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Khramov DE, Nedelyaeva OI, Konoshenkova AO, Volkov VS, Balnokin YV. Identification and selection of reference genes for analysis of gene expression by quantitative real-time PCR in the euhalophyte Suaeda altissima (L.) Pall. Commun Integr Biol 2024; 17:2372313. [PMID: 38988501 PMCID: PMC11236294 DOI: 10.1080/19420889.2024.2372313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024] Open
Abstract
Сoding sequences of seven housekeeping genes: actin SaACT7, ubiquitin-conjugating protein SaUBC10, glyceraldehyde-3-phosphate dehydrogenase SaGAPDH, protein of the large subunit of ribosomes SaL2, α-tubulin SaTUA, translation elongation factor SaeEF1α, and protein phosphatase SaPP2A were identified as candidate reference genes for expression analysis of target genes in the extremely salt tolerant plant Suaeda altissima (L.) Pall. The expression profiles of the genes differed. SaACT7 and SaeEF1α demonstrated the highest expression levels, while the lowest expression levels were found for SaPP2A and SaTUA. SaPP2A and SaeEF1α genes were the most stably expressed at different steady-state salinity levels and different nitrate concentrations in nutrient solutions (NSs). SaL2, SaPP2A, and SaeEF1α genes showed the greatest stability of expression when nitrate was added to nutrient solution of plants grown under conditions of nitrate deficiency. Less constant expression was demonstrated in this experiment by SaACT7 and SaTUA. SaL2, SaACT7, SaeEF1α, and SaUBC10 genes showed the smallest expression changes under salt shock. To validate the use of the most stably expressed genes for normalization of gene expression, we checked them as reference genes to study the expression of the nitrate transporter gene SaNPF6.3 in S. altissima roots under conditions of different salinity and different nitrate supply.
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Affiliation(s)
- Dmitrii E. Khramov
- Laboratory of Ion Transport and Salinity Tolerance, K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
| | - Olga I. Nedelyaeva
- Laboratory of Ion Transport and Salinity Tolerance, K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
| | - Alena O. Konoshenkova
- Laboratory of Ion Transport and Salinity Tolerance, K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
| | - Vadim S. Volkov
- Laboratory of Ion Transport and Salinity Tolerance, K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, CA, USA
| | - Yurii V. Balnokin
- Laboratory of Ion Transport and Salinity Tolerance, K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
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Jia X, Xiong Y, Xiong Y, Li D, Yu Q, Lei X, You M, Bai S, Zhang J, Ma X. Identification and Validation of Reference Genes for RT-qPCR Analysis in Reed Canary Grass during Abiotic Stress. Genes (Basel) 2023; 14:1790. [PMID: 37761930 PMCID: PMC10530813 DOI: 10.3390/genes14091790] [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: 08/24/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Reed canary grass (Phalaris arundinacea L.) is known for its tolerance to drought, heavy metals, and waterlogging, making it a popular choice for forage production and wetland restoration in the Qinghai-Tibet Plateau (QTP). To accurately assess gene expression in reed canary grass under different abiotic stresses, suitable reference genes need to be identified and validated. Thirteen candidate reference gene sequences were selected and screened using RT-qPCR to detect their expression levels in reed canary grass leaves under drought, salt, cadmium, and waterlogging stresses. Four algorithms were used to assess the stability of the expression levels of the candidate reference genes. The most stably expressed genes were UBC and H3 under drought Cd, ETF and CYT under salt stress, and ETF and TUB under waterlogging stress. GAPDH was found to be less stable under abiotic stresses. PIP-1, PAL, NAC 90, and WRKY 72A were selected as response genes for quantitative expression assessment under drought, salt, Cd, and waterlogging stresses to confirm the accuracy of the selected stable reference genes. These results provide a theoretical reference for assessing gene expression in reed canary grass under abiotic stresses.
