1
|
Song Y, Hanner RH, Meng B. Genome-wide screening of novel RT-qPCR reference genes for study of GLRaV-3 infection in wine grapes and refinement of an RNA isolation protocol for grape berries. PLANT METHODS 2021; 17:110. [PMID: 34711253 PMCID: PMC8554853 DOI: 10.1186/s13007-021-00808-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 10/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Grapevine, as an essential fruit crop with high economic values, has been the focus of molecular studies in diverse areas. Two challenges exist in the grapevine research field: (i) the lack of a rapid, user-friendly and effective RNA isolation protocol for mature dark-skinned berries and, (ii) the lack of validated reference genes that are stable for quantification of gene expression across desired experimental conditions. Successful isolation of RNA with sufficient yield and quality is essential for downstream analyses involving nucleic acids. However, ripe berries of dark-skinned grape cultivars are notoriously challenging in RNA isolation due to high contents of polyphenolics, polysaccharides, RNase and water. RESULTS We have optimized an RNA isolation protocol through modulating two factors at the lysis step that could impact results of RNA isolation - 2-ME concentration and berry mass. By finding the optimal combination among the two factors, our refined protocol was highly effective in isolating total RNA with high yield and quality from whole mature berries of an array of dark-skinned wine grape cultivars. Our protocol takes a much shorter time to complete, is highly effective, and eliminates the requirement for hazardous organic solvents. We have also shown that the resulting RNA preps were suitable for multiple downstream analyses, including the detection of viruses and amplification of grapevine genes using reverse transcription-polymerase chain reaction (RT-PCR), gene expression analysis via quantitative reverse transcription PCR (RT-qPCR), and RNA Sequencing (RNA-Seq). By using RNA-Seq data derived from Cabernet Franc, we have identified seven novel reference gene candidates (CYSP, NDUFS8, YLS8, EIF5A2, Gluc, GDT1, and EF-Hand) with stable expression across two tissue types, three developmental stages and status of infection with grapevine leafroll-associated virus 3 (GLRaV-3). We evaluated the stability of these candidate genes together with two conventional reference genes (actin and NAD5) using geNorm, NormFinder and BestKeeper. We found that the novel reference gene candidates outperformed both actin and NAD5. The three most stable reference genes were CYSP, NDUFS8 and YSL8, whereas actin and NAD5 were among the least stable. We further tested if there would be a difference in RT-qPCR quantification results when the most stable (CYSP) and the least stable (actin and NAD5) genes were used for normalization. We concluded that both actin and NAD5 led to erroneous RT-qPCR results in determining the statistical significance and fold-change values of gene expressional change. CONCLUSIONS We have formulated a rapid, safe and highly effective protocol for isolating RNA from recalcitrant berry tissue of wine grapes. The resulting RNA is of high quality and suitable for RT-qPCR and RNA-Seq. We have identified and validated a set of novel reference genes based on RNA-Seq dataset. We have shown that these new reference genes are superior over actin and NAD5, two of the conventional reference genes commonly used in early studies.
Collapse
Affiliation(s)
- Yashu Song
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road, Guelph, ON, N1G2W1, Canada.
| | - Robert H Hanner
- Department of Integrative Biology, University of Guelph, 50 Stone Road, Guelph, ON, N1G2W1, Canada
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road, Guelph, ON, N1G2W1, Canada
| |
Collapse
|
2
|
Vannozzi A, Palumbo F, Magon G, Lucchin M, Barcaccia G. The grapevine (Vitis vinifera L.) floral transcriptome in Pinot noir variety: identification of tissue-related gene networks and whorl-specific markers in pre- and post-anthesis phases. HORTICULTURE RESEARCH 2021; 8:200. [PMID: 34465729 PMCID: PMC8408131 DOI: 10.1038/s41438-021-00635-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/13/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
The comprehension of molecular processes underlying the development and progression of flowering in plants is a hot topic, not only because that often the products of interest for human and animal nutrition are linked to the development of fruits or seeds, but also because the processes of gametes formation occurring in sexual organs are at the basis of recombination and genetic variability which constitutes the matter on which evolution acts, whether understood as natural or human driven. In the present study, we used an NGS approach to produce a grapevine flower transcriptome snapshot in different whorls and tissues including calyx, calyptra, filament, anther, stigma, ovary, and embryo in both pre- and post-anthesis phases. Our investigation aimed at identifying hub genes that unequivocally distinguish the different tissues providing insights into the molecular mechanisms that are at the basis of floral whorls and tissue development. To this end we have used different analytical approaches, some now consolidated in transcriptomic studies on plants, such as pairwise comparison and weighted-gene coexpression network analysis, others used mainly in studies on animals or human's genomics, such as the tau (τ) analysis aimed at isolating highly and absolutely tissue-specific genes. The intersection of data obtained by these analyses allowed us to gradually narrow the field, providing evidence about the molecular mechanisms occurring in those whorls directly involved in reproductive processes, such as anther and stigma, and giving insights into the role of other whorls not directly related to reproduction, such as calyptra and calyx. We believe this work could represent an important genomic resource for functional analyses of grapevine floral organ growth and fruit development shading light on molecular networks underlying grapevine reproductive organ determination.
Collapse
Affiliation(s)
- Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, V. le dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Fabio Palumbo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, V. le dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, V. le dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Margherita Lucchin
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, V. le dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, V. le dell'Università 16, 35020, Legnaro, Padova, Italy.
| |
Collapse
|
3
|
Song Y, Hanner RH, Meng B. Probing into the Effects of Grapevine Leafroll-Associated Viruses on the Physiology, Fruit Quality and Gene Expression of Grapes. Viruses 2021; 13:v13040593. [PMID: 33807294 PMCID: PMC8066071 DOI: 10.3390/v13040593] [Citation(s) in RCA: 7] [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: 02/28/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 12/19/2022] Open
Abstract
Grapevine leafroll is one of the most widespread and highly destructive grapevine diseases that is responsible for great economic losses to the grape and wine industries throughout the world. Six distinct viruses have been implicated in this disease complex. They belong to three genera, all in the family Closteroviridae. For the sake of convenience, these viruses are named as grapevine leafroll-associated viruses (GLRaV-1, -2, -3, -4, -7, and -13). However, their etiological role in the disease has yet to be established. Furthermore, how infections with each GLRaV induce the characteristic disease symptoms remains unresolved. Here, we first provide a brief overview on each of these GLRaVs with a focus on genome structure, expression strategies and gene functions, where available. We then provide a review on the effects of GLRaV infection on the physiology, fruit quality, fruit chemical composition, and gene expression of grapevine based on the limited information so far reported in the literature. We outline key methodologies that have been used to study how GLRaV infections alter gene expression in the grapevine host at the transcriptomic level. Finally, we present a working model as an initial attempt to explain how infections with GLRaVs lead to the characteristic symptoms of grapevine leafroll disease: leaf discoloration and downward rolling. It is our hope that this review will serve as a starting point for grapevine virology and the related research community to tackle this vastly important and yet virtually uncharted territory in virus-host interactions involving woody and perennial fruit crops.
Collapse
Affiliation(s)
- Yashu Song
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Robert H. Hanner
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Correspondence: ; Tel.: +1-519-824-4120 (ext. 53876)
| |
Collapse
|
4
|
Selection and validation reference genes for qRT-PCR normalization in different cultivars during fruit ripening and softening of peach (Prunus persica). Sci Rep 2021; 11:7302. [PMID: 33790378 PMCID: PMC8012606 DOI: 10.1038/s41598-021-86755-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 03/18/2021] [Indexed: 02/01/2023] Open
Abstract
Quantitative real-time PCR (qRT-PCR) has been emerged as an effective method to explore the gene function and regulatory mechanisms. However, selecting appropriate reference gene (s) is a prerequisite for obtaining accurate qRT-PCR results. Peach is one of important fruit in Rosaceae and is widely cultivated worldwide. In this study, to explore reliable reference gene (s) in peach with different types during fruit ripening and softening (S1-S4), nine candidate reference genes (EF-1α, GAPDH, TBP, UBC, eIF-4α, TUB-A, TUB-B, ACTIN, and HIS) were selected from the whole-genome data. Then, the expression levels of the nine selected genes were detected using qRT-PCR in three peach types, including 'Hakuho' (melting type), 'Xiacui' (stony hard type), 'Fantasia' and 'NJC108' (non-melting type) cultivars were detected using qRT-PCR. Four software (geNorm, NormFinder, BestKeeper and RefFinder) were applied to evaluate the expression stability of these candidate reference genes. Gene expression was characterized in different peach types during fruit ripening and softening stages. The overall performance of each candidate in all samples was evaluated. The Actin gene (ACTIN) was a suitable reference gene and displayed excellent stability in 'Total' set, 'Hakuho' samples, S3 and S4 fruit developmental stages. Ubiquitin C gene (UBC) showed the best stability in most independent samples, including 'Fantasia', 'NJC108', S2 sets. Elongation factor-1α gene (EF-1α) was the most unstable gene across the set of all samples, 'NJC108' and S2 sets, while showed the highest stability in 'Xiacui' samples. The stability of candidate reference genes was further verified by analyzing the relative expression level of ethylene synthase gene of Prunus persica (PpACS1) in fruit ripening and softening periods of 'Hakuho'. Taken together, the results from this study provide a basis for future research on the mining of important functional genes, expression patterns and regulatory mechanisms in peach.
