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Sun H, Li C, Li S, Ma J, Li S, Li X, Gao C, Yang R, Ma N, Yang J, Yang P, He X, Hu T. Identification and validation of stable reference genes for RT-qPCR analyses of Kobresia littledalei seedlings. BMC PLANT BIOLOGY 2024; 24:389. [PMID: 38730341 PMCID: PMC11088182 DOI: 10.1186/s12870-024-04924-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 03/18/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Kobreisa littledalei, belonging to the Cyperaceae family is the first Kobresia species with a reference genome and the most dominant species in Qinghai-Tibet Plateau alpine meadows. It has several resistance genes which could be used to breed improved crop varieties. Reverse Transcription Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR) is a popular and accurate gene expression analysis method. Its reliability depends on the expression levels of reference genes, which vary by species, tissues and environments. However, K.littledalei lacks a stable and normalized reference gene for RT-qPCR analysis. RESULTS The stability of 13 potential reference genes was tested and the stable reference genes were selected for RT-qPCR normalization for the expression analysis in the different tissues of K. littledalei under two abiotic stresses (salt and drought) and two hormonal treatments (abscisic acid (ABA) and gibberellin (GA)). Five algorithms were used to assess the stability of putative reference genes. The results showed a variation amongst the methods, and the same reference genes showed tissue expression differences under the same conditions. The stability of combining two reference genes was better than a single one. The expression levels of ACTIN were stable in leaves and stems under normal conditions, in leaves under drought stress and in roots under ABA treatment. The expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) expression was stable in the roots under the control conditions and salt stress and in stems exposed to drought stress. Expression levels of superoxide dismutase (SOD) were stable in stems of ABA-treated plants and in the roots under drought stress. Moreover, RPL6 expression was stable in the leaves and stems under salt stress and in the stems of the GA-treated plants. EF1-alpha expression was stable in leaves under ABA and GA treatments. The expression levels of 28 S were stable in the roots under GA treatment. In general, ACTIN and GAPDH could be employed as housekeeping genes for K. littledalei under different treatments. CONCLUSION This study identified the best RT-qPCR reference genes for different K. littledalei tissues under five experimental conditions. ACTIN and GAPDH genes can be employed as the ideal housekeeping genes for expression analysis under different conditions. This is the first study to investigate the stable reference genes for normalized gene expression analysis of K. littledalei under different conditions. The results could aid molecular biology and gene function research on Kobresia and other related species.
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Affiliation(s)
- Haoyang Sun
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Chunping Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Siyu Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Jiaxin Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Shuo Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Xin Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Cai Gao
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Rongchen Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Nan Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Jing Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Xueqing He
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
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Venzhik Y, Deryabin A, Zhukova K. Au-Based Nanoparticles Enhance Low Temperature Tolerance in Wheat by Regulating Some Physiological Parameters and Gene Expression. PLANTS (BASEL, SWITZERLAND) 2024; 13:1261. [PMID: 38732476 PMCID: PMC11085431 DOI: 10.3390/plants13091261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/16/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
One of the key problems of biology is how plants adapt to unfavorable conditions, such as low temperatures. A special focus is placed on finding ways to increase tolerance in important agricultural crops like wheat. Au-based nanoparticles (Au-NPs) have been employed extensively in this area in recent years. Au-NPs can be produced fast and easily using low-cost chemical reagents. When employed in microdoses, Au-NPs are often non-toxic to plants, animals, and people. In addition, Au-NPs mainly have favorable impacts on plants. In this study, we investigated the effect of Au-NP seed nanopriming (diameter 15.3 nm, Au concentration 5-50 µg mL-1) on cold tolerance, as well as some physiological, biochemical and molecular parameters, of cold-sustainable wheat (Triticum aestivum L.) genotype Zlata. The treatment with Au-NPs improved tolerance to low temperatures in control conditions and after cold hardening. Au-NPs treatment boosted the intensity of growth processes, the quantity of photosynthetic pigments, sucrose in leaves, and the expressions of encoded RuBisCo and Wcor15 genes. The potential mechanisms of Au-NPs' influence on the cold tolerance of wheat varieties were considered.
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Affiliation(s)
- Yuliya Venzhik
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (A.D.); (K.Z.)
