under hormone treatment and abiotic stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2459-2470. [PMID: 34924704 PMCID: PMC8639980 DOI: 10.1007/s12298-021-01094-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED Real-time quantitative polymerase chain reaction is the most commonly used method to accurately detect gene expression patterns. The method requires stable internal reference genes to standardize the data. However, studies have shown that there is no stable expression of internal reference genes in different tissues and under different treatments. Therefore, in order to study the optimal reference genes of quinoa under different hormones and abiotic stress, leaves and stems from quinoa seedlings treated with low temperature (4 °C), salt (200 mmol/L) and abscisic acid (200 mmol/L) were used as experimental materials. Using ACT-1, eIF, EF1α, GAPDH, TUA, TUB-9, TUB-1, H2A and L8-1 as candidate reference genes, the expression stability of these 9 quinoa candidate reference genes under different hormone treatment and abiotic stress was evaluated by using geNorm, NormFinder and BestKeeper software. The results showed that TUB-1 gene under salt stress, L8-1 gene under low temperature stress, EF-1α gene induced by ABA. PLIM2c WLIM1and WLIM2b were selected to verify the candidate internal reference genes, and finally the expression of GAPDH was most unstable under the three treatments, which was not suitable to be the internal reference gene of quinoa under specific conditions, while EF1α showed good stability under the three different treatments and was suitable to be used as the internal reference gene. In conclusion, the results of this study could provide an important reference for quantifying the expression level of reference genes in quinoa. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01094-z.
Collapse
Affiliation(s)
- Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
| | - Baoqiang Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
| | - Xian Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
| | - Xiaohong Wei
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
| |
Collapse
|
22
|
Berruien NNA, Murray JF, Smith CL. Pregnancy influences the selection of appropriate reference genes in mouse tissue: Determination of appropriate reference genes for quantitative reverse transcription PCR studies in tissues from the female mouse reproductive axis. Gene 2021; 801:145855. [PMID: 34293448 DOI: 10.1016/j.gene.2021.145855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022]
Abstract
Selecting stably expressed reference genes which are not affected by physiological or pathophysiological conditions is crucial for reliable quantification in gene expression studies. This study examined the expression stability of a panel of twelve reference genes in tissues from the female mouse reproductive axis and the uterus. Gene expression studies were carried out using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). cDNA was synthesised from RNA extracted from hypothalami, pituitaries, ovaries and uteri of female mice at ages representing weaning, puberty and adulthood as well as pregnancy (13 ± 1 days post-coitus) (n = a minimum of 3 at each age and at pregnancy). The reference genes examined included 18 s, Actb, Atp5b, B2m, Canx, Cyc1, Eif4a2, Gapdh, Rpl13a, Sdha, Ubc and Ywhaz. The RT-qPCR raw data were imported into the qBASE+ software to analyse the expression stability using GeNorm. These data were also subsequently analysed using other software packages (Delta CT, Normfinder, BestKeeper). A comprehensive ranking was conducted considering all stability rankings generated from the different software analyses. B2m and Eif4a2 deviated from the acceptable range for amplification efficiency and therefore were excluded from the further analyses. The stability of the reference genes is influenced by the software used for the analysis with BestKeeper providing markedly different results than the other analyses. GeNorm analysis of tissues taken at different ages but not including pregnant animals, indicated that the expression of the reference genes is tissue specific with the most stable genes being: in the hypothalamus, Canx and Actb; in the pituitary, Sdha and Cyc1; in the ovary, 18s, Sdha and Ubc; and in the uterus, Ywhaz, Cyc1, Atp5b, 18s and Rpl13a. The optimal number of reference genes to be used was determined to be 2 in the first three tissues while in the uterus, the V-score generated by the GeNorm analysis was higher than 0.15 suggesting that 3 or more genes should be used for normalisation. Inclusion of tissues from pregnant mice changed the reference genes identified as being the most stable: Ubc and Sdha were the most stable genes in the hypothalamus, pituitary and the ovary. The addition of pregnant tissue had no effect on the stability of the genes in uterus (Ywhaz, Cyc1, Atp5b, 18s and Rpl13a). Identification of these stable reference genes will be of use to those interested in studying female fertility and researchers should be alert to the effects of pregnancy on reference gene stability. This study also signifies the importance of re-examining reference gene stability if the experimental conditions are changed, as shown with the introduction of pregnancy as a new factor in this research.
Collapse
Affiliation(s)
- Nasrin N A Berruien
- University of Westminster, School of Life Sciences, 115 New Cavendish Street, London W1W 6UW, United Kingdom
| | - Joanne F Murray
- University of Edinburgh, Centre for Discovery Brain Science, Hugh Robson Building, 15 George Square, Edinburgh EH8 9XD, United Kingdom
| | - Caroline L Smith
- University of Westminster, School of Life Sciences, 115 New Cavendish Street, London W1W 6UW, United Kingdom.
| |
Collapse
|
23
|
Sharma S, Vengavasi K, Kumar MN, Yadav SK, Pandey R. Expression of potential reference genes in response to macronutrient stress in rice and soybean. Gene 2021; 792:145742. [PMID: 34051336 DOI: 10.1016/j.gene.2021.145742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 05/13/2021] [Accepted: 05/24/2021] [Indexed: 02/04/2023]
Abstract
Given the complexity of nutrient stress responses and the availability of a few validated reference genes, we aimed to identify robust and stable reference genes for macronutrient stress in rice and soybean. Ten potential reference genes were evaluated using geNorm, NormFinder, BestKeeper, Comparative ΔCt method, and RefFinder algorithms under low and completely starved conditions of nitrogen (N), phosphorus (P), potassium (K), and sulphur (S). Results revealed distinct sets of reference gene pairs, showing stable expression under different experimental conditions. The gene pairs TIP41/UBC(9/10/18) and F-box/UBC10 were most stable in rice and soybean, respectively under N stress. Under P stress, UBC9/UBC10 in rice and F-Box/UBC10 in soybean were most stable. Similarly, TIP41/UBC10 in rice and RING FINGER/UBC9 in soybean were the best gene pairs under K stress while F-Box/TIP41 in rice and UBC9/UBC10 in soybean were the most stable gene pairs under S stress. These reference gene pairs were validated by quantifying the expression levels of high-affinity transporters like NRT2.1/NRT2.5, PT1, AKT1, and SULTR1 for N, P, K, and S stress, respectively. This study reiterates the importance of choosing reference genes based on crop species and the experimental conditions, in order to obtain concrete answers to missing links of gene regulation in response to macronutrient deficiencies.