Collapse
|
5
|
Zhang K, Fan W, Chen D, Jiang L, Li Y, Yao Z, Yang Y, Qiu D. Selection and validation of reference genes for quantitative gene expression normalization in Taxus spp. Sci Rep 2020; 10:22205. [PMID: 33335184 PMCID: PMC7747704 DOI: 10.1038/s41598-020-79213-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 12/04/2020] [Indexed: 11/09/2022] Open
Abstract
Quantitative real-time PCR (qRT-PCR) is commonly used to measure gene expression to further explore gene function, while suitable reference genes must be stably expressed under different experimental conditions to obtain accurate and reproducible data for relative quantification. Taxol or paclitaxel is an important anticancer compound mainly identified in Taxus spp. The molecular mechanism of the regulation of taxol biosynthesis is current research goal. However, in the case of Taxus spp., few reports were published on screening suitable reference genes as internal controls for qRT-PCR. Here, eight reference genes were selected as candidate reference genes for further study. Common statistical algorithms geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder were used to analyze the data from samples collected from a cell line of Taxus × media under various experimental conditions and from tissues of Taxus chinensis var. mairei. The expression patterns of TcMYC under salicylic acid treatment differed significantly, with the best and worst reference genes in the cell line. This study screened out suitable reference genes (GAPDH1 and SAND) under different treatments and tissues for the accurate and reliable normalization of the qRT-PCR expression data of Taxus spp. At the same time, this study will aid future research on taxol biosynthesis-related genes expression in Taxus spp., and can also be directly used to other related species.
Collapse
Affiliation(s)
- Kaikai Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.,College of Horticulture, Agricultural University of Hebei, Baoding, 071001, China
| | - Wei Fan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Duanfen Chen
- College of Horticulture, Agricultural University of Hebei, Baoding, 071001, China
| | - Luyuan Jiang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.,College of Horticulture, Agricultural University of Hebei, Baoding, 071001, China
| | - Yunfeng Li
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiwang Yao
- College of Horticulture, Agricultural University of Hebei, Baoding, 071001, China
| | - Yanfang Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| |
Collapse
|
6
|
Richter R, Rossmann S, Gabriel D, Töpfer R, Theres K, Zyprian E. Differential expression of transcription factor- and further growth-related genes correlates with contrasting cluster architecture in Vitis vinifera 'Pinot Noir' and Vitis spp. genotypes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3249-3272. [PMID: 32812062 PMCID: PMC7567691 DOI: 10.1007/s00122-020-03667-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/03/2020] [Indexed: 05/18/2023]
Abstract
Grapevine (Vitis vinifera L.) is an economically important crop that needs to comply with high quality standards for fruit, juice and wine production. Intense plant protection is required to avoid fungal damage. Grapevine cultivars with loose cluster architecture enable reducing protective treatments due to their enhanced resilience against fungal infections, such as Botrytis cinerea-induced gray mold. A recent study identified transcription factor gene VvGRF4 as determinant of pedicel length, an important component of cluster architecture, in samples of two loose and two compact quasi-isogenic 'Pinot Noir' clones. Here, we extended the analysis to 12 differently clustered 'Pinot Noir' clones from five diverse clonal selection programs. Differential gene expression of these clones was studied in three different locations over three seasons. Two phenotypically opposite clones were grown at all three locations and served for standardization. Data were correlated with the phenotypic variation of cluster architecture sub-traits. A set of 14 genes with consistent expression differences between loosely and compactly clustered clones-independent from season and location-was newly identified. These genes have annotations related to cellular growth, cell division and auxin metabolism and include two more transcription factor genes, PRE6 and SEP1-like. The differential expression of VvGRF4 in relation to loose clusters was exclusively found in 'Pinot Noir' clones. Gene expression studies were further broadened to phenotypically contrasting F1 individuals of an interspecific cross and OIV reference varieties of loose cluster architecture. This investigation confirmed PRE6 and six growth-related genes to show differential expression related to cluster architecture over genetically divergent backgrounds.
Collapse
Affiliation(s)
- Robert Richter
- Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, Julius Kühn Institute, 76833, Siebeldingen, Germany
| | - Susanne Rossmann
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Doreen Gabriel
- Federal Research Centre for Cultivated Plants, Institute for Crop and Soil Science, Julius Kühn Institute, Bundesallee 58, 38116, Brunswick, Germany
| | - Reinhard Töpfer
- Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, Julius Kühn Institute, 76833, Siebeldingen, Germany
| | - Klaus Theres
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Eva Zyprian
- Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, Julius Kühn Institute, 76833, Siebeldingen, Germany.
| |
Collapse
|
7
|
Maia M, Ferreira AEN, Nascimento R, Monteiro F, Traquete F, Marques AP, Cunha J, Eiras-Dias JE, Cordeiro C, Figueiredo A, Sousa Silva M. Integrating metabolomics and targeted gene expression to uncover potential biomarkers of fungal/oomycetes-associated disease susceptibility in grapevine. Sci Rep 2020; 10:15688. [PMID: 32973337 PMCID: PMC7515887 DOI: 10.1038/s41598-020-72781-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022] Open
Abstract
Vitis vinifera, one of the most cultivated fruit crops, is susceptible to several diseases particularly caused by fungus and oomycete pathogens. In contrast, other Vitis species (American, Asian) display different degrees of tolerance/resistance to these pathogens, being widely used in breeding programs to introgress resistance traits in elite V. vinifera cultivars. Secondary metabolites are important players in plant defence responses. Therefore, the characterization of the metabolic profiles associated with disease resistance and susceptibility traits in grapevine is a promising approach to identify trait-related biomarkers. In this work, the leaf metabolic composition of eleven Vitis genotypes was analysed using an untargeted metabolomics approach. A total of 190 putative metabolites were found to discriminate resistant/partial resistant from susceptible genotypes. The biological relevance of discriminative compounds was assessed by pathway analysis. Several compounds were selected as promising biomarkers and the expression of genes coding for enzymes associated with their metabolic pathways was analysed. Reference genes for these grapevine genotypes were established for normalisation of candidate gene expression. The leucoanthocyanidin reductase 2 gene (LAR2) presented a significant increase of expression in susceptible genotypes, in accordance with catechin accumulation in this analysis group. Up to our knowledge this is the first time that metabolic constitutive biomarkers are proposed, opening new insights into plant selection on breeding programs.