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Li Q, Song HL, Zhou T, Pei MN, Wang B, Yan SX, Liu YQ, Wu PJ, Hua YP. Differential Morpho-Physiological, Ionomic, and Phytohormone Profiles, and Genome-Wide Expression Profiling Involving the Tolerance of Allohexaploid Wheat ( Triticum aestivum L.) to Nitrogen Limitation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3814-3831. [PMID: 38329036 DOI: 10.1021/acs.jafc.3c08626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Common wheat (Triticum aestivum L.) is a global staple food, while nitrogen (N) limitation severely hinders plant growth, seed yield, and grain quality of wheat. Genetic variations in the responses to low N stresses among allohexaploid wheat (AABBDD, 2n = 6x = 42) genotypes emphasize the complicated regulatory mechanisms underlying low N tolerance and N use efficiency (NUE). In this study, hydroponic culture, inductively coupled plasma mass spectrometry, noninvasive microtest, high-performance liquid chromatography, RNA-seq, and bioinformatics were used to determine the differential growth performance, ionome and phytohormone profiles, and genome-wide expression profiling of wheat plants grown under high N and low N conditions. Transcriptional profiling of NPFs, NRT2s, CLCs, SLACs/SLAHs, AAPs, UPSs, NIAs, and GSs characterized the core members, such as TaNPF6.3-6D, TaNRT2.3-3D, TaNIA1-6B, TaGLN1;2-4B, TaAAP14-5A/5D, and TaUPS2-5A, involved in the efficient transport and assimilation of nitrate and organic N nutrients. The low-N-sensitivity wheat cultivar XM26 showed obvious leaf chlorosis and accumulated higher levels of ABA, JA, and SA than the low-N-tolerant ZM578 under N limitation. The TaMYB59-3D-TaNPF7.3/NRT1.5-6D module-mediated shoot-to-root translocation and leaf remobilization of nitrate was proposed as an important pathway regulating the differential responses between ZM578 and XM26 to low N. This study provides some elite candidate genes for the selection and breeding of wheat germplasms with low N tolerance and high NUE.
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Affiliation(s)
- Qiong Li
- Department of Brewing Engineering, Moutai Institute, Renhuai 564507, Guizhou, China
| | - Hai-Li Song
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Min-Nan Pei
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Bing Wang
- Department of Brewing Engineering, Moutai Institute, Renhuai 564507, Guizhou, China
| | - Song-Xian Yan
- Department of Resources and Environment, Moutai Institute, Renhuai 564507, Guizhou, China
| | - Yun-Qi Liu
- Zhongguancun Xuyue Non-invasive Micro-test Technology Industrial Alliance, Beijing 10080, China
| | - Peng-Jia Wu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
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Cao L, Zhang Q, Miao R, Zhao X, Ni Y, Li W, Feng R, Yang D. Reference gene selection for quantitative real-time PCR analysis of Hymenopellis radicata under abiotic stress. Fungal Biol 2024; 128:1567-1577. [PMID: 38341262 DOI: 10.1016/j.funbio.2023.11.004] [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: 08/09/2023] [Revised: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 02/12/2024]
Abstract
Hymenopellis radicata (H. radicata) is an edible fungus rich in protein and mineral elements, with high edible and medical value. And reference genes suitable for normalization of qRT-PCR data from this species have not been investigated. In this study, therefore, we selected 11 housekeeping genes common in biology. The expression levels of these housekeeping genes were measured in three different tissues and six different abiotic stress treatments in mycelium. They were evaluated for expression stability using online tools. The results showed that gene ACT could be stable expressed in all samples. The expressions of genes TUB and UBQ10 are the most stable under heat stress, ACT and EF are the most stable genes under salt stress, ACT and TUB are the most stable genes under oxidation stress, RPL6 and EF are the most stable genes under pH condition, ACT and RPB2 are the most stable genes under cadmium stress, and RPB2 and UBC are the most stable genes under drought condition. ACT and PP2A are the most stable genes at different tissue sites. This study is of great help to explore the gene expression pattern of H. radicata, and also provides reference for internal reference gene screening under other conditions.
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Affiliation(s)
- Luping Cao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, Gansu, China
| | - Qin Zhang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu 610299, Sichuan, China
| | - Renyun Miao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu 610299, Sichuan, China
| | - Xu Zhao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu 610299, Sichuan, China.
| | - Yanqing Ni
- College of Food and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China
| | - Wensheng Li
- College of Food and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China
| | - Rencai Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu 610299, Sichuan, China
| | - Delong Yang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, Gansu, China.