Collapse
Affiliation(s)
- Sandeep Sharma
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India
| | - Krishnapriya Vengavasi
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India
| | - M Nagaraj Kumar
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India
| | - Shiv Kumar Yadav
- Division of Seed Science and Technology, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India
| | - Renu Pandey
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India.
| |
Collapse
|
24
|
Nunes da Silva M, Vasconcelos MW, Pinto V, Balestra GM, Mazzaglia A, Gomez-Cadenas A, Carvalho SMP. Role of methyl jasmonate and salicylic acid in kiwifruit plants further subjected to Psa infection: biochemical and genetic responses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:258-266. [PMID: 33711719 DOI: 10.1016/j.plaphy.2021.02.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
The use of plant elicitors for controlling Pseudomonas syringae pv. actinidiae (Psa), the etiological agent of the kiwifruit bacterial canker (KBC), has been analysed in the past and, while salicylic acid (SA) seems to decrease disease susceptibility, methyl jasmonate (MJ) shows an opposite effect. However, the metabolic and genomic responses of Psa-infected plants following elicitation with these two compounds, as compared with non-elicited Psa-inoculated plants, are poorly understood, being the focus of this study. Micropropagated A. chinensis 'Hayward' plants were elicited with MJ or SA, and further inoculated with Psa. Fifteen days post-inoculation, Psa population in MJ-treated plants was increased by 7.4-fold, whereas SA elicitation led to decreased Psa colonization (0.5-fold), as compared with non-elicited inoculated plants. Additionally, elicitation with MJ or SA generally decreased polyphenols and lignin concentrations (by at least 20%) and increased total proteins (by at least 50%). MJ led to the upregulation of SOD, involved in plant antioxidant system, and reporter genes for the jasmonic acid (JA) (JIH and LOX1), abscisic acid (SnRK), SA (ICS1), and ethylene (ACAS1, ETR1 and SAM) pathways. Moreover, it increased ABA (40%) and decreased carotenoids (30%) concentrations. Contrastingly, comparing with non-elicited Psa-inoculated plants, SA application resulted in the downregulation of antioxidant system-related genes (SOD and APX) and of reporter genes for ethylene (ETR1) and JA (JIH and ETR1). This study contributes to the understanding of potential mechanisms involved in kiwifruit plant defences against Psa, highlighting the role of the JA, ABA and ethylene in plant susceptibility to the pathogen.
Collapse
Affiliation(s)
- M Nunes da Silva
- GreenUPorto - Research Centre for Sustainable Agrifood Production & DGAOT, Faculty of Sciences of University of Porto, Rua da Agrária 747, 4485-646, Vairão, Portugal; Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - M W Vasconcelos
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - V Pinto
- GreenUPorto - Research Centre for Sustainable Agrifood Production & DGAOT, Faculty of Sciences of University of Porto, Rua da Agrária 747, 4485-646, Vairão, Portugal
| | - G M Balestra
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100, Viterbo, Italy
| | - A Mazzaglia
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100, Viterbo, Italy
| | - A Gomez-Cadenas
- Departamento de Ciencias Agrarias y del Medio Natural, Universitat Jaume I, Avda. Vicent Sos Baynat, 12071, Castelló de la Plana, Spain
| | - S M P Carvalho
- GreenUPorto - Research Centre for Sustainable Agrifood Production & DGAOT, Faculty of Sciences of University of Porto, Rua da Agrária 747, 4485-646, Vairão, Portugal.
| |
Collapse
|
25
|
A Breach in Plant Defences: Pseudomonas syringae pv. actinidiae Targets Ethylene Signalling to Overcome Actinidia chinensis Pathogen Responses. Int J Mol Sci 2021; 22:ijms22094375. [PMID: 33922148 PMCID: PMC8122719 DOI: 10.3390/ijms22094375] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 01/12/2023] Open
Abstract
Ethylene interacts with other plant hormones to modulate many aspects of plant metabolism, including defence and stomata regulation. Therefore, its manipulation may allow plant pathogens to overcome the host’s immune responses. This work investigates the role of ethylene as a virulence factor for Pseudomonas syringae pv. actinidiae (Psa), the aetiological agent of the bacterial canker of kiwifruit. The pandemic, highly virulent biovar of this pathogen produces ethylene, whereas the biovars isolated in Japan and Korea do not. Ethylene production is modulated in planta by light/dark cycle. Exogenous ethylene application stimulates bacterial virulence, and restricts or increases host colonisation if performed before or after inoculation, respectively. The deletion of a gene, unrelated to known bacterial biosynthetic pathways and putatively encoding for an oxidoreductase, abolishes ethylene production and reduces the pathogen growth rate in planta. Ethylene production by Psa may be a recently and independently evolved virulence trait in the arms race against the host. Plant- and pathogen-derived ethylene may concur in the activation/suppression of immune responses, in the chemotaxis toward a suitable entry point, or in the endophytic colonisation.
Collapse
|
26
|
Soni P, Shivhare R, Kaur A, Bansal S, Sonah H, Deshmukh R, Giri J, Lata C, Ram H. Reference gene identification for gene expression analysis in rice under different metal stress. J Biotechnol 2021; 332:83-93. [PMID: 33794279 DOI: 10.1016/j.jbiotec.2021.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/27/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Real-time quantitative polymerase chain reaction (RT-qPCR) is the most common approach to quantify changes in gene expression. Appropriate internal reference genes are essential for normalization of data of RT-qPCR. In the present study, we identified suitable reference genes for analysis of gene expression in rice seedlings subjected to different heavy metal stresses such as deficiencies of iron and zinc and toxicities of cobalt, cadmium and nickel. First, from publically available RNA-Seq data we identified 10 candidate genes having stable expression. We also included commonly used house-keeping gene OsUBQ5 (Ubiquitin 5) in our analysis. Expression stability of all the 11 genes was determined by two independent tools, NormFinder and geNorm. Our results show that selected candidate reference genes have higher stability in their expression compared to that of OsUBQ5. Genes with locus ID LOC_Os03g16690, encoding an oxysterol-binding protein (OsOBP) and LOC_Os01g56580, encoding Casein Kinase_1a.3 (OsCK1a.3) were identified to be the most stably expressed reference genes under most of the conditions tested. Finally, the study reveals that it is better to use a specific reference gene for a specific heavy metal stress condition rather than using a common reference gene for multiple heavy metal stress conditions. The reference genes identified here would be very useful for gene expression studies under heavy metal stresses in rice.
Collapse
Affiliation(s)
- Praveen Soni
- Department of Botany, University of Rajasthan, Jaipur, 302004, India
| | - Radha Shivhare
- CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Amandeep Kaur
- National Agri-Food Biotechnology Institute, Mohali, 140308, India
| | - Sakshi Bansal
- National Agri-Food Biotechnology Institute, Mohali, 140308, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute, Mohali, 140308, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute, Mohali, 140308, India
| | - Jitender Giri
- National Institute of Plant Genome Research, New Delhi, 110067, India
| | - Charu Lata
- CSIR-National Institute of Science Communication and Information Resources, New Delhi, 110067, India.
| | - Hasthi Ram
- National Agri-Food Biotechnology Institute, Mohali, 140308, India; National Institute of Plant Genome Research, New Delhi, 110067, India.
| |
Collapse
|
27
|
Lv Y, Li Y, Liu X, Xu K. Identification of Ginger ( Zingiber officinale Roscoe) Reference Genes for Gene Expression Analysis. Front Genet 2020; 11:586098. [PMID: 33240331 PMCID: PMC7670040 DOI: 10.3389/fgene.2020.586098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/09/2020] [Indexed: 11/24/2022] Open
Abstract
Quantitative real-time PCR (qRT-PCR) is widely used in the detection of gene expression level. However, there is no suitable ginger reference gene for qPCR analysis. Therefore, it is the primary task to select and validate the appropriate ginger reference gene to normalize the expression of target genes. In this study, 14 candidate reference genes were selected and analyzed in different tissues (leaf, and rhizome), different development stages, different varieties, and abiotic stress (ABA and salt stress). Expression stability was calculated using geNorm and NormFinder, Bestkeeper, and RefFinder. For abiotic stress and total conditions, 28S and COX were identified as the most stable genes. In addition, RPII was the most stable in the different development stages and different varieties. TEF2 and RPL2 were the least stably expressed in the tissue and all the conditions. In order to verify the feasibility of these genes as reference genes, we used the most stable and least stable reference genes to normalize the expression levels of ZoSPS genes under different conditions. This work can provide theoretical support for future research on ginger gene expression.