Collapse
Affiliation(s)
- Marisa Maia
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - António E N Ferreira
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Rui Nascimento
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Filipa Monteiro
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017, Lisbon, Portugal
| | - Francisco Traquete
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Ana P Marques
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Jorge Cunha
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV), Quinta da Almoinha, 2565-191, Dois Portos, Portugal
| | - José E Eiras-Dias
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV), Quinta da Almoinha, 2565-191, Dois Portos, Portugal
| | - Carlos Cordeiro
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Andreia Figueiredo
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
| | - Marta Sousa Silva
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
| |
Collapse
|
8
|
Dayer S, Scharwies JD, Ramesh SA, Sullivan W, Doerflinger FC, Pagay V, Tyerman SD. Comparing Hydraulics Between Two Grapevine Cultivars Reveals Differences in Stomatal Regulation Under Water Stress and Exogenous ABA Applications. FRONTIERS IN PLANT SCIENCE 2020; 11:705. [PMID: 32636852 PMCID: PMC7316991 DOI: 10.3389/fpls.2020.00705] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/05/2020] [Indexed: 05/23/2023]
Abstract
Hydraulics of plants that have different strategies of stomatal regulation under water stress are relatively poorly understood. We explore how root and shoot hydraulics, stomatal conductance (g s), leaf and root aquaporin (AQP) expression, and abscisic acid (ABA) concentration in leaf xylem sap ([ABA]xylemsap) may be coordinated under mild water stress and exogenous ABA applications in two Vitis vinifera L. cultivars traditionally classified as near-isohydric (Grenache) and near-anisohydric (Syrah). Under water stress, Grenache exhibited stronger adjustments of plant and root hydraulic conductances and greater stomatal sensitivity to [ABA]xylemsap than Syrah resulting in greater conservation of soil moisture but not necessarily more isohydric behavior. Correlations between leaf (Ψleaf) and predawn (ΨPD) water potentials between cultivars suggested a "hydrodynamic" behavior rather than a particular iso-anisohydric classification. A significant decrease of Ψleaf in well-watered ABA-fed vines supported a role of ABA in the soil-leaf hydraulic pathway to regulate g s. Correlations between leaf and root AQPs expression levels under water deficit could explain the response of leaf (K leaf) and root (Lp r) hydraulic conductances in both cultivars. Additional studies under a wider range of soil water deficits are required to explore the possible differential regulation of g s and plant hydraulics in different cultivars and experimental conditions.
Collapse
Affiliation(s)
- Silvina Dayer
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, Australia
| | - Johannes D. Scharwies
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, Australia
| | - Sunita A. Ramesh
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, Australia
| | - Wendy Sullivan
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, Australia
| | | | - Vinay Pagay
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, Australia
| | - Stephen D. Tyerman
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| |
Collapse
|
9
|
Deng Y, Li Y, Sun H. Selection of reference genes for RT-qPCR normalization in blueberry (Vaccinium corymbosum × angustifolium) under various abiotic stresses. FEBS Open Bio 2020; 10:1418-1435. [PMID: 32438500 PMCID: PMC7396441 DOI: 10.1002/2211-5463.12903] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 05/07/2020] [Accepted: 05/18/2020] [Indexed: 11/06/2022] Open
Abstract
As a small fruit rich in anthocyanins, blueberry (Vaccinium corymbosum × angustifolium) has become a focus of research in recent years for identifying genes related to anthocyanin transport and stress resistance mechanisms based on transcriptome sequencing. However, the lack of validated, stably expressed reference genes greatly limits the functional study of blueberry genes. Therefore, in this study, we selected 14 candidate reference genes from a blueberry transcriptome database and used three algorithms (geNorm, NormFinder and BestKeeper) to evaluate the expression stability of these genes in various organs at different fruit developmental stages under five abiotic stress conditions. EF1α, EIF and TBP were observed to be the most stable and were thus chosen as reference genes for quantitative real-time PCR. Measurement of the relative expression of VcMATE1 (European Nucleotide Archive accession number KF875433) in blueberry further verified the reliability of these reference genes, which may have great utility for determining the accuracy of gene expression analyses in future research on blueberry.
Collapse
Affiliation(s)
- Yu Deng
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Yadong Li
- Engineering Center of Genetic Breeding and Innovative Utilization of Small Fruits of Jilin Province, College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Haiyue Sun
- Engineering Center of Genetic Breeding and Innovative Utilization of Small Fruits of Jilin Province, College of Horticulture, Jilin Agricultural University, Changchun, China
| |
Collapse
|
10
|
Hu Y, Gao YR, Yang LS, Wang W, Wang YJ, Wen YQ. The cytological basis of powdery mildew resistance in wild Chinese Vitis species. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 144:244-253. [PMID: 31593897 DOI: 10.1016/j.plaphy.2019.09.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
The wild Chinese grapevines (Vitis spp.) show varying levels of resistance to powdery mildew caused by Erysiphe necator that is an economically important disease of cultivated grapevines (Vitis vinifera). However, little information is available regarding the cytological mechanisms of powdery mildew resistance in these wild relatives. Here, we studied the cytological responses of three wild Chinese grapevine accessions after they were infected with E. necator (En) NAFU1 in comparison to the susceptible V. vinifera cv. 'Thompson Seedless' grape. The hyphal growth and sporulation of En NAFU1 were significantly restricted in wild species compared to 'Thompson Seedless', which appears to be associated with early cell wall deposition at the attempt sites, encasement of haustoria, and hypersensitive response-like cell death of penetrated epidermal cells. Moreover, endogenous free salicylic acid (SA) was more abundant in wild Chinese Vitis species than in 'Thompson Seedless' under pathogen-free condition. During En NAFU1 colonization, SA conjugates accumulated higher in wild grapevines than in 'Thompson Seedless'. In addition, the species-specific expression patterns of defense-associated genes during En NAFU1 colonization indicated that mechanisms underlying powdery mildew resistance are divergent among different wild Chinese Vitis species. These results contribute to understanding of mechanisms underlying defense responses of wild Chinese Vitis species against powdery mildew.
Collapse
Affiliation(s)
- Yang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling, 712100, Shaanxi, China
| | - Yu-Rong Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling, 712100, Shaanxi, China
| | - Lu-Shan Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling, 712100, Shaanxi, China
| | - Wei Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling, 712100, Shaanxi, China
| | - Yue-Jin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling, 712100, Shaanxi, China
| | - Ying-Qiang Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
11
|
Ciaffi M, Paolacci AR, Paolocci M, Alicandri E, Bigini V, Badiani M, Muganu M. Transcriptional regulation of stilbene synthases in grapevine germplasm differentially susceptible to downy mildew. BMC PLANT BIOLOGY 2019; 19:404. [PMID: 31521112 PMCID: PMC6744718 DOI: 10.1186/s12870-019-2014-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 09/02/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND To limit the impact of the downy mildew disease of grapevine and reduce the need to recur to chemical treatments, an effective strategy might be recovering adaptive resistance traits in both cultivated and wild V. vinifera germplasm. Considering that stilbenes represent the most important class of phytoalexins in the Vitaceae, the constitutive expression and transcriptional activation of all the functional members of the stilbene synthase gene family were analysed in a group of nine grapevine genotypes following artificial infection with the oomycete Plasmopara viticola, the causal agent of the disease. In addition, in the same genotypes we analyzed the expression of genes encoding for two transcription factors involved in the transcriptional regulation of the stilbene synthase genes, namely VvMYB14 and VvMYB15, and of genes encoding for chalcone synthases. RESULTS Downy mildew incidence and severity ranged from nihil to high in the grapevine genotypes considered, being low to moderate in a subgroup of V. vinifera genotypes. The constitutive expression of the stilbene synthase genes as well as the extent of their transcriptional activation following P. viticola inoculation appeared to be inversely related to the proneness to develop disease symptoms upon infection. In a specular manner, following P. viticola inoculation all the chalcone synthase genes were up-regulated in the susceptible grapevine genotypes and down-regulated in the resistant ones. The infection brought by P. viticola appeared to elicit a co-ordinated and sequential transcriptional activation of distinct stilbene synthase genes subsets, each of which may be regulated by a distinct and specific MYB transcription factor. CONCLUSIONS The present results suggest that the induction of stilbene biosynthesis may contribute to the basal immunity against the downy mildew of grapevine, thus representing an adaptive resistance trait to recover, in both cultivated and wild V. vinifera germplasm. During the early stages of P. viticola infection, an antagonistic interaction between flavonol and stilbene biosynthesis might occur, whose outcome might determine the subsequent extent of disease symptoms. Further studies are needed to decipher the possible regulatory mechanisms involved in the antagonistic crosstalk between these two metabolic pathways in resistant and susceptible genotypes in response to P. viticola.