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Affiliation(s)
- Xuejie Jia
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
| | - Daxu Li
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Qinqin Yu
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Minghong You
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Shiqie Bai
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621002, China
| | - Jianbo Zhang
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
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Liu H, Liu J, Chen P, Zhang X, Wang K, Lu J, Li Y. Selection and Validation of Optimal RT-qPCR Reference Genes for the Normalization of Gene Expression under Different Experimental Conditions in Lindera megaphylla. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112185. [PMID: 37299163 DOI: 10.3390/plants12112185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/18/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Lindera megaphylla, a broad-leaved evergreen that is used as a landscape ornamental plant and medicinal plant, is an ecologically important and dominant tree species. However, little is known about the molecular mechanisms of its growth, development, and metabolism. The selection of suitable reference genes is critical for molecular biological analyses. To date, no research on reference genes as a foundation for gene expression analysis has been undertaken in L. megaphylla. In this study, 14 candidate genes were selected from the transcriptome database of L. megaphylla for RT-qPCR assay under different conditions. Results showed that helicase-15 and UBC28 were most stable in different tissues of seedlings and adult trees. For different leaf developmental stages, the best combination of reference genes was ACT7 and UBC36. UBC36 and TCTP were the best under cold treatment, while PAB2 and CYP20-2 were the best under heat treatment. Finally, a RT-qPCR assay of LmNAC83 and LmERF60 genes were used to further verify the reliability of selected reference genes above. This work is the first to select and evaluate the stability of reference genes for the normalization of gene expression analysis in L. megaphylla and will provide an important foundation for future genetic studies of this species.
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Affiliation(s)
- Hongli Liu
- International Union Laboratory of Landscape Architecture of Henan, College of Landscape Architecture and Arts, Henan Agricultural University, Zhengzhou 450003, China
| | - Jing Liu
- International Union Laboratory of Landscape Architecture of Henan, College of Landscape Architecture and Arts, Henan Agricultural University, Zhengzhou 450003, China
| | - Peng Chen
- International Union Laboratory of Landscape Architecture of Henan, College of Landscape Architecture and Arts, Henan Agricultural University, Zhengzhou 450003, China
| | - Xin Zhang
- International Union Laboratory of Landscape Architecture of Henan, College of Landscape Architecture and Arts, Henan Agricultural University, Zhengzhou 450003, China
| | - Ke Wang
- Zhengzhou Botanical Garden, Zhengzhou 450042, China
| | - Jiuxing Lu
- International Union Laboratory of Landscape Architecture of Henan, College of Landscape Architecture and Arts, Henan Agricultural University, Zhengzhou 450003, China
| | - Yonghua Li
- International Union Laboratory of Landscape Architecture of Henan, College of Landscape Architecture and Arts, Henan Agricultural University, Zhengzhou 450003, China
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Soltani Najafabadi M, Amirbakhtiar N. Evaluating and Validating Sunflower Reference Genes for Q-PCR Studies Under High Temperature Condition. IRANIAN JOURNAL OF BIOTECHNOLOGY 2023; 21:e3357. [PMID: 37228632 PMCID: PMC10203189 DOI: 10.30498/ijb.2023.338375.3357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 01/07/2023] [Indexed: 05/27/2023]
Abstract
Background Q-PCR is the method of choice for PCR- based transcriptomics and validating microarray-based and RNA-seq results. Proper application of this technology requires proper normalization to correct as much as possible errors propagating during RNA extraction and cDNA synthesis. Objectives The investigation was performed to find stable reference genes in sunflower under shifting in ambient temperature. Materials and Methods Sequences of five well-known reference genes of Arabidopsis (Actin, Ubiquitin, Elongation factor-1, GAPDH, and SAND) and one well-known reference gene inhuman, Importin, were subjected to BLASTX against sunflower databases and the relevant genes were subjected to primer designing for q-PCR. Two sunflower inbred lines were cultivated at two dates so that anthesis occurred at nearly 30 °C and 40 °C (heat stress). The experiment was repeated for two years. Q-PCR was run on samples taken for two planting date separately at the beginning of anthesis for each genotype from leaf, taproots, receptacle base, immature and mature disc flowers and on pooled samples comprising of the tissues for each genotype, planting dates and also all tissues for both genotypes and both planting dates. Basic statistical properties of each candidate gene across all the samples were calculated. Furthermore, gene expression stability analysis was done for six candidate reference genes on Cq mean of two years using three independent algorithms, geNorm, Bestkeeper, and Refinder. Results Designed primers for Actin2, SAND, GAPDH, Ubiquitin, EF-1a, and Importin yielded a single peak in melting curve analysis indicating specificity of the PCR reaction. Basic statistical analysis showed that Actin2 and EF-1a had the highest and lowest expression levels across all the samples, respectively. Actin2 appeared to be the most stable reference gene across all the samples based on the three used algorithms. Pairwise variation analysis revealed that for samples taken under ambient temperature of 30 °C, Actin2, EF-1a, SAND and for those taken under ambient temperature of 40 °C, Actin2, EF-1a, Importin and SAND have to be used for normalization in q-PCR studies. Moreover, it is suggested that normalization to be based on Actin2, SAND and EF-1a for vegetative tissues and Actin2, EF-1a, SAND and Importin for reproductive tissues. Conclusions In the present research, proper reference genes for normalization of gene expression studies under heat stress conditions were introduced. Moreover, the presence of genotype-by- planting date interaction effects and tissue specific gene expression pattern on the behavior of the most three stable reference genes was indicated.