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Hussein MAA, Alqahtani MM, Alwutayd KM, Aloufi AS, Osama O, Azab ES, Abdelsattar M, Hassanin AA, Okasha SA. Exploring Salinity Tolerance Mechanisms in Diverse Wheat Genotypes Using Physiological, Anatomical, Agronomic and Gene Expression Analyses. PLANTS (BASEL, SWITZERLAND) 2023; 12:3330. [PMID: 37765494 PMCID: PMC10535590 DOI: 10.3390/plants12183330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
Salinity is a widespread abiotic stress that devastatingly impacts wheat growth and restricts its productivity worldwide. The present study is aimed at elucidating biochemical, physiological, anatomical, gene expression analysis, and agronomic responses of three diverse wheat genotypes to different salinity levels. A salinity treatment of 5000 and 7000 ppm gradually reduced photosynthetic pigments, anatomical root and leaf measurements and agronomic traits of all evaluated wheat genotypes (Ismailia line, Misr 1, and Misr 3). In addition, increasing salinity levels substantially decreased all anatomical root and leaf measurements except sclerenchyma tissue upper and lower vascular bundle thickness compared with unstressed plants. However, proline content in stressed plants was stimulated by increasing salinity levels in all evaluated wheat genotypes. Moreover, Na+ ions content and antioxidant enzyme activities in stressed leaves increased the high level of salinity in all genotypes. The evaluated wheat genotypes demonstrated substantial variations in all studied characters. The Ismailia line exhibited the uppermost performance in photosynthetic pigments under both salinity levels. Additionally, the Ismailia line was superior in the activity of superoxide dismutase (SOD), catalase activity (CAT), peroxidase (POX), and polyphenol oxidase (PPO) enzymes followed by Misr 1. Moreover, the Ismailia line recorded the maximum anatomical root and leaf measurements under salinity stress, which enhanced its tolerance to salinity stress. The Ismailia line and Misr 3 presented high up-regulation of H+ATPase, NHX2 HAK, and HKT genes in the root and leaf under both salinity levels. The positive physiological, anatomical, and molecular responses of the Ismailia line under salinity stress were reflected on agronomic performance and exhibited superior values of all evaluated agronomic traits.
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Affiliation(s)
- Mohammed A. A. Hussein
- Department of Botany (Genetics), Faculty of Agriculture, Suez Canal University, Ismailia 41522, Egypt;
| | - Mesfer M. Alqahtani
- Department of Biological Sciences, Faculty of Science and Humanities, Shaqra University, Ad-Dawadimi 11911, Saudi Arabia;
| | - Khairiah M. Alwutayd
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Abeer S. Aloufi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Omnia Osama
- Environmental Stress Lab (ESL), Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza 12619, Egypt;
| | - Enas S. Azab
- Agricultural Botany Department, Faculty of Agriculture, Suez Canal University, Ismailia 41522, Egypt;
| | - Mohamed Abdelsattar
- Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza 12619, Egypt;
| | - Abdallah A. Hassanin
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Salah A. Okasha
- Department of Agronomy, Faculty of Agriculture, Suez Canal University, Ismailia 41522, Egypt
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Renganathan VG, Renuka R, Vanniarajan C, Raveendran M, Elangovan A. Selection and validation of reliable reference genes for quantitative real-time PCR in Barnyard millet (Echinochloa spp.) under varied abiotic stress conditions. Sci Rep 2023; 13:15573. [PMID: 37731036 PMCID: PMC10511452 DOI: 10.1038/s41598-023-40526-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 08/11/2023] [Indexed: 09/22/2023] Open
Abstract
Quantitative real-time polymerase chain reaction (RT-qPCR) using a stable reference gene is widely used for gene expression research. Barnyard millet (Echinochloa spp.) is an ancient crop in Asia and Africa that is widely cultivated for food and fodder. It thrives well under drought, salinity, cold, and heat environmental conditions, besides adapting to any soil type. To date, there are no gene expression studies performed to identify the potential candidate gene responsible for stress response in barnyard millet, due to lack of reference gene. Here, 10 candidate reference genes, Actin (ACT), α-tubulin (α-TUB), β-tubulin (β-TUB), RNA pol II (RP II), elongation factor-1 alpha (EF-1α), adenine phosphoribosyltransferase (APRT), TATA-binding protein-like factor (TLF), ubiquitin-conjugating enzyme 2 (UBC2), ubiquitin-conjugating enzyme E2L5 (UBC5) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), were selected from mRNA sequences of E. crus-galli and E. colona var frumentacea. Five statistical algorithms (geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder) were applied to determine the expression stabilities of these genes in barnyard millet grown under four different abiotic stress (drought, salinity, cold and heat) exposed at different time points. The UBC5 and ɑ-TUB in drought, GAPDH in salinity, GAPDH and APRT in cold, and EF-1α and RP II in heat were the most stable reference genes, whereas ß-TUB was the least stable irrespective of stress conditions applied. Further Vn/Vn + 1 analysis revealed two reference genes were sufficient to normalize gene expression across all sample sets. The suitability of identified reference genes was validated with Cu-ZnSOD (SOD1) in the plants exposed to different abiotic stress conditions. The results revealed that the relative quantification of the SOD1 gene varied according to reference genes and the number of reference genes used, thus highlighting the importance of the choice of a reference gene in such experiments. This study provides a foundational framework for standardizing RT-qPCR analyses, enabling accurate gene expression profiling in barnyard millet.