Collapse
Affiliation(s)
- Mario Ciaffi
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c, I-01100 Viterbo, Italy
| | - Anna Rita Paolacci
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c, I-01100 Viterbo, Italy
| | - Marco Paolocci
- Dipartimento di Scienze Agrarie e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c, I-01100 Viterbo, Italy
| | - Enrica Alicandri
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c, I-01100 Viterbo, Italy
| | - Valentina Bigini
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c, I-01100 Viterbo, Italy
| | - Maurizio Badiani
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Loc. Feo di Vito, I-89129 Reggio Calabria, Italy
| | - Massimo Muganu
- Dipartimento di Scienze Agrarie e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c, I-01100 Viterbo, Italy
| |
Collapse
|
12
|
Reineke A, Selim M. Elevated atmospheric CO 2 concentrations alter grapevine (Vitis vinifera) systemic transcriptional response to European grapevine moth (Lobesia botrana) herbivory. Sci Rep 2019; 9:2995. [PMID: 30816321 PMCID: PMC6395777 DOI: 10.1038/s41598-019-39979-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/04/2019] [Indexed: 12/24/2022] Open
Abstract
Atmospheric carbon dioxide (CO2) concentrations are among the chief factors shaping the mode and magnitude of interactions between plants and herbivorous insects. Here, we describe the first global analysis of systemic transcriptomic responses of grapevine Vitis vinifera plants to feeding of European grapevine moth Lobesia botrana larvae at future elevated CO2 concentrations. The study was conducted on mature, fruit-bearing grapevine plants under ambient and elevated CO2 concentrations in a grapevine free-air carbon dioxide enrichment (FACE) facility. Grapevine transcriptional response to herbivory was clearly dependent on phenological stage, with a higher number of differentially expressed genes identified at fruit development compared to berry ripening. At fruit development, more transcripts were differentially expressed as a response to herbivory under elevated compared to ambient CO2 concentrations. Classification of the respective transcripts revealed that in particular genes involved in metabolic pathways, biosynthesis of secondary metabolites and plant-pathogen interactions were significantly enriched. Most of these genes had similar expression patterns under both CO2 concentrations, with a higher fold-change under elevated CO2 concentrations. Differences in expression levels of a subset of herbivory responsive genes were further validated by RT-qPCR. Our study indicates that future elevated CO2 concentrations will affect interactions between grapevine plants and one of its key insect pests, with consequences for future relevance of L. botrana in worldwide viticulture.
Collapse
Affiliation(s)
- Annette Reineke
- Geisenheim University, Department of Crop Protection, Von-Lade-Str. 1, D-65366, Geisenheim, Germany.
| | - Moustafa Selim
- Geisenheim University, Department of Crop Protection, Von-Lade-Str. 1, D-65366, Geisenheim, Germany
| |
Collapse
|
13
|
Zhou L, Niu J, Quan S. Identification of appropriate reference genes for RT-qPCR analysis in Juglans regia L. PLoS One 2018; 13:e0209424. [PMID: 30562379 PMCID: PMC6298729 DOI: 10.1371/journal.pone.0209424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 12/05/2018] [Indexed: 01/03/2023] Open
Abstract
Reverse transcription quantitative real-time PCR (RT-qPCR) is a popular adopted technique to detect gene expression, and the selection of appropriate reference genes is crucial for data normalization. In the present study, seven candidate reference genes were screened to evaluate their expression stability in various flower buds, leaf buds, tissues and cultivars of the English walnut (Juglans regia L.) based on four algorithms (geNorm, Normfinder, Bestkeeper and RefFinder). The results demonstrated that TUA, EF1 and TUB were appropriate reference genes for flower buds at different stages of female flower buds differentiation; TUB and 18S rRNA were best for leaf buds at different stages of female flower buds differentiation; TUB and TUA were suitable for different cultivars; and ACT2, 18S rRNA and GAPDH were useful for different tissues. Moreover, the expression of ACT was not stable among different flower buds, leaf buds and cultivars. The stability of reference genes were confirmed through the analysis of the expression of SPL18 gene. These results will contribute to a reliable normalization of gene expression in J. regia.
Collapse
Affiliation(s)
- Li Zhou
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, P.R. China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, P.R. China
| | - Jianxin Niu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, P.R. China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, P.R. China
- * E-mail:
| | - Shaowen Quan
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, P.R. China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, P.R. China
| |
Collapse
|
14
|
Lu X, Liu Y, Zhao L, Liu Y, Zhao M. Selection of reliable reference genes for RT-qPCR during methyl jasmonate, salicylic acid and hydrogen peroxide treatments in Ganoderma lucidum. World J Microbiol Biotechnol 2018; 34:92. [DOI: 10.1007/s11274-018-2476-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/07/2018] [Indexed: 12/01/2022]
|
15
|
Flores-Herrera P, Arredondo-Zelada O, Marshall SH, Gómez FA. Selection and validation of reliable housekeeping genes to evaluate Piscirickettsia salmonis gene expression. INFECTION GENETICS AND EVOLUTION 2018; 63:151-157. [PMID: 29860100 DOI: 10.1016/j.meegid.2018.05.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 05/15/2018] [Accepted: 05/30/2018] [Indexed: 12/30/2022]
Abstract
Piscirickettsia salmonis is a highly aggressive facultative intracellular bacterium that challenges the sustainability of Chilean salmon production. Due to the limited knowledge of its biology, there is a need to identify key molecular markers that could help define the pathogenic potential of this bacterium. We think a model system should be implemented that efficiently evaluates the expression of putative bacterial markers by using validated, stable, and highly specific housekeeping genes to properly select target genes, which could lead to identifying those responsible for infection and disease induction in naturally infected fish. Here, we selected a set of validated reference or housekeeping genes for RT-qPCR expression analyses of P. salmonis under different growth and stress conditions, including an in vitro infection kinetic. After a thorough screening, we selected sdhA as the most reliable housekeeping gene able to represent stable and highly specific host reference genes for RT-qPCR-driven P. salmonis analysis.
Collapse
Affiliation(s)
- Patricio Flores-Herrera
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Av. Universidad 330 Curauma, Valparaíso, Chile.
| | - Oscar Arredondo-Zelada
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Av. Universidad 330 Curauma, Valparaíso, Chile
| | - Sergio H Marshall
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Av. Universidad 330 Curauma, Valparaíso, Chile.
| | - Fernando A Gómez
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Av. Universidad 330 Curauma, Valparaíso, Chile.
| |
Collapse
|
16
|
Liu S, Zhang C, Chao N, Lu J, Zhang Y. Cloning, Characterization, and Functional Investigation of VaHAESA from Vitis amurensis Inoculated with Plasmopara viticola. Int J Mol Sci 2018; 19:E1204. [PMID: 29659493 PMCID: PMC5979312 DOI: 10.3390/ijms19041204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 03/26/2018] [Accepted: 04/06/2018] [Indexed: 12/14/2022] Open
Abstract
Plant pattern recognition receptors (PRRs) are essential for immune responses and establishing symbiosis. Plants detect invaders via the recognition of pathogen-associated molecular patterns (PAMPs) by PRRs. This phenomenon is termed PAMP-triggered immunity (PTI). We investigated disease resistance in Vitis amurensis to identify PRRs that are important for resistance against downy mildew, analyzed the PRRs that were upregulated by incompatible Plasmopara viticola infection, and cloned the full-length cDNA of the VaHAESA gene. We then analyzed the structure, subcellular localization, and relative disease resistance of VaHAESA. VaHAESA and PRR-receptor-like kinase 5 (RLK5) are highly similar, belonging to the leucine-rich repeat (LRR)-RLK family and localizing to the plasma membrane. The expression of PRR genes changed after the inoculation of V. amurensis with compatible and incompatible P. viticola; during early disease development, transiently transformed V. vinifera plants expressing VaHAESA were more resistant to pathogens than those transformed with the empty vector and untransformed controls, potentially due to increased H₂O₂, NO, and callose levels in the transformants. Furthermore, transgenic Arabidopsis thaliana showed upregulated expression of genes related to the PTI pathway and improved disease resistance. These results show that VaHAESA is a positive regulator of resistance against downy mildew in grapevines.
Collapse
Affiliation(s)
- Shaoli Liu
- The Viticulture and Enology Program, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Chi Zhang
- The Viticulture and Enology Program, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Nan Chao
- Center for Plant Biology, TSinghua University, Beijing 100084, China.
| | - Jiang Lu
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200024, China.