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Affiliation(s)
- Masood Soltani Najafabadi
- National Plant Genebank, Seed and Plant Improvement Institute, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Nazanin Amirbakhtiar
- National Plant Genebank, Seed and Plant Improvement Institute, Agricultural Research, Education, and Extension Organization, Karaj, Iran
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Sowa S, Sozoniuk M, Toporowska J, Kowalczyk K, Paczos-Grzęda E. Validation of reference genes as an internal control for studying Avena sativa-Puccinia coronata interaction by RT-qPCR. Sci Rep 2022; 12:14601. [PMID: 36028746 PMCID: PMC9418433 DOI: 10.1038/s41598-022-18746-z] [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: 04/21/2022] [Accepted: 08/18/2022] [Indexed: 11/11/2022] Open
Abstract
In this study we evaluated eleven candidate reference genes in Avena sativa during compatible and incompatible interactions with two different pathotypes of Puccinia coronata f. sp. avenae in six time points post-inoculation. The identification of genes with high expression stability was performed by four algorithms (geNorm, NormFinder, BestKeeper and ΔCt method). The results obtained confirmed that the combination of two genes would be sufficient for reliable normalization of the expression data. In general, the most stable in the tested plant-pathogen system were HNR (heterogeneous nuclear ribonucleoprotein 27C) and EF1A (elongation factor 1-alpha). ARF (ADP-ribosylation factor) and EIF4A (eukaryotic initiation factor 4A-3) could also be considered as exhibiting high expression stability. CYP (cyclophilin) was shown by all assessment methods to be the worst candidate for normalization in this dataset. To date, this is the first report of reference genes selection in A. sativa–P. coronata interaction system. Identified reference genes enable reliable and comprehensive RT-qPCR analysis of oat gene expression in response to crown rust infection. Understanding the molecular mechanisms involved in the host–pathogen interactions may expand knowledge of durable resistance strategies beneficial to modern oat breeding.
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Affiliation(s)
- Sylwia Sowa
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland.
| | - Magdalena Sozoniuk
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland
| | - Joanna Toporowska
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland
| | - Krzysztof Kowalczyk
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland
| | - Edyta Paczos-Grzęda
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland
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Selection and Optimization of Reference Genes for MicroRNA Expression Normalization by qRT-PCR in Chinese Cedar ( Cryptomeria fortunei) under Multiple Stresses. Int J Mol Sci 2021; 22:ijms22147246. [PMID: 34298866 PMCID: PMC8304282 DOI: 10.3390/ijms22147246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 01/22/2023] Open
Abstract
MicroRNA (miRNA) expression analysis is very important for investigating its functions. To date, no research on reference genes (RGs) for miRNAs in gymnosperms, including Cryptomeria fortunei, has been reported. Here, ten miRNAs (i.e., pab-miR159a, cln-miR162, cas-miR166d, pab-miR395b, ppt-miR894, cln-miR6725, novel1, novel6, novel14 and novel16) and three common RGs (U6, 5S and 18S) were selected as candidate RGs. qRT-PCR was used to analyse their expressions in C. fortunei under various experimental conditions, including multiple stresses (cold, heat, drought, salt, abscisic acid and gibberellin) and in various tissues (roots, stems, tender needles, cones and seeds). Four algorithms (delta Ct, geNorm, NormFinder and BestKeeper) were employed to assess the stability of candidate RG expression; the geometric mean and RefFinder program were used to comprehensively evaluate RG stability. According to the results, novel16, cln-miR6725, novel1 and U6 were the most stable RGs for studying C. fortunei miRNA expression. In addition, the expression of three target miRNAs (aly-miR164c-5p, aly-miR168a-5p and smo-miR396) was examined to verify that the selected RGs are suitable for miRNA expression normalisation. This study may aid further investigations of miRNA expression/function in the response of C. fortunei to abiotic stress and provides an important basis for the standardisation of miRNA expression in other gymnosperm species.