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Affiliation(s)
- Vellaichamy Gandhimeyyan Renganathan
- Department of Biotechnology, Centre of Excellence for Innovations, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Raman Renuka
- Department of Biotechnology, Centre of Excellence for Innovations, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India.
| | - Chockalingam Vanniarajan
- Anbil Dharmalingam Agricultural College & Research Institute, Tamil Nadu Agricultural University, Tiruchirappalli, India
| | - Muthurajan Raveendran
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Allimuthu Elangovan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
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Alyahya N, Taybi T. Comparative transcriptomic profiling reveals differentially expressed genes and important related metabolic pathways in shoots and roots of a Saudi wheat cultivar (Najran) under salinity stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1225541. [PMID: 37588415 PMCID: PMC10425591 DOI: 10.3389/fpls.2023.1225541] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/28/2023] [Indexed: 08/18/2023]
Abstract
High salinity of soil is a threatening constraint for agricultural output worldwide. The adverse effects of salt stress on plants can be revealed in different manners, from phenotypic to genetic changes. A comparative RNA-Sequencing analysis was done in roots and shoots of bread wheat, Najran cultivar between plants grown under unstressed control condition (0 mM NaCl) and salt treatment (200 mM NaCl). More than 135 million and 137 million pair-end reads were obtained from root and shoot samples, respectively. Of which, the mapped reads to Triticum aestivum genome IWGSC_V51 ranged from 83.9% to 85% in the root and 71.6% to 79% in the shoot. Interestingly, a comparison of transcriptomic profiling identified that total number of significantly differentially expressed genes (DEGs) examined in the roots was much higher than that found in the shoots under NaCl treatment, 5829 genes were differentially expressed in the roots whereas 3495 genes in the shoots. The salt-induced change in the transcriptome was confirmed by RT-qPCR using a set of randomly selected genes. KEGG enrichment analysis classified all DEGs in both roots and shoots into 25 enriched KEGG pathways from three main KEGG classes: Metabolism, organismal systems and genetic information processing. According to that, the most significantly regulated pathways in the root and shoot tissues were glutathione metabolism and biosynthesis of secondary metabolites such as phenylpropanoids and galactose metabolism suggesting that these pathways might participate in wheat salt tolerance. The findings highlight the importance of the control of oxidative stress via Glutathione and phenylpropanoids and the regulation of galactose metabolism in the roots and shoots for salt-tolerance in wheat. They open promising prospects for engineering salt-tolerance in this important crop via targeted improvement of the regulation of key genes in the production of these compounds.