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Yali Zhang
- The Viticulture and Enology Program, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| |
Collapse
|
17
|
Zhang S, Ding F, Peng H, Huang Y, Lu J. Molecular cloning of a CC-NBS-LRR gene from Vitis quinquangularis and its expression pattern in response to downy mildew pathogen infection. Mol Genet Genomics 2017; 293:61-68. [PMID: 28864888 DOI: 10.1007/s00438-017-1360-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/08/2017] [Indexed: 12/19/2022]
Abstract
Downy mildew, caused by Plasmopara viticola, can result in a substantial decrease in grapevine productivity. Vitis vinifera is a widely cultivated grapevine species, which is susceptible to this disease. Repeated pesticide applications are harmful for both the environment and human health. Thus, it is essential to develop varieties/cultivars that are resistant to downy mildew and other diseases. In our previous studies, we investigated the natural resistance of the Chinese wild grapevine V. quinquangularis accession 'PS' against P. viticola and obtained several candidate resistance (R) genes that may play important roles in plant disease resistance. In the present study, we isolated a CC-NBS-LRR-type R gene from 'PS' and designated it VqCN. Its open reading frame is 2676 bp which encodes a protein of 891 amino acids with a predicted molecular mass of 102.12 kDa and predicted isoelectric point of 6.53. Multiple alignments with other disease resistant (R) proteins revealed a conserved phosphate-binding loop (P-loop), resistance nucleotide binding site, a hydrophobic domain (GLPL) and methionine-histidine-aspartate (MHD) motifs, which are typical components of nucleotide-binding site leucine-rich repeat proteins, as well as a coiled-coil region in the N-terminus. Quantitative real-time polymerase chain reaction analysis showed that the transcript of VqCN was rapidly and highly induced after infection with P. viticola in 'PS'. Moreover, the leaves of susceptible 'Cabernet Sauvignon' transiently expressing VqCN manifested increased resistance to P. viticola. The results indicated that VqCN might play a positive role in protecting grapevine against infection with P. viticola. Cloning and functional analysis of a putative resistance gene provide a basis for disease-resistance breeding.
Collapse
Affiliation(s)
- Shuwei Zhang
- Guangxi Crop Genetic Improvement and Biotechnology Key Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Feng Ding
- Guangxi Crop Genetic Improvement and Biotechnology Key Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Hongxiang Peng
- Horticultural Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yu Huang
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Jiang Lu
- Guangxi Crop Genetic Improvement and Biotechnology Key Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
| |
Collapse
|
18
|
Comparative analysis of constitutive proteome between resistant and susceptible tomato genotypes regarding to late blight. Funct Integr Genomics 2017; 18:11-21. [DOI: 10.1007/s10142-017-0570-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/18/2017] [Accepted: 08/23/2017] [Indexed: 01/07/2023]
|
19
|
Reference gene selection for normalization of RT-qPCR gene expression data from Actinidia deliciosa leaves infected with Pseudomonas syringae pv. actinidiae. Sci Rep 2015; 5:16961. [PMID: 26581656 PMCID: PMC4652207 DOI: 10.1038/srep16961] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/22/2015] [Indexed: 12/17/2022] Open
Abstract
Normalization of data, by choosing the appropriate reference genes (RGs), is fundamental for obtaining reliable results in reverse transcription-quantitative PCR (RT-qPCR). In this study, we assessed Actinidia deliciosa leaves inoculated with two doses of Pseudomonas syringae pv. actinidiae during a period of 13 days for the expression profile of nine candidate RGs. Their expression stability was calculated using four algorithms: geNorm, NormFinder, BestKeeper and the deltaCt method. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and protein phosphatase 2A (PP2A) were the most stable genes, while β-tubulin and 7s-globulin were the less stable. Expression analysis of three target genes, chosen for RGs validation, encoding the reactive oxygen species scavenging enzymes ascorbate peroxidase (APX), superoxide dismutase (SOD) and catalase (CAT) indicated that a combination of stable RGs, such as GAPDH and PP2A, can lead to an accurate quantification of the expression levels of such target genes. The APX level varied during the experiment time course and according to the inoculum doses, whereas both SOD and CAT resulted down-regulated during the first four days, and up-regulated afterwards, irrespective of inoculum dose. These results can be useful for better elucidating the molecular interaction in the A. deliciosa/P. s. pv. actinidiae pathosystem and for RGs selection in bacteria-plant pathosystems.
Collapse
|
20
|
Müller OA, Grau J, Thieme S, Prochaska H, Adlung N, Sorgatz A, Bonas U. Genome-Wide Identification and Validation of Reference Genes in Infected Tomato Leaves for Quantitative RT-PCR Analyses. PLoS One 2015; 10:e0136499. [PMID: 26313760 PMCID: PMC4552032 DOI: 10.1371/journal.pone.0136499] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/04/2015] [Indexed: 11/18/2022] Open
Abstract
The Gram-negative bacterium Xanthomonas campestris pv. vesicatoria (Xcv) causes bacterial spot disease of pepper and tomato by direct translocation of type III effector proteins into the plant cell cytosol. Once in the plant cell the effectors interfere with host cell processes and manipulate the plant transcriptome. Quantitative RT-PCR (qRT-PCR) is usually the method of choice to analyze transcriptional changes of selected plant genes. Reliable results depend, however, on measuring stably expressed reference genes that serve as internal normalization controls. We identified the most stably expressed tomato genes based on microarray analyses of Xcv-infected tomato leaves and evaluated the reliability of 11 genes for qRT-PCR studies in comparison to four traditionally employed reference genes. Three different statistical algorithms, geNorm, NormFinder and BestKeeper, concordantly determined the superiority of the newly identified reference genes. The most suitable reference genes encode proteins with homology to PHD finger family proteins and the U6 snRNA-associated protein LSm7. In addition, we identified pepper orthologs and validated several genes as reliable normalization controls for qRT-PCR analysis of Xcv-infected pepper plants. The newly identified reference genes will be beneficial for future qRT-PCR studies of the Xcv-tomato and Xcv-pepper pathosystems, as well as for the identification of suitable normalization controls for qRT-PCR studies of other plant-pathogen interactions, especially, if related plant species are used in combination with bacterial pathogens.
Collapse
Affiliation(s)
- Oliver A. Müller
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Jan Grau
- Institute for Informatics, Department of Bioinformatics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Sabine Thieme
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Heike Prochaska
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Norman Adlung
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Anika Sorgatz
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Ulla Bonas
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail:
| |
Collapse
|
21
|
Identification of suitable grapevine reference genes for qRT-PCR derived from heterologous species. Mol Genet Genomics 2015; 291:483-92. [DOI: 10.1007/s00438-015-1081-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/15/2015] [Indexed: 11/27/2022]
|
22
|
Borges AF, Fonseca C, Ferreira RB, Lourenço AM, Monteiro S. Reference gene validation for quantitative RT-PCR during biotic and abiotic stresses in Vitis vinifera. PLoS One 2014; 9:e111399. [PMID: 25340748 PMCID: PMC4207820 DOI: 10.1371/journal.pone.0111399] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 09/30/2014] [Indexed: 11/18/2022] Open
Abstract
Grapevine is one of the most cultivated fruit crop worldwide with Vitis vinifera being the species with the highest economical importance. Being highly susceptible to fungal pathogens and increasingly affected by environmental factors, it has become an important agricultural research area, where gene expression analysis plays a fundamental role. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is currently amongst the most powerful techniques to perform gene expression studies. Nevertheless, accurate gene expression quantification strongly relies on appropriate reference gene selection for sample normalization. Concerning V. vinifera, limited information still exists as for which genes are the most suitable to be used as reference under particular experimental conditions. In this work, seven candidate genes were investigated for their stability in grapevine samples referring to four distinct stresses (Erysiphe necator, wounding and UV-C irradiation in leaves and Phaeomoniella chlamydospora colonization in wood). The expression stability was evaluated using geNorm, NormFinder and BestKeeper. In all cases, full agreement was not observed for the three methods. To provide comprehensive rankings integrating the three different programs, for each treatment, a consensus ranking was created using a non-weighted unsupervised rank aggregation method. According to the last, the three most suitable reference genes to be used in grapevine leaves, regardless of the stress, are UBC, VAG and PEP. For the P. chlamydospora treatment, EF1, CYP and UBC were the best scoring genes. Acquaintance of the most suitable reference genes to be used in grapevine samples can contribute for accurate gene expression quantification in forthcoming studies.