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Validation of Reference Genes for Studying Different Abiotic Stresses in Oat ( Avena sativa L.) by RT-qPCR. PLANTS 2021; 10:plants10071272. [PMID: 34206660 PMCID: PMC8309034 DOI: 10.3390/plants10071272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 12/27/2022]
Abstract
Oat (Avena sativa L.) is a widely cultivated cereal with high nutritional value and it is grown mainly in temperate regions. The number of studies dealing with gene expression changes in oat continues to increase, and to obtain reliable RT-qPCR results it is essential to establish and use reference genes with the least possible influence caused by experimental conditions. However, no detailed study has been conducted on reference genes in different tissues of oat under diverse abiotic stress conditions. In our work, nine candidate reference genes (ACT, TUB, CYP, GAPD, UBC, EF1, TBP, ADPR, PGD) were chosen and analysed by four statistical methods (GeNorm, Normfinder, BestKeeper, RefFinder). Samples were taken from two tissues (leaves and roots) of 13-day-old oat plants exposed to five abiotic stresses (drought, salt, heavy metal, low and high temperatures). ADPR was the top-rated reference gene for all samples, while different genes proved to be the most stable depending on tissue type and treatment combinations. TUB and EF1 were most affected by the treatments in general. Validation of reference genes was carried out by PAL expression analysis, which further confirmed their reliability. These results can contribute to reliable gene expression studies for future research in cultivated oat.
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Zhang Y, Zhu L, Xue J, Yang J, Hu H, Cui J, Xu J. Selection and Verification of Appropriate Reference Genes for Expression Normalization in Cryptomeria fortunei under Abiotic Stress and Hormone Treatments. Genes (Basel) 2021; 12:genes12060791. [PMID: 34064253 PMCID: PMC8224294 DOI: 10.3390/genes12060791] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/15/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Cryptomeria fortunei has become one of the main timber afforestation species in subtropical high-altitude areas of China due to its fast growth, good material quality, and strong adaptability, showing broad application prospects. Quantitative real-time PCR (qRT-PCR) is the most accurate and widely used gene expression evaluation technique, and selecting appropriate reference genes (RGs) is essential for normalizing qRT-PCR results. However, suitable RGs for gene expression normalization in C. fortunei have not been reported. Here, we tested the expression stability for 12 RGs in C. fortunei under various experimental conditions (simulated abiotic stresses (cold, heat, drought, and salinity) and hormone treatments (methyl jasmonate, abscisic acid, salicylic acid, and gibberellin) and in different tissues (stems, tender needles, needles, cones, and seeds) using four algorithms (delta Ct, geNorm, NormFinder, and BestKeeper). Then, geometric mean rankings from these algorithms and the RefFinder program were used to comprehensively evaluate RG stability. The results indicated CYP, actin, UBC, and 18S as good choices for studying C. fortunei gene expression. qRT-PCR analysis of the expression patterns of three target genes (CAT and MAPK1/6) further verified that the selected RGs were suitable for gene expression normalization. This study provides an important basis for C. fortunei gene expression standardization and quantification.