Collapse
Affiliation(s)
- Yao Lv
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.,Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Tai'an, China.,Key Laboratory of Biology of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Tai'an, China.,State Key Laboratory of Crop Biology, Tai'an, China
| | - Yanyan Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xiaohui Liu
- School of Environment, Tsinghua University, Qingdao, China
| | - Kun Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.,Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Tai'an, China.,Key Laboratory of Biology of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Tai'an, China.,State Key Laboratory of Crop Biology, Tai'an, China
| |
Collapse
|
28
|
Nunes da Silva M, Vasconcelos MW, Gaspar M, Balestra GM, Mazzaglia A, Carvalho SMP. Early Pathogen Recognition and Antioxidant System Activation Contributes to Actinidia arguta Tolerance Against Pseudomonas syringae Pathovars actinidiae and actinidifoliorum. FRONTIERS IN PLANT SCIENCE 2020; 11:1022. [PMID: 32793252 PMCID: PMC7387506 DOI: 10.3389/fpls.2020.01022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/22/2020] [Indexed: 05/03/2023]
Abstract
Actinidia chinensis and A. arguta have distinct tolerances to Pseudomonas syringae pv. actinidiae (Psa), but the reasons underlying the inter-specific variation remain unclear. This study aimed to integrate the metabolic and molecular responses of these two kiwifruit species against the highly pathogenic Psa and the less pathogenic P. syringae pv. actinidifoliorum (Pfm) bacterial strains. Disease development was monitored weekly till 21 days post inoculation (dpi), analysing a broad number and variety of parameters including: colony forming units (CFU), foliar symptoms, total chlorophylls, lipid peroxidation, soluble polyphenols, lignin and defense-related gene expression. At the end of the experimental period A. chinensis inoculated with Psa presented the highest endophytic bacterial population, whereas A. arguta inoculated with Pfm showed the lowest values, also resulting in a lower extent of leaf symptoms. Metabolic responses to infection were also more pronounced in A. chinensis with decreased total chlorophylls (up to 55%) and increased lipid peroxidation (up to 53%), compared with non-inoculated plants. Moreover, at 14 dpi soluble polyphenols and lignin concentrations were significantly higher (112 and 26%, respectively) in Psa-inoculated plants than in controls, while in A. arguta no significant changes were observed in those metabolic responses, except for lignin concentration which was, in general, significantly higher in Psa-inoculated plants (by at least 22%), comparing with control and Pfm-inoculated plants. Genes encoding antioxidant enzymes (SOD, APX and CAT) were upregulated at an earlier stage in Psa-inoculated A. arguta than in A. chinensis. In contrast, genes related with phenylpropanoids (LOX1) and ethylene (SAM) pathways were downregulated in A. arguta, but upregulated in A. chinensis in the later phases of infection. Expression of Pto3, responsible for pathogen recognition, occurred 2 dpi in A. arguta, but only 14 dpi in A. chinensis. In conclusion, we found that A. arguta is more tolerant to Psa and Pfm infection than A. chinensis and its primary and secondary metabolism is less impacted. A. arguta higher tolerance seems to be related with early pathogen recognition, the activation of plant antioxidant system, and to the suppression of ET and JA pathways from an earlier moment after infection.
Collapse
Affiliation(s)
- M. Nunes da Silva
- GreenUPorto—Research Centre on Sustainable Agrifood Production, Faculty of Sciences, University of Porto, Vairão, Portugal
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - M. W. Vasconcelos
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - M. Gaspar
- GreenUPorto—Research Centre on Sustainable Agrifood Production, Faculty of Sciences, University of Porto, Vairão, Portugal
| | - G. M. Balestra
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi della Tuscia, Viterbo, Italy
| | - A. Mazzaglia
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi della Tuscia, Viterbo, Italy
| | - Susana M. P. Carvalho
- GreenUPorto—Research Centre on Sustainable Agrifood Production, Faculty of Sciences, University of Porto, Vairão, Portugal
| |
Collapse
|
29
|
Bobrovskikh A, Zubairova U, Kolodkin A, Doroshkov A. Subcellular compartmentalization of the plant antioxidant system: an integrated overview. PeerJ 2020; 8:e9451. [PMID: 32742779 PMCID: PMC7369019 DOI: 10.7717/peerj.9451] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/09/2020] [Indexed: 01/22/2023] Open
Abstract
The antioxidant system (AOS) maintains the optimal concentration of reactive oxygen species (ROS) in a cell and protects it against oxidative stress. In plants, the AOS consists of seven main classes of antioxidant enzymes, low-molecular antioxidants (e.g., ascorbate, glutathione, and their oxidized forms) and thioredoxin/glutaredoxin systems which can serve as reducing agents for antioxidant enzymes. The number of genes encoding AOS enzymes varies between classes, and same class enzymes encoded by different gene copies may have different subcellular localizations, functional loads and modes of evolution. These facts hereafter reinforce the complex nature of AOS regulation and functioning. Further studies can describe new trends in the behavior and functioning of systems components, and provide new fundamental knowledge about systems regulation. The system is revealed to have a lot of interactions and interplay pathways between its components at the subcellular level (antioxidants, enzymes, ROS level, and hormonal and transcriptional regulation). These facts should be taken into account in further studies during the AOS modeling by describing the main pathways of generating and utilizing ROS, as well as the associated signaling processes and regulation of the system on cellular and organelle levels, which is a complicated and ambitious task. Another objective for studying the phenomenon of the AOS is related to the influence of cell dynamics and circadian rhythms on it. Therefore, the AOS requires an integrated and multi-level approach to study. We focused this review on the existing scientific background and experimental data used for the systems biology research of the plant AOS.
Collapse
Affiliation(s)
- Aleksandr Bobrovskikh
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Ulyana Zubairova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
| | - Alexey Kolodkin
- University of Amsterdam, Amsterdam, Netherlands
- The University of Luxembourg, Luxembourg Centre for Systems Biomedicine, Luxembourg, Luxembourg
| | - Alexey Doroshkov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
| |
Collapse
|
30
|
Jose S, Abbey J, Jaakola L, Percival D. Selection and validation of reliable reference genes for gene expression studies from Monilinia vaccinii-corymbosi infected wild blueberry phenotypes. Sci Rep 2020; 10:11688. [PMID: 32678232 PMCID: PMC7366731 DOI: 10.1038/s41598-020-68597-9] [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: 12/04/2019] [Accepted: 03/19/2020] [Indexed: 01/24/2023] Open
Abstract
Monilinia blight disease caused by Monilinia vaccinii-corymbosi (Reade) Honey (M.vc) causes severe damage and economic losses in wild blueberry growing regions. Molecular mechanisms regulating defence responses of wild blueberry phenotypes towards this causal fungus are not yet fully known. A reliable quantification of gene expression using quantitative real time PCR (qPCR) is fundamental for measuring changes in target gene expression. A crucial aspect of accurate normalisation is the choice of appropriate reference genes. This study evaluated the expression stability of seven candidate reference genes (GAPDH, UBC9, UBC28, TIP41, CaCSa, PPR and RH8) in floral tissues of diploid and tetraploid wild blueberry phenotypes challenged with M.vc. The expression stability was calculated using five algorithms: geNorm, NormFinder, BestKeeper, deltaCt and RefFinder. The results indicated that UBC9 and GAPDH were the most stable reference genes, while RH8 and PPR were the least stable ones. To further validate the suitability of the analyzed reference genes, the expression level of a pathogenesis related protein gene (i.e., PR3) was analysed for both phenotypes at four time points of infection. Our results may be beneficial for future studies involving the quantification of relative gene expression levels in wild blueberry species.