Collapse
Affiliation(s)
- Alexandre Filipe Borges
- Disease & Stress Biology Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Disease & Stress Biology Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
- * E-mail:
| | - Catarina Fonseca
- Disease & Stress Biology Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Ricardo Boavida Ferreira
- Disease & Stress Biology Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Disease & Stress Biology Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Maria Lourenço
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Sara Monteiro
- Disease & Stress Biology Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| |
Collapse
|
23
|
Jeong JK, Kang MH, Gurunathan S, Cho SG, Park C, Seo HG, Kim JH. Evaluation of reference genes in mouse preimplantation embryos for gene expression studies using real-time quantitative RT-PCR (RT-qPCR). BMC Res Notes 2014; 7:675. [PMID: 25256308 PMCID: PMC4181407 DOI: 10.1186/1756-0500-7-675] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 09/05/2014] [Indexed: 01/26/2023] Open
Abstract
Background Real-time quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) is the most sensitive, and valuable technique for rare mRNA detection. However, the expression profiles of reference genes under different experimental conditions, such as different mouse strains, developmental stage, and culture conditions have been poorly studied. Results mRNA stability of the actb, gapdh, sdha, ablim, ywhaz, sptbn, h2afz, tgfb1, 18 s and wrnip genes was analyzed. Using the NormFinder program, the most stable genes are as follows: h2afz for the B6D2F-1 and C57BL/6 strains; sptbn for ICR; h2afz for KOSOM and CZB cultures of B6D2F-1 and C57BL/6 strain-derived embryos; wrnip for M16 culture of B6D2F-1 and C57BL/6 strain-derived embryos; ywhaz, tgfb1, 18 s, 18 s, ywhaz, and h2afz for zygote, 2-cell, 4-cell, 8-cell, molular, and blastocyst embryonic stages cultured in KSOM medium, respectively; h2afz, wrnip, wrnip, h2afz, ywhaz, and ablim for zygote, 2-cell, 4-cell, 8-cell, molular, and blastocyst stage embryos cultured in CZB medium, respectively; 18 s, h2afz, h2afz, actb, h2afz, and wrnip for zygote, 2-cell, 4-cell, 8-cell, molular, and blastocyst stage embryos cultured in M16 medium, respectively. Conclusions These results demonstrated that candidate reference genes for normalization of target gene expression using RT-qPCR should be selected according to mouse strains, developmental stage, and culture conditions. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-675) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Jin-Hoi Kim
- Department of Animal Biotechnology, KonKuk University, Seoul 143-701, Republic of Korea.
| |
Collapse
|
24
|
Guerriero G, Legay S, Hausman JF. Alfalfa Cellulose synthase gene expression under abiotic stress: a Hitchhiker's guide to RT-qPCR normalization. PLoS One 2014; 9:e103808. [PMID: 25084115 PMCID: PMC4118957 DOI: 10.1371/journal.pone.0103808] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/07/2014] [Indexed: 01/22/2023] Open
Abstract
Abiotic stress represents a serious threat affecting both plant fitness and productivity. One of the promptest responses that plants trigger following abiotic stress is the differential expression of key genes, which enable to face the adverse conditions. It is accepted and shown that the cell wall senses and broadcasts the stress signal to the interior of the cell, by triggering a cascade of reactions leading to resistance. Therefore the study of wall-related genes is particularly relevant to understand the metabolic remodeling triggered by plants in response to exogenous stresses. Despite the agricultural and economical relevance of alfalfa (Medicago sativa L.), no study, to our knowledge, has addressed specifically the wall-related gene expression changes in response to exogenous stresses in this important crop, by monitoring the dynamics of wall biosynthetic gene expression. We here identify and analyze the expression profiles of nine cellulose synthases, together with other wall-related genes, in stems of alfalfa plants subjected to different abiotic stresses (cold, heat, salt stress) at various time points (e.g. 0, 24, 72 and 96 h). We identify 2 main responses for specific groups of genes, i.e. a salt/heat-induced and a cold/heat-repressed group of genes. Prior to this analysis we identified appropriate reference genes for expression analyses in alfalfa, by evaluating the stability of 10 candidates across different tissues (namely leaves, stems, roots), under the different abiotic stresses and time points chosen. The results obtained confirm an active role played by the cell wall in response to exogenous stimuli and constitute a step forward in delineating the complex pathways regulating the response of plants to abiotic stresses.
Collapse
Affiliation(s)
- Gea Guerriero
- Department Environment and Agro-biotechnologies (EVA), Centre de Recherche Public, Gabriel Lippmann, Belvaux, Luxembourg
| | - Sylvain Legay
- Department Environment and Agro-biotechnologies (EVA), Centre de Recherche Public, Gabriel Lippmann, Belvaux, Luxembourg
| | - Jean-Francois Hausman
- Department Environment and Agro-biotechnologies (EVA), Centre de Recherche Public, Gabriel Lippmann, Belvaux, Luxembourg
| |
Collapse
|
25
|
Nopo-Olazabal C, Condori J, Nopo-Olazabal L, Medina-Bolivar F. Differential induction of antioxidant stilbenoids in hairy roots of Vitis rotundifolia treated with methyl jasmonate and hydrogen peroxide. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 74:50-69. [PMID: 24269870 DOI: 10.1016/j.plaphy.2013.10.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/29/2013] [Indexed: 06/02/2023]
Abstract
Stilbenoids are polyphenolic phytoalexins that exhibit potential health applications in humans. Hairy root cultures of muscadine grape (Vitis rotundifolia Michx.) were used to study the biochemical and molecular regulation of stilbenoid biosynthesis upon treatment with 100 μM methyl jasmonate (MeJA) or 10 mM hydrogen peroxide (H2O2) over a 96-h period. Resveratrol, piceid, and ε-viniferin were identified in higher concentrations in the tissue whereas resveratrol was the most abundant stilbenoid in the medium under either treatment. An earlier increase in resveratrol accumulation was observed for the MeJA-treated group showing a maximum at 12 h in the tissue and 18 h in the medium. Furthermore, the antioxidant capacity of extracts from the tissue and medium was determined by the 2,2'-azinobis[3-ethylbenzthiazoline sulfonic acid] (ABTS) and the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays showing correlation with the stilbenoid content. Fourteen candidate reference genes for qPCR were tested under the described experimental conditions and resulted in the selection of 5 reference genes. Quantitative analyses of transcripts for phenylalanine ammonia-lyase (PAL), resveratrol synthase (RS), and two stilbene synthases (STS and STS2) showed the highest RNA level induction at 3 h for both treatments with a higher induction for the MeJA treatment. In contrast, the flavonoid-related chalcone synthase (CHS) transcripts showed induction and a decrease in expression for MeJA and H2O2 treatments, respectively. The observed responses could be related to an oxidative burst triggered by the exposure to abiotic stressor compounds with signaling function such as MeJA and H2O2 which have been previously related to the synthesis of secondary metabolites.