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Affiliation(s)
- Yingting Zhang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (L.Z.); (J.X.); (J.Y.); (H.H.); (J.C.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Lijuan Zhu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (L.Z.); (J.X.); (J.Y.); (H.H.); (J.C.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Jinyu Xue
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (L.Z.); (J.X.); (J.Y.); (H.H.); (J.C.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Junjie Yang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (L.Z.); (J.X.); (J.Y.); (H.H.); (J.C.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Hailiang Hu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (L.Z.); (J.X.); (J.Y.); (H.H.); (J.C.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Jiebing Cui
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (L.Z.); (J.X.); (J.Y.); (H.H.); (J.C.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Jin Xu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (L.Z.); (J.X.); (J.Y.); (H.H.); (J.C.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: ; Tel.: +86-25-8542-7319
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Yu T, Kuwahara S, Ohno T, Iwahashi H. Recycling salmon meat by decontamination under mild conditions using high-pressure carbon dioxide. WASTE MANAGEMENT (NEW YORK, N.Y.) 2021; 124:102-109. [PMID: 33611154 DOI: 10.1016/j.wasman.2021.01.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/26/2021] [Accepted: 01/30/2021] [Indexed: 06/12/2023]
Abstract
The 2011-2016 reports from the Food and Agriculture Organization of the United Nations has stated that annual food loss and waste occurs on a massive scale in fisheries and aquaculture. This study aimed to explore advanced technologies to recycle wasted salmon as an industrial resource with high commercial value by applying enzymatic hydrolysis under HPCD. Our results showed that HPCD treatment at 50 °C and 1 MPa for 16 h effectively prevents salmon from microbial contamination. Real-time PCR analysis demonstrated that HPCD was also able to inhibit an increase in bacteria at moderate temperatures. Based on NGS analysis, there was a very low abundance of Bacillus and some histamine producers, such as Pseudomonas, Acinetobacter, Enterobacter, and Klebsiella, detected in samples treated using HPCD at 50 °C and 1 MPa for 16 h. Hydrolysate analysis showed that HPCD treatment at 1 MPa did not affect the hydrolysates from salmon. It is anticipated that the results from this study will support the application of HPCD in industrial enzymatic hydrolysis and increase the sustainability of bio-based materials.
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Affiliation(s)
- Tonghuan Yu
- The United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan.
| | - Shinichi Kuwahara
- Faculty of Applied Biological Science, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan.
| | - Tomoki Ohno
- Faculty of Applied Biological Science, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan.
| | - Hitoshi Iwahashi
- Faculty of Applied Biological Science, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan.
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Maldonado-Taipe N, Patirange DSR, Schmöckel SM, Jung C, Emrani N. Validation of suitable genes for normalization of diurnal gene expression studies in Chenopodium quinoa. PLoS One 2021; 16:e0233821. [PMID: 33705394 PMCID: PMC7951847 DOI: 10.1371/journal.pone.0233821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/18/2021] [Indexed: 11/18/2022] Open
Abstract
Quinoa depicts high nutritional quality and abiotic stress resistance, attracting strong interest in the last years. To unravel the function of candidate genes for agronomically relevant traits, studying their transcriptional activities by RT-qPCR is an important experimental approach. The accuracy of such experiments strongly depends on precise data normalization. To date, validation of potential candidate genes for normalization of diurnal expression studies has not been performed in C. quinoa. We selected eight candidate genes based on transcriptome data and literature survey, including conventionally used reference genes. We used three statistical algorithms (BestKeeper, geNorm and NormFinder) to test their stability and added further validation by a simulation-based strategy. We demonstrated that using different reference genes, including those top ranked by stability, causes significant differences among the resulting diurnal expression patterns. Our results show that isocitrate dehydrogenase enzyme (IDH-A) and polypyrimidine tract-binding protein (PTB) are suitable genes to normalize diurnal expression data of two different quinoa accessions. Moreover, we validated our reference genes by normalizing two known diurnally regulated genes, BTC1 and BBX19. The validated reference genes obtained in this study will improve the accuracy of RT-qPCR data normalization and facilitate gene expression studies in quinoa.
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Affiliation(s)
| | | | - Sandra M. Schmöckel
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
- Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Nazgol Emrani
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
- * E-mail:
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Selection and Validation of Reference Genes for RT-qPCR Analysis in Spinacia oleracea under Abiotic Stress. BIOMED RESEARCH INTERNATIONAL 2021; 2021:4853632. [PMID: 33623781 PMCID: PMC7875621 DOI: 10.1155/2021/4853632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/16/2021] [Indexed: 11/17/2022]
Abstract
Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is an accurate and convenient method for mRNA quantification. Selection of optimal reference gene(s) is an important step in RT-qPCR experiments. However, the stability of housekeeping genes in spinach (Spinacia oleracea) under various abiotic stresses is unclear. Evaluating the stability of candidate genes and determining the optimal gene(s) for normalization of gene expression in spinach are necessary to investigate the gene expression patterns during development and stress response. In this study, ten housekeeping genes, 18S ribosomal RNA (18S rRNA), actin, ADP ribosylation factor (ARF), cytochrome c oxidase subunit 5C (COX), cyclophilin (CYP), elongation factor 1-alpha (EF1α), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone H3 (H3), 50S ribosomal protein L2 (RPL2), and tubulin alpha chain (TUBα) from spinach, were selected as candidates in roots, stems, leaves, flowers, and seedlings in response to high temperature, CdCl2, NaCl, NaHCO3, and Na2CO3 stresses. The expression of these genes was quantified by RT-qPCR and evaluated by NormFinder, BestKeeper, and geNorm. 18S rRNA, actin, ARF, COX, CYP, EF1α, GAPDH, H3, and RPL2 were detected as optimal reference genes for gene expression analysis of different organs and stress responses. The results were further confirmed by the expression pattern normalized with different reference genes of two heat-responsive genes. Here, we optimized the detection method of the gene expression pattern in spinach. Our results provide the optimal candidate reference genes which were crucial for RT-qPCR analysis.