Collapse
Affiliation(s)
- Sherin Jose
- Wild Blueberry Research Program, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada.
| | - Joel Abbey
- Wild Blueberry Research Program, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Laura Jaakola
- Climate Laboratory Holt, Department of Arctic and Marine Biology, The Arctic University of Norway, 9037, Tromsø, Norway.,NIBIO, Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1431, Ås, Norway
| | - David Percival
- Wild Blueberry Research Program, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| |
Collapse
|
31
|
Köhsler M, Leitsch D, Müller N, Walochnik J. Validation of reference genes for the normalization of RT-qPCR gene expression in Acanthamoeba spp. Sci Rep 2020; 10:10362. [PMID: 32587282 PMCID: PMC7316857 DOI: 10.1038/s41598-020-67035-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 05/28/2020] [Indexed: 01/06/2023] Open
Abstract
Acanthamoebae are potentially pathogenic organisms, with a highly unique, yet still insufficiently investigated metabolism. Many open questions can be addressed by gene expression studies, however, for Acanthamoeba reliable standards have not yet been established. In this study, suitable reference genes (RGs) for RT-qPCR in Acanthamoeba were comprehensively evaluated, comparing different Acanthamoeba strains and employing four different algorithms (NormFinder, GeNorm, BestKeeper and RefFinder). Expression stability was assessed under various conditions and the potentials of the most promising RGs for accurate normalization of target genes were evaluated. Expression stability of RGs varied depending on conditions and employed algorithms, however, the genes for the 18S rRNA and the hypoxanthine phosphoribosyl transferase seem to be widely suitable RGs. Normalization with a combination of two carefully chosen RGs resulted in reliable expression data for target genes, while normalization with unsuitable RGs led to significant misinterpretation of expression profiles. Thus, a careful evaluation of RGs prior to expression studies is essential.
Collapse
Affiliation(s)
- Martina Köhsler
- Institute of Specific Prophylaxis und Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - David Leitsch
- Institute of Specific Prophylaxis und Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Norbert Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Julia Walochnik
- Institute of Specific Prophylaxis und Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
32
|
Dudziak K, Sozoniuk M, Szczerba H, Kuzdraliński A, Kowalczyk K, Börner A, Nowak M. Identification of stable reference genes for qPCR studies in common wheat ( Triticum aestivum L.) seedlings under short-term drought stress. PLANT METHODS 2020; 16:58. [PMID: 32355504 PMCID: PMC7183717 DOI: 10.1186/s13007-020-00601-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/16/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Quantitative PCR (qPCR) is one of the most common and accurate methods of gene expression analysis. However, the biggest challenge for this kind of examinations is normalization of the results, which requires the application of dependable internal controls. The selection of appropriate reference genes (RGs) is one of the most crucial points in qPCR data analysis and for correct assessment of gene expression. Because of the fact that many reports indicate that the expression profiles of typically used RGs can be unstable in certain experimental conditions, species or tissues, reference genes with stable expression levels should be selected individually for each experiment. In this study, we analysed a set of ten candidate RGs for wheat seedlings under short-term drought stress. Our tests included five 'traditional' RGs (GAPDH, ACT, UBI, TUB, and TEF1) and five novel genes developed by the RefGenes tool from the Genevestigator database. RESULTS Expression stability was assessed using five different algorithms: geNorm, NormFinder, BestKeeper, RefFinder and the delta Ct method. In the final ranking, we identified three genes: CJ705892, ACT, and UBI, as the best candidates for housekeeping genes. However, our data indicated a slight variation between the different algorithms that were used. We revealed that the novel gene CJ705892, obtained by means of in silico analysis, showed the most stable expression in the experimental tissue and condition. CONCLUSIONS Our results support the statement, that novel genes selected for certain experimental conditions have a more stable level of expression in comparison to routinely applied RGs, like genes encoding actin, tubulin or GAPDH. Selected CJ705892 gene can be used as a housekeeping gene in the expression analysis in wheat seedlings under short-term drought. The results of our study will be useful for subsequent analyses of gene expression in wheat tissues subjected to drought.
Collapse
Affiliation(s)
- Karolina Dudziak
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950 Lublin, Poland
- Chair and Department of Biochemistry and Molecular Biology, Medical University of Lublin, Chodźki 1, 20-093 Lublin, Poland
| | - Magdalena Sozoniuk
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950 Lublin, Poland
| | - Hubert Szczerba
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland
| | - Adam Kuzdraliński
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland
| | - Krzysztof Kowalczyk
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950 Lublin, Poland
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Stadt Seeland, 06466 Gatersleben, Germany
| | - Michał Nowak
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950 Lublin, Poland
| |
Collapse
|
33
|
Gao P, Wang J, Wen J. Selection of reference genes for tissue/organ samples of adults of Eucryptorrhynchus scrobiculatus. PLoS One 2020; 15:e0228308. [PMID: 32012184 PMCID: PMC6996836 DOI: 10.1371/journal.pone.0228308] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 01/13/2020] [Indexed: 11/22/2022] Open
Abstract
Eucryptorrhynchus scrobiculatus is an important wood-boring pest of Ailanthus altissima in China, where it causes a large number of these trees to weaken or even die. To identify genes related to economic traits or specific cellular processes in E. scrobiculatus, gene expression in multiple tissue/organ samples is commonly surveyed, and reference genes are required in this process as a control for normalization. In the present study, 18 candidate reference genes from E. scrobiculatus were identified, and the expression levels of these reference genes were estimated through quantitative real-time PCR. Differences in expression levels were analyzed with four algorithms (geNorm, NormFinder, BestKeeper and delta Ct) and comprehensively with RefFinder. With the most stable levels of expression in different tissues, RPL13, RPS3 and RPL36 were determined to be suitable for use as candidate reference genes. Moreover, the expression profile of one target gene (glycoside hydrolase family 45, GH45) confirmed the reliability of the selected candidate reference genes. This study provides the first set of suitable candidate reference genes for gene expression studies in E. scrobiculatus, and the findings will facilitate subsequent transcriptomics and functional gene research on this pest.