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Affiliation(s)
- Norah Alyahya
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- Department of Biology, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Tahar Taybi
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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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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Lu Y, Fricke W. Changes in root hydraulic conductivity in wheat (Triticum aestivum L.) in response to salt stress and day/night can best be explained through altered activity of aquaporins. PLANT, CELL & ENVIRONMENT 2023; 46:747-763. [PMID: 36600451 PMCID: PMC10107167 DOI: 10.1111/pce.14535] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/07/2022] [Accepted: 01/01/2023] [Indexed: 05/27/2023]
Abstract
Salt stress reduces plant water flow during day and night. It is not known to which extent root hydraulic properties change in parallel. To test this idea, hydroponically grown wheat plants were grown at four levels of salt stress (50, 100, 150 and 200 mM NaCl) for 5-8d before harvest (d14-18) and subjected to a range of analyses to determine diurnal changes in hydraulic conductivity (Lp) at cell, root and plant level. Cell pressure probe analyses showed that the Lp of cortex cells was differentially affected by salt stress during day and night, and that the response to salt stress differed between the main axis of roots and lateral roots. The Aquaporin (AQP) inhibitor H2 O2 reduced Lp to a common, across treatments, level as observed in salt-stressed plants during the night. Analyses of transpiring plants and exuding root systems provided values of root Lp which were in the same range as values modeled based on cell-Lp. The results can best be explained through a change in root Lp in response to salt stress and day/night, which results from an altered activity of AQPs. qPCR gene expression analyses point to possible candidate AQP isoforms.
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Affiliation(s)
- Yingying Lu
- School of Biology and Environmental SciencesUniversity College DublinDublinIreland
| | - Wieland Fricke
- School of Biology and Environmental SciencesUniversity College DublinDublinIreland
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Hua YP, Zhang YF, Zhang TY, Chen JF, Song HL, Wu PJ, Yue CP, Huang JY, Feng YN, Zhou T. Low iron ameliorates the salinity-induced growth cessation of seminal roots in wheat seedlings. PLANT, CELL & ENVIRONMENT 2023; 46:567-591. [PMID: 36358019 DOI: 10.1111/pce.14486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/21/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Wheat plants are ubiquitously simultaneously exposed to salinity and limited iron availability caused by soil saline-alkalisation. Through this study, we found that both low Fe and NaCl severely inhibited the growth of seminal roots in wheat seedlings; however, sufficient Fe caused greater growth cessation of seminal roots than low Fe under salt stress. Low Fe improved the root meristematic division activity, not altering the mature cell sizes compared with sufficient Fe under salt stress. Foliar Fe spray and split-root experiments showed that low Fe-alleviating the salinity-induced growth cessation of seminal roots was dependent on local low Fe signals in the roots. Ionomics combined with TEM/X-ray few differences in the root Na+ uptake and vacuolar Na+ sequestration between two Fe levels under salt stress. Phytohormone profiling and metabolomics revealed salinity-induced overaccumulation of ACC/ethylene and tryptophan/auxin in the roots under sufficient Fe than under low Fe. Differential gene expression, pharmacological inhibitor addition and the root growth performance of transgenic wheat plants revealed that the rootward auxin efflux and was responsible for the low Fe-mediated amelioration of the salinity-induced growth cessation of seminal roots. Our findings will provide novel insights into the modulation of crop root growth under salt stress.
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Affiliation(s)
- Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Yi-Fan Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Tian-Yu Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jun-Fan Chen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Hai-Li Song
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Peng-Jia Wu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Cai-Peng Yue
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jin-Yong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying-Na Feng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
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11
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Lu Y, Jeffers R, Raju A, Kenny T, Ratchanniyasamu E, Fricke W. Does night-time transpiration provide any benefit to wheat (Triticum aestivum L.) plants which are exposed to salt stress? PHYSIOLOGIA PLANTARUM 2023; 175:e13839. [PMID: 36511643 PMCID: PMC10107941 DOI: 10.1111/ppl.13839] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/09/2022] [Indexed: 05/27/2023]
Abstract
The study aimed to test whether night-time transpiration provides any potential benefit to wheat plants which are subjected to salt stress. Hydroponically grown wheat plants were grown at four levels of salt stress (50, 100, 150, and 200 mM NaCl) for 5-8 days prior to harvest (day 14-18). Salt stress caused large decreases in transpiration and leaf elongation rates during day and night. The quantitative relation between the diurnal use of water for transpiration and leaf growth was comparatively little affected by salt. Night-time transpirational water loss occurred predominantly through stomata in support of respiration. Diurnal gas exchange and leaf growth were functionally linked to each other through the provision of resources (carbon, energy) and an increase in leaf surface area. Diurnal rates of water use associated with leaf cell expansive growth were highly correlated with the water potential of the xylem, which was dominated by the tension component. The tissue-specific expression level of nine candidate aquaporin genes in elongating and mature leaf tissue was little affected by salt stress or day/night changes. Growing plants under conditions of reduced night-time transpirational water loss by increasing the relative humidity (RH) during the night to 95% had little effect on the growth response to salt stress, nor was the accumulation of Na+ and Cl- in shoot tissue altered. We conclude that night-time gas exchange supports the growth in leaf area over a 24 h day/night period. Night-time transpirational water loss neither decreases nor increases the tolerance to salt stress in wheat.