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Li T, Chen X, Lin S. Physiological and transcriptomic responses to N-deficiency and ammonium: Nitrate shift in Fugacium kawagutii (Symbiodiniaceae). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 753:141906. [PMID: 32890873 DOI: 10.1016/j.scitotenv.2020.141906] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 06/11/2023]
Abstract
Symbiodiniaceae are the source of essential coral symbionts of reef building corals. The growth and density of endosymbiotic Symbiodiniaceae within the coral host is dependent on nutrient availability, yet little is known about how Symbiodiniaceae respond to the dynamics of the nutrients, including switch between different chemical forms and changes in abundance. In this study, we investigated physiological, cytometric, and transcriptomic responses in Fugacium kawagutii to nitrogen (N)-nutrient deficiency and different chemical N forms (nitrate and ammonium) in batch culture conditions. We mainly found that ammonium was consumed faster than nitrate when provided separately, and was preferentially utilized over nitrate when both N compounds were supplied at 1:2, 1:1 and 2:1 molarity ratios. Besides, N-deficiency caused decreases in growth, energy production, antioxidative capacity and investment in photosynthate transport but increased energy consumption. Growing on ammonium produced a similar cell yield as nitrate, but with a reduced investment in nutrient transport and assimilation; yet at high concentrations ammonium exhibited inhibitory effects. These findings together have important implications in N-nutrient regulation of coral symbiosis. In addition, we identified ten highly and stably expressed genes as candidate reference genes, which will be potentially useful for gene expression studies in the future.
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Affiliation(s)
- Tangcheng Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Xibei Chen
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao 266237, China; Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
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Liang X, Chen Q, Wu C, Liu Y, Fang Y. Reference gene validation in Eotetranychus sexmaculatus (Acari: Tetranychidae) feeding on mite-susceptible and mite-resistant rubber tree germplasms. EXPERIMENTAL & APPLIED ACAROLOGY 2020; 82:211-228. [PMID: 32886259 DOI: 10.1007/s10493-020-00542-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Reliable reference genes are quite important in calculating gene transcript levels by using real-time quantitative reverse transcription-PCR (RT-qPCR). Eotetranychus sexmaculatus is known as a dangerous mite causing significant yield reduction of rubber tree latex; however, selection of appropriate reference genes for validation of target gene expression in E. sexmaculatus has not been conducted yet. In the present study, nine candidate reference genes were analyzed for their expression stability in different life stages of E. sexmaculatus by using common algorithms including comparative ΔCq method, geNorm, NormFinder and BestKeeper. In addition, a comprehensive analysis software (RefFinder) was used to assign an overall final rank for each candidate gene. The results showed that β-actin and β-TUB were the best two reference genes and were subjected to evaluate expression of two protective enzyme genes (EsCu/ZnSOD and EsCAT1) in E. sexmaculatus. We found that the expression of EsCu/ZnSOD and EsCAT1 in E. sexmaculatus feeding on mite-resistant rubber tree germplasm was significantly lower compared with those feeding on mite-susceptible germplasm. These results will facilitate research in revealing molecular mechanisms underlying rubber tree resistance to the spider mite.