Collapse
Affiliation(s)
- Peng Gao
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, P. R. China
| | - Jingzhen Wang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, P. R. China
| | - Junbao Wen
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, P. R. China
- * E-mail:
| |
Collapse
|
34
|
Bai B, Ren J, Bai F, Hao L. Selection and validation of reference genes for gene expression studies in Pseudomonas brassicacearum GS20 using real-time quantitative reverse transcription PCR. PLoS One 2020; 15:e0227927. [PMID: 31986172 PMCID: PMC6984700 DOI: 10.1371/journal.pone.0227927] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/02/2020] [Indexed: 12/28/2022] Open
Abstract
Pseudomonas brassicacearum GS20 is an antagonistic strain of bacteria recently isolated from the rhizosphere of Codonopsis pilosula. No validated reference gene has been indentified from P. brassicacearum to use in the normalization of real-time quantitative reverse transcription-PCR data. Therefore, in this study, nine candidate reference genes (recA, gyrA, rpoD, proC, gmk, rho, 16S, ftsz, and secA) were assessed at different growth phases and under various growth conditions. The expression stability of these candidate genes was evaluated using BestKeeper, NormFinder and GeNorm. In general, the results showed rho, rpoD and gyrA were the most suitable reference genes for P. brassicacearum GS20. The relative expression of iron-regulated gene (fhu) was normalized to verify the reliability of the proposed reference genes under iron-replete and iron-limited conditions. The trend in relative expression was consistent with the change in siderophore production under different iron conditions. This study presents reliable reference genes for transcriptional studies in P. brassicacearum GS20 under the chosen experimental conditions.
Collapse
Affiliation(s)
- Bianxia Bai
- College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
- The Department of Biological Science and Technology, Changzhi University, Changzhi, Shanxi, China
- Ecological and Environmental Research Institute of Taihang Mountain, Changzhi, Shanxi, China
| | - Jiahong Ren
- The Department of Biological Science and Technology, Changzhi University, Changzhi, Shanxi, China
- Ecological and Environmental Research Institute of Taihang Mountain, Changzhi, Shanxi, China
- * E-mail: (LH); (JR)
| | - Fenling Bai
- The Department of Biological Science and Technology, Changzhi University, Changzhi, Shanxi, China
- Ecological and Environmental Research Institute of Taihang Mountain, Changzhi, Shanxi, China
| | - Lin Hao
- College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
- * E-mail: (LH); (JR)
| |
Collapse
|
35
|
Yu M, Man Y, Wang Y. Light- and Temperature-Induced Expression of an R2R3-MYB Gene Regulates Anthocyanin Biosynthesis in Red-Fleshed Kiwifruit. Int J Mol Sci 2019; 20:ijms20205228. [PMID: 31652509 PMCID: PMC6829553 DOI: 10.3390/ijms20205228] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 12/15/2022] Open
Abstract
The R2R3 MYB genes associated with the flavonoid/anthocyanidin pathway feature two repeats, and represent the most abundant classes of MYB genes in plants; however, the physiological role and regulatory function of most R2R3 MYBs remain poorly understood in kiwifruit (Actinidia). Here, genome-wide analysis identified 155 R2R3-MYBs in the ‘Red 5′ version of the Actinidia chinensis genome. Out of 36 anthocyanin-related AccR2R3-MYBs, AcMYB10 was the most highly expressed in inner pericarp of red-fleshed kiwifruit. The expression of AcMYB10 was highly correlated with anthocyanin accumulation in natural pigmentation during fruit ripening and light-/temperature-induced pigmentation in the callus. AcMYB10 is localized in the nuclei and has transcriptional activation activity. Overexpression of AcMYB10 elevates anthocyanin accumulation in transgenic A. chinensis. In comparison, A. chinensis fruit infiltrated with virus-induced gene silencing showed delayed red coloration, lower anthocyanin content, and lower expression of AcMYB10. The transient expression experiment in Nicotiana tabacum leaves and Actinidia arguta fruit indicated the interaction of AcMYB10 with AcbHLH42 might strongly activate anthocyanin biosynthesis by activating the transcription of AcLDOX and AcF3GT. In conclusion, this study provides novel molecular information about R2R3-MYBs in kiwifruit, advances our understanding of light- and temperature-induced anthocyanin accumulation, and demonstrates the important function of AcMYB10 in the biosynthesis of anthocyanin in kiwifruit.
Collapse
Affiliation(s)
- Min Yu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yuping Man
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Yanchang Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
| |
Collapse
|
36
|
Ronaldson-Bouchard K, Yeager K, Teles D, Chen T, Ma S, Song L, Morikawa K, Wobma HM, Vasciaveo A, Ruiz EC, Yazawa M, Vunjak-Novakovic G. Engineering of human cardiac muscle electromechanically matured to an adult-like phenotype. Nat Protoc 2019; 14:2781-2817. [PMID: 31492957 PMCID: PMC7195192 DOI: 10.1038/s41596-019-0189-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 05/13/2019] [Indexed: 12/19/2022]
Abstract
The application of tissue-engineering approaches to human induced pluripotent stem (hiPS) cells enables the development of physiologically relevant human tissue models for in vitro studies of development, regeneration, and disease. However, the immature phenotype of hiPS-derived cardiomyocytes (hiPS-CMs) limits their utility. We have developed a protocol to generate engineered cardiac tissues from hiPS cells and electromechanically mature them toward an adult-like phenotype. This protocol also provides optimized methods for analyzing these tissues' functionality, ultrastructure, and cellular properties. The approach relies on biological adaptation of cultured tissues subjected to biomimetic cues, applied at an increasing intensity, to drive accelerated maturation. hiPS cells are differentiated into cardiomyocytes and used immediately after the first contractions are observed, when they still have developmental plasticity. This starting cell population is combined with human dermal fibroblasts, encapsulated in a fibrin hydrogel and allowed to compact under passive tension in a custom-designed bioreactor. After 7 d of tissue formation, the engineered tissues are matured for an additional 21 d by increasingly intense electromechanical stimulation. Tissue properties can be evaluated by measuring contractile function, responsiveness to electrical stimuli, ultrastructure properties (sarcomere length, mitochondrial density, networks of transverse tubules), force-frequency and force-length relationships, calcium handling, and responses to β-adrenergic agonists. Cell properties can be evaluated by monitoring gene/protein expression, oxidative metabolism, and electrophysiology. The protocol takes 4 weeks and requires experience in advanced cell culture and machining methods for bioreactor fabrication. We anticipate that this protocol will improve modeling of cardiac diseases and testing of drugs.
Collapse
Affiliation(s)
| | - Keith Yeager
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Diogo Teles
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Timothy Chen
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Stephen Ma
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - LouJin Song
- Departments of Rehabilitation and Regenerative Medicine, and of Pharmacology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Kumi Morikawa
- Departments of Rehabilitation and Regenerative Medicine, and of Pharmacology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Holly M Wobma
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Edward C Ruiz
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Masayuki Yazawa
- Departments of Rehabilitation and Regenerative Medicine, and of Pharmacology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
- Department of Medicine, Columbia University, New York, NY, USA.