Collapse
Affiliation(s)
- Cesar Nopo-Olazabal
- Arkansas Biosciences Institute, Arkansas State University, P.O. Box 639, State University, AR 72467, USA
| | - Jose Condori
- Arkansas Biosciences Institute, Arkansas State University, P.O. Box 639, State University, AR 72467, USA
| | - Luis Nopo-Olazabal
- Arkansas Biosciences Institute, Arkansas State University, P.O. Box 639, State University, AR 72467, USA; Department of Biological Sciences, Arkansas State University, State University, AR 72467, USA
| | - Fabricio Medina-Bolivar
- Arkansas Biosciences Institute, Arkansas State University, P.O. Box 639, State University, AR 72467, USA; Department of Biological Sciences, Arkansas State University, State University, AR 72467, USA.
| |
Collapse
|
26
|
Kundu A, Patel A, Pal A. Defining reference genes for qPCR normalization to study biotic and abiotic stress responses in Vigna mungo. PLANT CELL REPORTS 2013; 32:1647-58. [PMID: 23868569 DOI: 10.1007/s00299-013-1478-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/05/2013] [Accepted: 07/08/2013] [Indexed: 05/20/2023]
Abstract
Expression of ACT, EF1A; H2A, EF1A, ACT and 18S, TUB showed stability under MYMIV, salinity and drought stress, respectively; these are recommended as reference genes for qPCR normalization in Vigna mungo. Accurate gene expression profiling through qPCR depends on selection of appropriate reference gene(s) for normalization. Due to lack of unanimous internal standard, suitable constitutively expressed reference genes are selected that exhibit stable expression under diverse experimental conditions. In this communication, a comparative evaluation of stability among seven V. mungo genes encoding actin (ACT), histone H2A (H2A), elongation factor 1-alpha (EF1A), 18S rRNA (18S), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), cyclophilin (CYP) and tubulin (TUB) under biotic (MYMIV) and abiotic (drought and salinity) stress conditions has been attempted. Specificity and amplification efficiency for each primer pair were verified; however, cumulative assessment of their accumulated transcripts revealed no uniformity. Therefore, individual stability and suitability of these seven candidates have been assessed in silico, by two widely used algorithms, geNorm and Normfinder. Based on the computed results, high stability was obtained for ACT and EF1A during MYMIV stress, while H2A, EFIA and ACT were found to be most suitable in salinity stress experiments and TUB and 18S during drought treatments. Combinations of ACT/TUB or ACT/EFIA were recommended for their use in the pooled analysis, while expression of 18S and CYP showed greater variations and therefore considered unsuitable as reference genes. Additionally, precise quantification of the target gene VmPRX under these stresses was shown to be a function of reference genes' stability, which tends to get affected when normalized with the least stable genes. Hence, use of these normalizers will facilitate accurate and reliable analyses of gene expression in V. mungo.
Collapse
Affiliation(s)
- Anirban Kundu
- Division of Plant Biology, Bose Institute, Kolkata, 700054, West Bengal, India
| | | | | |
Collapse
|
27
|
Figueiredo A, Loureiro A, Batista D, Monteiro F, Várzea V, Pais MS, Gichuru EK, Silva MC. Validation of reference genes for normalization of qPCR gene expression data from Coffea spp. hypocotyls inoculated with Colletotrichum kahawae. BMC Res Notes 2013; 6:388. [PMID: 24073624 PMCID: PMC3849654 DOI: 10.1186/1756-0500-6-388] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 09/25/2013] [Indexed: 02/03/2023] Open
Abstract
Background Coffee production in Africa represents a significant share of the total export revenues and influences the lives of millions of people, yet severe socio-economic repercussions are annually felt in result of the overall losses caused by the coffee berry disease (CBD). This quarantine disease is caused by the fungus Colletotrichum kahawae Waller and Bridge, which remains one of the most devastating threats to Coffea arabica production in Africa at high altitude, and its dispersal to Latin America and Asia represents a serious concern. Understanding the molecular genetic basis of coffee resistance to this disease is of high priority to support breeding strategies. Selection and validation of suitable reference genes presenting stable expression in the system studied is the first step to engage studies of gene expression profiling. Results In this study, a set of ten genes (S24, 14-3-3, RPL7, GAPDH, UBQ9, VATP16, SAND, UQCC, IDE and β-Tub9) was evaluated to identify reference genes during the first hours of interaction (12, 48 and 72 hpi) between resistant and susceptible coffee genotypes and C. kahawae. Three analyses were done for the selection of these genes considering the entire dataset and the two genotypes (resistant and susceptible), separately. The three statistical methods applied GeNorm, NormFinder, and BestKeeper, allowed identifying IDE as one of the most stable genes for all datasets analysed, and in contrast GADPH and UBQ9 as the least stable ones. In addition, the expression of two defense-related transcripts, encoding for a receptor like kinase and a pathogenesis related protein 10, were used to validate the reference genes selected. Conclusion Taken together, our results provide guidelines for reference gene(s) selection towards a more accurate and widespread use of qPCR to study the interaction between Coffea spp. and C. kahawae.
Collapse
Affiliation(s)
- Andreia Figueiredo
- Plant Systems Biology Lab, Center of Biodiversity, Functional & Integrative Genomics (BioFIG), Science Faculty of Lisbon University, Lisbon 1749-016, Portugal.
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Monteiro F, Sebastiana M, Pais MS, Figueiredo A. Reference gene selection and validation for the early responses to downy mildew infection in susceptible and resistant Vitis vinifera cultivars. PLoS One 2013; 8:e72998. [PMID: 24023800 PMCID: PMC3762845 DOI: 10.1371/journal.pone.0072998] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 07/16/2013] [Indexed: 01/04/2023] Open
Abstract
The pivotal role of cultivated grapevine (Vitis vinifera L.) in many countries economy is compromised by its high susceptibility to Plasmopara viticola, the causal agent of downy mildew disease. Recent research has identified a set of genes related to resistance which may be used to track downy mildew infection. Quantification of the expression of these resistance genes requires normalizing qPCR data using reference genes with stable expression in the system studied. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. For the biotic stress effect, EF1α, SAND and SMD3 were the most constant for the susceptible cultivar Trincadeira and EF1α, GAPDH, UBQ for the resistant cultivar Regent. In addition, the expression of three defense-related transcripts, encoding for subtilisin-like protein, CYP and PR10, was analysed, for both datasets, during inoculation time-course. Taken together, our results provide guidelines for reference gene(s) selection towards a more accurate and widespread use of qPCR to study the first hours of interaction between different grapevine cultivars and P. viticola.
Collapse
Affiliation(s)
- Filipa Monteiro
- Plant Systems Biology Lab, Center of Biodiversity, Functional & Integrative Genomics (BioFIG), Science Faculty of Lisbon University, Lisboa, Portugal
- * E-mail: (AF); (FM)
| | - Mónica Sebastiana
- Plant Systems Biology Lab, Center of Biodiversity, Functional & Integrative Genomics (BioFIG), Science Faculty of Lisbon University, Lisboa, Portugal
| | - Maria Salomé Pais
- Plant Systems Biology Lab, Center of Biodiversity, Functional & Integrative Genomics (BioFIG), Science Faculty of Lisbon University, Lisboa, Portugal
| | - Andreia Figueiredo
- Plant Systems Biology Lab, Center of Biodiversity, Functional & Integrative Genomics (BioFIG), Science Faculty of Lisbon University, Lisboa, Portugal
- * E-mail: (AF); (FM)
| |
Collapse
|
29
|
Wang L, Wang Y, Zhou P. Validation of reference genes for quantitative real-time PCR during Chinese wolfberry fruit development. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 70:304-10. [PMID: 23811043 DOI: 10.1016/j.plaphy.2013.05.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 05/21/2013] [Indexed: 05/12/2023]
Abstract
Lycium barbarum L., a woody bush that grows in Eurasia and North Africa, is an ornamental and medicinal plant. Its fruits have been used for centuries in China as a traditional herbal medicine and as a valuable nourishing tonic. There has been no report describing the selection of reference genes for stringent normalization for quantitative PCR (qPCR) in L. barbarum. The present study identified reliable reference genes for normalization of qPCR data in L. barbarum during fruit development from among eight candidate genes (GAPDH, TEF G, EF 1a, UBQ, TUB a, SAMS, EF2 and Hsp80) using the geNorm and NormFinder statistical algorithms. The results showed that the best-ranked references genes differed across the samples. A combination of GAPDH and EF1a would be appropriate as a reference panel for normalizing gene expression data across fruit developmental stages. A combination of EF 1a and SAMS would be appropriate as a reference panel for normalizing gene expression data at the stage A tested, whereas the combination of TUB a, and TEF G was the most suitable for stage B. EF2 and Hsp80 exhibited the most stable expression under stage C and stage D. NormFinder ranking of reference gene candidates was slightly different from that determined by geNorm. These results provide guidelines for the selection of reference genes under different development stages and also represent a foundation for more accurate and widespread use of qRT-PCR in L. barbarum gene analysis.