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Affiliation(s)
- Xiao Liang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Qing Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
| | - Chunling Wu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Ying Liu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yongjun Fang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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Selvakesavan RK, Franklin G. Nanoparticles Affect the Expression Stability of Housekeeping Genes in Plant Cells. Nanotechnol Sci Appl 2020; 13:77-88. [PMID: 32884247 PMCID: PMC7431599 DOI: 10.2147/nsa.s265641] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/30/2020] [Indexed: 02/05/2023] Open
Abstract
Purpose We report on the expression stability of several housekeeping/reference genes that can be used in the normalization of target gene expression in quantitative real-time PCR (qRT-PCR) analysis of plant cells challenged with metal nanoparticles (NPs). Materials and Methods Uniform cell suspension cultures of Hypericum perforatum were treated with 25 mg/l silver and gold NPs (14-15 nm in diameter). Cells were collected after 0.5, 4.0, and 12 h. The total RNA isolated from the cells was analyzed for the stability of ACT2, ACT3, ACT7, EF1-α, GAPDH, H2A, TUB-α, TUB-β, and 18S rRNA genes using qRT-PCR. The cycle threshold (Ct) values of the genes were analyzed using the geNorm, NormFinder, BestKeeper, and RefFinder statistical algorithms to rank gene stability. The stability of the top-ranked genes was validated by normalizing the expression of HYP1. Results The expression of the tested housekeeping genes varied with treatment duration and NP types. EF1-α in gold NP treatment and TUB-α and EF1-α in silver NP treatment ranked among the top three positions. However, none of the genes retained their top ranking with time and across NP types. Conclusion EF1-α can be used as a reference for treatment involving both silver and gold NPs in H. perforatum cells. TUB-α can be used only for silver NP-treated cells. The expression instability of most of the housekeeping genes highlights the importance of systematic standardization of reference genes for NP treatment conditions to draw proper conclusions on the target gene expression.
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Affiliation(s)
| | - Gregory Franklin
- Institute of Plant Genetics of the Polish Academy of Sciences, Poznan 60-479, Poland
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Carex muskingumensis and Osmotic Stress: Identification of Reference Genes for Transcriptional Profiling by RT-qPCR. Genes (Basel) 2020; 11:genes11091022. [PMID: 32878033 PMCID: PMC7563777 DOI: 10.3390/genes11091022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 01/16/2023] Open
Abstract
Carex muskingumensis is a highly valued perennial ornamental grass cultivated worldwide. However, there is limited genetic data regarding this species. Selection of proper reference genes (RGs) for reverse transcription quantitative PCR (RT-qPCR) data normalization has become an essential step in gene expression analysis. In this study, we aimed to examine expression stability of nine candidate RGs in C. muskingumensis plants, subjected to osmotic stress, generated either by salinity or PEG treatment. The identification of genes exhibiting high expression stability was performed by four algorithms (geNorm, NormFinder, BestKeeper and deltaCt method). The results showed that the combination of two genes would be sufficient for reliable expression data normalization. ADP (ADP-ribosylation factor) and TBP (TATA-box-binding protein) were identified as the most stably expressed under salinity treatment, while eIF4A (eukaryotic initiation factor 4A) and TBP were found to show the highest stability under PEG-induced drought. A set of three genes (ADP, eIF4A and TBP) displayed the highest expression stability across all experimental samples tested in this study. To our best knowledge, this is the first report regarding RGs selection in C. muskingumensis. It will provide valuable starting point information for conducting further analyses in this and related species concerning their responses to water shortage and salinity stress.