| |
Collapse
|
37
|
Identification of suitable reference genes for normalization of RT-qPCR data in eggplant fruit and shoot borer (Leucinodes orbonalis Guenée). Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00346-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
38
|
Integrated Use of Aureobasidium pullulans Strain CG163 and Acibenzolar-S-Methyl for Management of Bacterial Canker in Kiwifruit. PLANTS 2019; 8:plants8080287. [PMID: 31443158 PMCID: PMC6724088 DOI: 10.3390/plants8080287] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/02/2019] [Accepted: 08/12/2019] [Indexed: 11/21/2022]
Abstract
An isolate of Aureobasidium pullulans (strain = CG163) and the plant defence elicitor acibenzolar-S-methyl (ASM) were investigated for their ability to control leaf spot in kiwifruit caused by Pseudomonassyringae pv. actinidiae biovar 3 (Psa). Clonal Actinidia chinensis var. deliciosa plantlets (‘Hayward’) were treated with ASM, CG163 or ASM + CG163 at seven and one day before inoculation with Psa. ASM (0.2 g/L) was applied either as a root or foliar treatments and CG163 was applied as a foliar spray containing 2 × 107 CFU/mL. Leaf spot incidence was significantly reduced by all treatments compared with the control. The combination of ASM + CG163 had greater efficacy (75%) than either ASM (55%) or CG163 (40%) alone. Moreover, treatment efficacy correlated positively with the expression of defence-related genes: pathogenesis-related protein 1 (PR1), β-1,3-glucosidase, Glucan endo 1,3-β-glucosidase (Gluc_PrimerH) and Class IV chitinase (ClassIV_Chit), with greater gene upregulation in plants treated with ASM + CG163 than by the individual treatments. Pathogen population studies indicated that CG163 had significant suppressive activity against epiphytic populations of Psa. Endophytic populations were reduced by ASM + CG163 but not by the individual treatments, and by 96–144 h after inoculation were significantly lower than the control. Together these data suggest that ASM + CG163 have complementary modes of action that contribute to greater control of leaf spotting than either treatment alone.
Collapse
|
39
|
mRNA extraction of Xanthomonas fragariae in strawberry and validation of reference genes for the RT-qPCR for study of bacterial gene expression. Mol Biol Rep 2019; 46:5723-5733. [PMID: 31368022 DOI: 10.1007/s11033-019-05006-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/26/2019] [Indexed: 01/11/2023]
Abstract
This is the first study which describes a unique procedure of isolating of high-quality, intact RNA from strawberry leaves of Xanthomonas fragariae, three most suitable reference genes, crucial for the normalization of RT-qPCR data for this pathogen and accurate expression analysis of target genes. In our study, various mathematic algorithms: NormFinder geNorm, BestKeeper, the delta CT method, RefFinder were adopted for validation of most stable reference genes from nine candidate genes (ffh, glyA, gyrA, gyrB, proC, pykA, recA, rpoB, rpoD). The analyses allowing to select three most suitable pioneer reference genes, gyrB, ffh, and pykA, that we recommend for the normalization of RT-qPCR data and for the study of the expression of target genes in Xf. Moreover, their combination as references allowed for an accurate expression analysis and computation of the fold change of the flhF and iroN2 genes in Xf. These two genes are important for the success of the colonization of plant tissue and pathogenicity and sequences of primers designed to study these genes, are presented.
Collapse
|
40
|
Selection of Suitable Reference Genes in Pinus massoniana Lamb. Under Different Abiotic Stresses for qPCR Normalization. FORESTS 2019. [DOI: 10.3390/f10080632] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The normalization of data by choosing suitable reference genes is fundamental for obtaining accurate and reliable results in quantitative real-time polymerase chain reaction (qPCR) analyses. In this study, the expression stability of 12 candidate reference genes of Pinus massoniana under different abiotic stresses was evaluated using four statistical algorithms: geNorm, NormFinder, BestKeeper, and RefFinder. The results indicate that the following genes could be used as reference genes under different treatments: Actin 2 (ACT2) and F-box family gene (F-box) for salinity treatment, cyclophilin (CYP) and alpha-tubulin (TUA) for ABA treatment, actin 7 (ACT7) and CYP for drought treatment, actin 1 (ACT1) and ACT7 for cold treatment, ACT1 and CYP for heat treatment, and TUA and ACT2 for the “Total” group. To validate the suitability of the selected reference genes in this study, the Short-Root protein (SHR), Alpha-pinene synthase (APS), and Pyrabactin resistance-like protein (PYL) gene expression patterns were analyzed. The expression patterns had significant biases when the most unstable reference genes were used for normalization, compared with when the optimum reference gene or gene combinations were used for normalization. These results will be beneficial for further studies on gene transcription in early-stage, unlignified seedlings of P. massoniana.
Collapse
|
41
|
Chen C, Wu J, Hua Q, Tel-Zur N, Xie F, Zhang Z, Chen J, Zhang R, Hu G, Zhao J, Qin Y. Identification of reliable reference genes for quantitative real-time PCR normalization in pitaya. PLANT METHODS 2019; 15:70. [PMID: 31333756 PMCID: PMC6613322 DOI: 10.1186/s13007-019-0455-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 07/01/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND A suitable reference gene is an important prerequisite for guarantying accurate and reliable results in quantitative real-time PCR (qRT-PCR) analyses. However, there is no absolute universality in reference genes among different species. It's hard to find an ideal reference gene to fit for different tissues and growth periods. Pitaya (Hylocereus) is commercially produced as a new fruit crop at a large scale in tropical and subtropical regions. To date, there is no report on the identification of the most reliable reference genes for qRT-PCR normalization in pitaya. RESULTS In this study, six candidate reference genes i.e. Actin(1), GAPDH, UBC(1), UBC(2) EF1-α(1) and histone(1) were selected from thirty-nine typical candidate reference genes to determine the most stable reference genes for qRT-PCR normalization in different tissues, temperature stresses and fruit developmental stages of pitaya. Among the six candidate reference genes, Actin(1) and EF1-α(1) were the most stable gene according to calculations of three statistical methods (GeNorm, NormFinder and BestKeeper) while UBC(1) and UBC(2) showed the lowest expression stability. The six candidate reference genes were further validated by comparing expression profiles of key genes related to betalain biosynthesis at flesh coloration stages of Guanhuahong (Hylocereus monacanthus) and Guanhuabai (H. undatus) pitayas. Actin(1) was recommended the best reference gene for accurate normalization of qRT-PCR data. CONCLUSIONS In this study, the stability of the selected reference genes for normalizing the qRT-PCR data were identified from pitaya. Actin(1) was the most stably expressed genes in different tissues and fruit developmental stages in pitaya. The present work provides the first data of reference gene identification for pitaya and will facilitate further studies in molecular biology and gene function on Hylocereus and other closely related species.
Collapse
Affiliation(s)
- Canbin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of South China Horticultural Crop Biology and Germplasm Enhancement, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Jingyu Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of South China Horticultural Crop Biology and Germplasm Enhancement, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Qingzhu Hua
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of South China Horticultural Crop Biology and Germplasm Enhancement, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Noemi Tel-Zur
- French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990 Sede Boqer, Israel
| | - Fangfang Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of South China Horticultural Crop Biology and Germplasm Enhancement, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Zhike Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of South China Horticultural Crop Biology and Germplasm Enhancement, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Jianye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of South China Horticultural Crop Biology and Germplasm Enhancement, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Rong Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of South China Horticultural Crop Biology and Germplasm Enhancement, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Guibing Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of South China Horticultural Crop Biology and Germplasm Enhancement, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Jietang Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of South China Horticultural Crop Biology and Germplasm Enhancement, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Yonghua Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of South China Horticultural Crop Biology and Germplasm Enhancement, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| |
Collapse
|
42
|
Dessels C, Pepper MS. Reference Gene Expression in Adipose-Derived Stromal Cells Undergoing Adipogenic Differentiation. Tissue Eng Part C Methods 2019; 25:353-366. [PMID: 31062665 PMCID: PMC6589494 DOI: 10.1089/ten.tec.2019.0076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023] Open
Abstract
IMPACT STATEMENT As the use of adipose-derived stromal cells (ASCs) in clinical trials increases, so does the amount of experimental data from research groups, many of which use human ASCs to study adipogenesis in obesity. Different conditions are constantly being applied to ASCs in vitro, to obtain a therapeutic product for potential downstream applications. Few articles have looked at the effect of different conditions on ASC reference gene (RG) expression and stability, which was the aim of this research, as such this article will assist other researchers to make an informed decision about RG selection for gene expression studies using ASCs including those for adipogenesis.