Collapse
Affiliation(s)
- Lijuan Wang
- Ningxia University, 750021 Yinchuan, PR China.
| | | | | |
Collapse
|
30
|
Pou A, Medrano H, Flexas J, Tyerman SD. A putative role for TIP and PIP aquaporins in dynamics of leaf hydraulic and stomatal conductances in grapevine under water stress and re-watering. PLANT, CELL & ENVIRONMENT 2013; 36:828-43. [PMID: 23046275 DOI: 10.1111/pce.12019] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We examined the role of aquaporins (AQPs) in regulating leaf hydraulic conductance (Kleaf ) in Vitis vinifera L. (cv Chardonnay) by studying effects of AQP inhibitors, and AQP gene expression during water stress (WS) and recovery (REC). Kleaf was measured after 3 h of petiole perfusion with different solutions and to introduce inhibitors. The addition of 0.1 mm HgCl2 to 15 mm KCl reduced Kleaf compared with perfusion in 15 mM KNO3 or KCl, and these solutions were used for leaves from control, WS and REC plants. Perfusion for 3 h did not significantly alter stomatal conductance (gs ) though expression of VvTIP1;1 was increased. WS decreased Kleaf by about 30% and was correlated with gs . The expression of VvTIP2;1 and VvPIP2;1 correlated with Kleaf , and VvTIP2;1 was highly correlated with gs . There was no association between the expression of particular AQPs during WS and REC and inhibition of Kleaf by HgCl2 ; however, HgCl2 treatment itself increased expression of VvPIP2;3 and decreased expression of VvPIP2;1. Inhibition by HgCl2 of Kleaf only at early stages of WS and then after REC suggested that apoplasmic pathways become more important during WS. This was confirmed using fluorescent dyes confined to apoplasm or preferentially accumulated in symplasm.
Collapse
Affiliation(s)
- Alicia Pou
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia
| | | | | | | |
Collapse
|
31
|
Kou SJ, Wu XM, Liu Z, Liu YL, Xu Q, Guo WW. Selection and validation of suitable reference genes for miRNA expression normalization by quantitative RT-PCR in citrus somatic embryogenic and adult tissues. PLANT CELL REPORTS 2012; 31:2151-63. [PMID: 22865195 DOI: 10.1007/s00299-012-1325-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 07/11/2012] [Accepted: 07/16/2012] [Indexed: 05/09/2023]
Abstract
UNLABELLED miRNAs have recently been reported to modulate somatic embryogenesis (SE), a key pathway of plant regeneration in vitro. For expression level detection and subsequent function dissection of miRNAs in certain biological processes, qRT-PCR is one of the most effective and sensitive techniques, for which suitable reference gene selection is a prerequisite. In this study, three miRNAs and eight non-coding RNAs (ncRNA) were selected as reference candidates, and their expression stability was inspected in developing citrus SE tissues cultured at 20, 25, and 30 °C. Stability of the eight non-miRNA ncRNAs was further validated in five adult tissues without temperature treatment. The best single reference gene for SE tissues was snoR14 or snoRD25, while for the adult tissues the best one was U4; although they were not as stable as the optimal multiple references snoR14 + U6 for SE tissues and snoR14 + U5 for adult tissues. For expression normalization of less abundant miRNAs in SE tissues, miR3954 was assessed as a viable reference. Single reference gene snoR14 outperformed multiple references for the overall SE and adult tissues. As one of the pioneer systematic studies on reference gene identification for plant miRNA normalization, this study benefits future exploration on miRNA function in citrus and provides valuable information for similar studies in other higher plants. KEY MESSAGE Three miRNAs and eight non-coding RNAs were tested as reference candidates on developing citrus SE tissues. Best single references snoR14 or snoRD25 and optimal multiple references snoR14 + U6, snoR14 + U5 were identified.
Collapse
Affiliation(s)
- Shu-Jun Kou
- Key Laboratory of Horticultural Plant Biology Ministry of Education, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | | | | | | | | |
Collapse
|
32
|
Shi J, Liu M, Shi J, Zheng G, Wang Y, Wang J, Chen Y, Lu C, Yin W. Reference gene selection for qPCR in Ammopiptanthus mongolicus under abiotic stresses and expression analysis of seven ROS-scavenging enzyme genes. PLANT CELL REPORTS 2012; 31:1245-54. [PMID: 22451089 DOI: 10.1007/s00299-012-1245-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 02/14/2012] [Accepted: 02/21/2012] [Indexed: 05/08/2023]
Abstract
Ammopiptanthus mongolicus, the only evergreen broadleaf shrub endemic to the northwest desert of China, is a valuable species for plant abiotic stress research. No report has so far described the selection of reference genes to get stringent normalization for qPCR in A. mongolicus. This work identified reliable reference genes for normalization of qPCR data in A. mongolicus under abiotic stresses from 14 reference gene candidates (UBQ, Tub1, Tub2, Abc1, Ubc1, Ubc2, Ubc4, Ubc5, eIF1, eIF2, eIF3, eIF4, EF1, EF2), and used the most suitable combination of reference genes to normalize the expression profiles of seven ROS-scavenging enzyme genes (AmSOD, AmAPX, AmGPX, AmCAT, AmGLR, AmPrx, and AmTrx). We set a series of 22 experimental samples covering the control and different time points under cold, dry, salt, and heat stresses. According to geNorm and NormFinder, the combination of eIF1 and eIF3 was best for accurate normalization across all the treatments, confirmed by normalizing qPCR data with AmHsp90. In contrast, these data show that Tub1, Abc1, and EF1 are not suitable reference gene candidates. After being normalized against eIF1 and eIF3, the seven ROS-scavenging enzyme genes exhibited differentially up- or down-regulated expression patterns. AmSOD and AmGPX were up-regulated by all four treatments, indicating that they may participate in an anti-oxidative mechanism under abiotic stresses in A. mongolicus. AmCAT exhibited a much higher expression level than AmAPX, AmPrx, and AmGPX, suggesting a principle role in detoxifying excessive H₂O₂. AmSOD, AmGPX and AmAPX showing the most abundant transcripts under heat, AmCAT and AmGLR under drought, and AmPrx under salt, were observed. Expression patterns of the seven ROS-scavenging enzyme genes suggest different antioxidant protection roles of these genes under abiotic stresses. These results are valuable for future research on gene expression and abiotic stress tolerance in A. mongolicus.
Collapse
Affiliation(s)
- Jing Shi
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Coito JL, Rocheta M, Carvalho L, Amâncio S. Microarray-based uncovering reference genes for quantitative real time PCR in grapevine under abiotic stress. BMC Res Notes 2012; 5:220. [PMID: 22564373 PMCID: PMC3837474 DOI: 10.1186/1756-0500-5-220] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 04/18/2012] [Indexed: 11/15/2022] Open
Abstract
Background Quantitative real time polymerase chain reaction is becoming the primary tool for detecting mRNA and transcription data analysis as it shows to have advantages over other more commonly used techniques. Nevertheless, it also presents a few shortcomings, with the most import being the need for data normalisation, usually with a reference gene. Therefore the choice of the reference gene(s) is of great importance for correct data analysis. Microarray data, when available, can be of great assistance when choosing reference genes. Grapevine was submitted to water stress and heat stress as well as a combination of both to test the stability of the possible reference genes. Results Using the analysis of microarray data available for grapevine, six possible reference genes were selected for RT-qPCR validation: PADCP, ubiq, TIF, TIF-GTP, VH1-IK, aladin-related. Two additional genes that are commonly used as reference genes were included: act and L2. The stability of those genes was tested in leaves of grapevine in both field plants and in greenhouse plants under water or heat stress or a combination of both. Gene stability was analyzed with the softwares GeNorm, NormFinder and the ΔCq method resulting in several combinations of reference genes suitable for data normalisation. In order to assess the best combination, the reference genes were tested in putative stress marker genes (PCO, Galsynt, BKCoAS and HSP17) also chosen from the same microarray, in water stress, heat stress and the combination of both. Conclusions Each method selected different gene combinations (PADCP + act, TIF + TIF-GTP and ubiq + act). However, as none of the combinations diverged significantly from the others used to normalize the expression of the putative stress marker genes, then any combination is suitable for data normalisation under the conditions tested. Here we prove the accuracy of choosing grapevine reference genes for RT-qPCR through a microarray analysis.
Collapse
Affiliation(s)
- João L Coito
- Centro de Botânica Aplicado à Agricultura, Departamento de Recursos Naturais, Ambiente e Território, Instituto Superior de Agronomia, Universidade Técnica de Lisboa, Lisbon, Portugal
| | | | | | | |
Collapse
|