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Zhang L, Wang Y, Zhang Q, Jiang Y, Zhang H, Li R. Overexpression of HbMBF1a, encoding multiprotein bridging factor 1 from the halophyte Hordeum brevisubulatum, confers salinity tolerance and ABA insensitivity to transgenic Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2020; 102:1-17. [PMID: 31655970 PMCID: PMC6976555 DOI: 10.1007/s11103-019-00926-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/13/2019] [Indexed: 05/11/2023]
Abstract
HbMBF1a was isolated and characterized in H. brevisubulatum, and overexpressed HbMBF1a could enhance the salt tolerance and ABA insensitivity in Arabidopsis thaliana. The transcript levels of stress-responsive genes were significantly increased in the transgenic lines under salt and ABA conditions. Salinity is an abiotic stress that considerably affects plant growth, yield, and distribution. Hordeum brevisubulatum is a halophyte that evolved to become highly tolerant to salinity. Multiprotein bridging factor 1 (MBF1) is a transcriptional coactivator and an important regulator of stress tolerance. In this study, we isolated and characterized HbMBF1a based on the transcriptome data of H. brevisubulatum grown under saline conditions. We overexpressed HbMBF1a in Arabidopsis thaliana and compared the phenotypes of the transgenic lines and the wild-type in response to stresses. The results indicated that HbMBF1a expression was induced by salt and ABA treatments during the middle and late stages. The overexpression of HbMBF1a in A. thaliana resulted in enhanced salt tolerance and ABA insensitivity. More specifically, the enhanced salt tolerance manifested as the increased seed germination and seedling growth and development. Similarly, under ABA treatments, the cotyledon greening rate and seedling root length were higher in the HbMBF1a-overexpressing lines, suggesting the transgenic plants were better adapted to high exogenous ABA levels. Furthermore, the transcript levels of stress-responsive genes were significantly increased in the transgenic lines under salt and ABA conditions. Thus, HbMBF1a is a positive regulator of salt and ABA responses, and the corresponding gene may be useful for producing transgenic plants that are salt tolerant and/or ABA insensitive, with few adverse effects. This study involved a comprehensive analysis of HbMBF1a. The results may provide the basis and insight for the application of MBF1 family genes for developing stress-tolerant crops.
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Affiliation(s)
- Lili Zhang
- Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, 100097 China
| | - Yunxiao Wang
- Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, 100097 China
| | - Qike Zhang
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024 China
| | - Ying Jiang
- Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, 100097 China
| | - Haiwen Zhang
- Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, 100097 China
| | - Ruifen Li
- Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, 100097 China
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Solanki S, Ameen G, Zhao J, Flaten J, Borowicz P, Brueggeman RS. Visualization of spatial gene expression in plants by modified RNAscope fluorescent in situ hybridization. PLANT METHODS 2020; 16:71. [PMID: 32467719 PMCID: PMC7229616 DOI: 10.1186/s13007-020-00614-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/11/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND In situ analysis of biomarkers such as DNA, RNA and proteins are important for research and diagnostic purposes. At the RNA level, plant gene expression studies rely on qPCR, RNAseq and probe-based in situ hybridization (ISH). However, for ISH experiments poor stability of RNA and RNA based probes commonly results in poor detection or poor reproducibility. Recently, the development and availability of the RNAscope RNA-ISH method addressed these problems by novel signal amplification and background suppression. This method is capable of simultaneous detection of multiple target RNAs down to the single molecule level in individual cells, allowing researchers to study spatio-temporal patterning of gene expression. However, this method has not been optimized thus poorly utilized for plant specific gene expression studies which would allow for fluorescent multiplex detection. Here we provide a step-by-step method for sample collection and pretreatment optimization to perform the RNAscope assay in the leaf tissues of model monocot plant barley. We have shown the spatial distribution pattern of HvGAPDH and the low expressed disease resistance gene Rpg1 in leaf tissue sections of barley and discuss precautions that should be followed during image analysis. RESULTS We have shown the ubiquitous HvGAPH and predominantly stomatal guard cell associated subsidiary cell expressed Rpg1 expression pattern in barley leaf sections and described the improve RNAscope methodology suitable for plant tissues using confocal laser microscope. By addressing the problems in the sample collection and incorporating additional sample backing steps we have significantly reduced the section detachment and experiment failure problems. Further, by reducing the time of protease treatment, we minimized the sample disintegration due to over digestion of barley tissues. CONCLUSIONS RNAscope multiplex fluorescent RNA-ISH detection is well described and adapted for animal tissue samples, however due to morphological and structural differences in the plant tissues the standard protocol is deficient and required optimization. Utilizing barley specific HvGAPDH and Rpg1 RNA probes we report an optimized method which can be used for RNAscope detection to determine the spatial expression and semi-quantification of target RNAs. This optimized method will be immensely useful in other plant species such as the widely utilized Arabidopsis.
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Affiliation(s)
- Shyam Solanki
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163 USA
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108-6050 USA
| | - Gazala Ameen
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163 USA
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108-6050 USA
| | - Jin Zhao
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108-6050 USA
| | - Jordan Flaten
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58108-6050 USA
| | - Pawel Borowicz
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58108-6050 USA
| | - Robert S. Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163 USA
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108-6050 USA
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