Collapse
Affiliation(s)
- Carla Dessels
- Institute for Cellular and Molecular Medicine, Department of Immunology, and SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Michael Sean Pepper
- Institute for Cellular and Molecular Medicine, Department of Immunology, and SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
43
|
Hossain MS, Ahmed R, Haque MS, Alam MM, Islam MS. Identification and validation of reference genes for real-time quantitative RT-PCR analysis in jute. BMC Mol Biol 2019; 20:13. [PMID: 31035927 PMCID: PMC6489354 DOI: 10.1186/s12867-019-0130-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/16/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND With the availability of genome sequences, gene expression analysis of jute has drawn considerable attention for understanding the regulatory mechanisms of fiber development and improving fiber quality. Gene expression profiles of a target gene can provide valuable clues towards the understanding of its biological function. Reverse transcription quantitative real-time PCR (qRT-PCR) is the best method for targeted gene expression analysis due to its sensitivity and reproducibility. However, calculating relative expression requires reference genes, which must be stable across various biological conditions. For this purposes, 11 prospective genes namely, 28S RNA, ACT7, CYP, EF1A, EF2, ETIF3E, GAPDH, PP2Ac, PTB, UBC2 and UBI1 were evaluated for their potential use as reference genes in jute. RESULTS The expression stabilities of eleven prospective genes were analyzed in various jute plant tissues, such as the root, stick, bark, leaf, flower, seed and fiber, as well as under abiotic (waterlogged, drought and salinity) and biotic stress (infestation with Macrophomina phaseolina) conditions with different time points. All 11 genes were variably expressed in different tissues and stress conditions. To find suitable reference genes in different sample sets, a comprehensive approach based on four statistical algorithms such as GeNorm, BestKeeper, NormFinder the ΔCt was used. The PP2Ac and EF2 genes were the most stably expressed across the different tissues. ACT7 and UBC2 were suitable reference genes under drought stress, and CYP and PP2Ac were the most appropriate after inoculation with Macrophomina phaseolina. Under salinity stress, PP2Ac and UBC2 were the best genes, and ACT7 and PP2Ac were the most suitable under waterlogged conditions. CONCLUSION Expression stability of reference genes from jute varied in different tissues and selected experimental conditions. Our results provide a valuable resource for the accurate normalization of gene expression experiments in fiber research for important bast fiber crops.
Collapse
Affiliation(s)
- Md. Sabbir Hossain
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Rasel Ahmed
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Md. Samiul Haque
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Md. Monjurul Alam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Md. Shahidul Islam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
| |
Collapse
|
44
|
Yang M, Wu S, You W, Jaisi A, Xiao Y. Selection of Reference Genes for Expression Analysis in Chinese Medicinal Herb Huperzia serrata. Front Pharmacol 2019; 10:44. [PMID: 30774594 PMCID: PMC6367274 DOI: 10.3389/fphar.2019.00044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/14/2019] [Indexed: 12/21/2022] Open
Abstract
Huperzine A (HupA) is a powerful and selective inhibitor of acetylcholinesterase. It has attracted widespread attention endangering the ultimate plant sources of Lycopodiaceae family. In this study, we used Huperzia serrata, extensively used in Traditional Chinese medicine (TCM), a slow growing vascular plant as the model plant of the Lycopodiaceae family to develop and validate the reference genes. We aim to use gene expression platform to understand the gene expression of different tissues and developmental stages of this medicinal herb. Eight candidate reference genes were selected based on RNA-seq data and evaluated with qRT-PCR. The expression of L/ODC and cytochrome P450s genes known for their involvement in lycopodium alkaloid biosynthesis, were also studied to validate the selected reference genes. The most stable genes were TBP, GAPDH, and their combination (TBP + GAPDH). We report for the first time the reference gene of H. serrata’s different tissues which would provide important insights into understanding their biological functions comparing other Lycopodiaceae plants and facilitate a good biopharming approach.
Collapse
Affiliation(s)
- Mengquan Yang
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shiwen Wu
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenjing You
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Amit Jaisi
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS-JIC Centre of Excellence in Plant and Microbial Sciences, Shanghai, China
| |
Collapse
|
45
|
Abdin M, Ahmad J, Nasrullah N, Quadri N, Nissar U, Kumar S. Selection of suitable reference genes for reverse transcription-quantitative polymerase chain reaction normalization in Artemisia annua L. plants at different stages of growth and development. Pharmacogn Mag 2019. [DOI: 10.4103/pm.pm_600_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
46
|
Gao S, Wang G, Huang Z, Lei X, Bian Y, Liu Y, Huang W. Selection of Reference Genes for qRT-PCR Analysis in Lentinula edodes after Hot-Air Drying. Molecules 2018; 24:molecules24010136. [PMID: 30602709 PMCID: PMC6337709 DOI: 10.3390/molecules24010136] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 12/24/2018] [Accepted: 12/25/2018] [Indexed: 12/31/2022] Open
Abstract
Volatile sulfur compounds gradually develop in Lentinula edodes after hot-air drying, and many genes are involved in the generation of these sulfur compounds. The expression stability of reference genes may vary in a particular experimental treatment when analyzing their expressions by quantitative real-time polymerase chain reaction (qRT-PCR). In this study, the expression profile of 17 candidate genes was assessed in L. edodes under treatment at 50 °C for 0, 1, 2, and 3 h, and the expression stability of each reference gene was analyzed by three statistical algorithms, including geNorm, NormFinder, and BestKeeper. Results indicated that the two optimal reference genes for mycelium and fruiting body were CAC and DAHP as well as CAC and NUP, respectively. Additionally, CAC and DAHP were found to be the two most stable reference genes across the mycelium and fruiting body set. Our results will provide a genetic foundation for further research on the metabolism genes of sulfur compounds in L. edodes.
Collapse
Affiliation(s)
- Shuangshuang Gao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Gangzheng Wang
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Zhicheng Huang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Xiaoyu Lei
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Yinbing Bian
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Ying Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Wen Huang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| |
Collapse
|
47
|
Ashrafi M, Azimi Moqadam MR, Moradi P, Mohsenifard E, Shekari F. Evaluation and validation of housekeeping genes in two contrast species of thyme plant to drought stress using real-time PCR. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:54-60. [PMID: 30172853 DOI: 10.1016/j.plaphy.2018.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/06/2018] [Accepted: 08/06/2018] [Indexed: 06/08/2023]
Abstract
To decrease errors and increase accuracy and reliability of quantitative real-time PCR (qRT-PCR) results, the use of a reference gene is inevitable. Despite the industrial importance of genus Thymus, not any validated reference gene has not been reported for T. kotschyanus and T. vulgaris which could limit such investigations. In this study, the expression stability of seven housekeeping genes including Actin, Cyclophilin-18, elongation factor-1A, glyceraldehyde-3-phosphate dehydrogenase, 18S ribosomal RNA, Cullin, and Polypyrimidine tract-binding protein were evaluated in T. kotschyanus and T. vulgaris which grown at four levels of drought stress using geNorm, NormFinder, and BestKeeper algorithms. Histone deacetylase-6 (HDA-6) gene was also used for validation of evaluated reference genes. In T. vulgaris, all of the algorithms similarly ranked elongation factor-1A and glyceraldehyde-3-phosphate dehydrogenase as the two most stably expressed genes. In T. kotschyanus, only NormFinder and BestKeeper had a similar ranking and identified Actin and glyceraldehyde-3-phosphate dehydrogenase as the two most stably expressed genes, but geNorm algorithm ranked elongation factor-1A and glyceraldehyde-3-phosphate dehydrogenase as the best two reference genes. On the other hand, all algorithms ranked 18S rRNA and Cyclophilin-18 as the least stable genes in T. kotschyanus and T. vulgaris, respectively. Validation results indicated that there was a significant change (0.53-3.19 fold change) in relative expression of HDA-6 normalized by the best stable gene compare to the least ranked gene. Our study presented the first systematic validation of reference gene(s) selection in T. kotschyanus and T. vulgaris and provided useful information to obtain more accurate qRT-PCR results in these species.
Collapse
Affiliation(s)
- Mohsen Ashrafi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | | | - Parviz Moradi
- Research Division of Natural Resources, Zanjan Agricultural and Natural Resources Research and Education Centre, AREEO, Zanjan, Iran
| | - Ehsan Mohsenifard
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | - Farid Shekari
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| |
Collapse
|
48
|
Selection of suitable reference genes for qRT-PCR normalisation under different experimental conditions in Eucommia ulmoides Oliv. Sci Rep 2018; 8:15043. [PMID: 30301911 PMCID: PMC6177395 DOI: 10.1038/s41598-018-33342-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/26/2018] [Indexed: 01/09/2023] Open
Abstract
Normalisation of data, by choosing the appropriate reference genes, is fundamental for obtaining reliable results in quantitative real-time PCR (qPCR). This study evaluated the expression stability of 11 candidate reference genes with different varieties, developmental periods, tissues, and abiotic stresses by using four statistical algorithms: geNorm, NormFinder, BestKeeper, and RefFinder. The results indicated that ubiquitin-conjugating enzyme S (UBC) and ubiquitin-conjugating enzyme E2 (UBC E2) could be used as reference genes for different E. ulmoides varieties and tissues, UBC and histone H4 (HIS4) for different developmental periods, beta-tubulin (TUB) and UBC for cold treatment, ubiquitin extension protein (UBA80) and HIS4 for drought treatment, and ubiquitin-60S ribosomal protein L40 (UBA52) and UBC E2 for salinity treatment. UBC and UBC E2 for the group “Natural growth” and “Total”, UBA80 and UBC for the group “Abiotic stresses”. To validate the suitability of the selected reference genes in this study, mevalonate kinase (MK), phenylalanine ammonia-lyase (PAL), and 4-coumarate-CoA ligase (4CL) gene expression patterns were analysed. When the most unstable reference genes were used for normalisation, the expression patterns had significant biases compared with the optimum reference gene combinations. These results will be beneficial for more accurate quantification of gene expression levels in E. ulmoides.
Collapse
|
49
|
Jatav PK, Sharma A, Dahiya DK, Khan A, Agarwal A, Kothari SL, Kachhwaha S. Identification of suitable internal control genes for transcriptional studies in Eleusine coracana under different abiotic stress conditions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:793-807. [PMID: 30150855 PMCID: PMC6103957 DOI: 10.1007/s12298-018-0544-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/14/2018] [Accepted: 05/02/2018] [Indexed: 06/08/2023]
Abstract
Finger millet [Eleusine coracana (L.) Gaertn] is an excellent food and forage crop of arid and semiarid areas in Africa and Asia. It is well adapted to drought, heat, high salinity, poor soil fertility and low pH with an efficient C4 carbon fixation mechanism for high yield potential. To normalize the target gene expression data, the identification of suitable reference genes is essential. Ten candidate reference genes were selected and their expression stability was analyzed in various samples treated with different abiotic stress conditions. Five different statistical algorithms: geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder were used to determine the stability of these genes. Our results revealed GAPDH, EEF1a, ACT and CYC as highly stable reference genes and PP2A and eIF4A as least stable reference genes across all the samples and suggesting that these genes could be used for accurate transcript normalization under abiotic stress. To the best of our knowledge, this is the first report on identification of suitable reference genes for accurate transcript normalization using qRT-PCR in finger millet under abiotic stress.
Collapse
Affiliation(s)
- Pradeep K. Jatav
- Department of Botany, University of Rajasthan, Jaipur, 302004 India
| | - Ankita Sharma
- National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - Dinesh K. Dahiya
- Post Graduate Institute of Veterinary Education and Research, Jaipur, 302020 India
| | - Arif Khan
- Post Graduate Institute of Veterinary Education and Research, Jaipur, 302020 India
| | - Atika Agarwal
- Department of Botany, University of Rajasthan, Jaipur, 302004 India
| | - S. L. Kothari
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, 302006 India
| | - Sumita Kachhwaha
- Department of Botany, University of Rajasthan, Jaipur, 302004 India
- Bioinformatics Infrastructure Facility, University of Rajasthan, Jaipur, 302004 India
| |
Collapse
|
50
|
Selection and validation of suitable reference genes for qRT-PCR analysis in pear leaf tissues under distinct training systems. PLoS One 2018; 13:e0202472. [PMID: 30138340 PMCID: PMC6107188 DOI: 10.1371/journal.pone.0202472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/04/2018] [Indexed: 12/13/2022] Open
Abstract
Training systems generally alter tree architecture, which modulates light microclimate within the canopy, for the purpose of improving photosynthetic efficiency and fruit quality. Gene expression quantification is one of the most important methods for exploring the molecular mechanisms underlying the influence of training systems on pear photosynthesis, and suitable reference genes for gene expression normalization are a prerequisite for this method. In this study, the expression stability of nine common and four novel candidate genes were evaluated in 14 different pear leaf samples in two training systems, including those at four developmental stages (training_period) and from different parts of the trees (training_space), using two distinct algorithms, geNorm and NormFinder. Our results revealed that SKD1 (Suppressor of K+Transport Growth Defect1)/ YLS8 (Yellow Leaf Specific 8) and ARM (Armadillo) were the most stable single reference genes for the ‘training_period’ and ‘training_space’ subsets, respectively, although these single genes were not as stable as the optimal pairs of reference genes, SKD1+YLS8 and ARM+YLS8, respectively. Furthermore, the expression levels of the PpsAPX (Ascorbate peroxidase) gene showed that the arbitrary use of reference genes without previous testing could lead to misinterpretation of data. This work constitutes the first systematic analysis regarding the selection of superior reference genes in training system studies, facilitating the elucidation of gene function in pear and providing valuable information for similar studies in other higher plants.
Collapse
|