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Affiliation(s)
- Yingying Lu
- School of Biology and Environmental SciencesUniversity College DublinDublinRepublic of Ireland
| | - Ruth Jeffers
- School of Biology and Environmental SciencesUniversity College DublinDublinRepublic of Ireland
| | - Anakha Raju
- School of Biology and Environmental SciencesUniversity College DublinDublinRepublic of Ireland
| | - Tamara Kenny
- School of Biology and Environmental SciencesUniversity College DublinDublinRepublic of Ireland
| | | | - Wieland Fricke
- School of Biology and Environmental SciencesUniversity College DublinDublinRepublic of Ireland
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12
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Hu A, Yang X, Zhu J, Wang X, Liu J, Wang J, Wu H, Zhang H, Zhang H. Selection and validation of appropriate reference genes for RT-qPCR analysis of Nitraria sibirica under various abiotic stresses. BMC PLANT BIOLOGY 2022; 22:592. [PMID: 36526980 PMCID: PMC9758788 DOI: 10.1186/s12870-022-03988-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Nitraria sibirica Pall. is a halophytic shrub with strong environmental adaptability that can survive in extremely saline-alkali and drought-impacted environments. Gene expression analysis aids in the exploration of the molecular mechanisms of plant responses to abiotic stresses. RT-qPCR is the most common technique for studying gene expression. Stable reference genes are a prerequisite for obtaining accurate target gene expression results in RT-qPCR analysis. RESULTS In this study, a total of 10 candidate reference genes were selected from the transcriptome of N. sibirica, and their expression stability in leaves and roots under different treatment conditions (salt, alkali, drought, cold, heat and ABA) was evaluated with the geNorm, NormFinder, BestKeeper, comparative ΔCt and RefFinder programs. The results showed that the expression stability of the candidate reference genes was dependent on the tissue and experimental conditions tested. ACT7 combined with R3H, GAPDH, TUB or His were the most stable reference genes in the salt- or alkali-treated leaves, salt-treated roots and drought-treated roots, respectively; R3H and GAPDH were the most suitable combination for drought-treated leaves, heat-treated root samples and ABA-treated leaves; DIM1 and His maintained stable expression in roots under alkali stress; and TUB combined with R3H was stable in ABA-treated roots. TBCB and GAPDH exhibited stable expression in heat-treated leaves; TBCB, R3H, and ERF3A were stable in cold-treated leaves; and the three most stable reference genes for cold-treated roots were TBCB, ACT11 and DIM1. The reliability of the selected reference genes was further confirmed by evaluating the expression patterns of the NsP5CS gene under the six treatment conditions. CONCLUSION This study provides a theoretical reference for N. sibirica gene expression standardization and quantification under various abiotic stress conditions and will help to reveal the molecular mechanisms that confer stress tolerance to N. sibirica.
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Affiliation(s)
- Aishuang Hu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, 063299, Tangshan, China
- Hebei saline-alkali Land Greening Technology Innovation Center, 063299, Tangshan, China
| | - Xiuyan Yang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Jianfeng Zhu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Xiuping Wang
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, 063299, Tangshan, China
- Hebei saline-alkali Land Greening Technology Innovation Center, 063299, Tangshan, China
| | - Jiaxin Liu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Jiping Wang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Haiwen Wu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Huilong Zhang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China.
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China.
| | - Huaxin Zhang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China.
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China.
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13
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Hua YP, Chen JF, Zhou T, Zhang TY, Shen DD, Feng YN, Guan PF, Huang SM, Zhou ZF, Huang JY, Yue CP. Multiomics reveals an essential role of long-distance translocation in regulating plant cadmium resistance and grain accumulation in allohexaploid wheat (Triticum aestivum). JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7516-7537. [PMID: 36063365 DOI: 10.1093/jxb/erac364] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Cadmium (Cd) is a highly toxic heavy metal that readily enters cereals, such as wheat, via the roots and is translocated to the shoots and grains, thereby posing high risks to human health. However, the vast and complex genome of allohexaploid wheat makes it challenging to understand Cd resistance and accumulation. In this study, a Cd-resistant cultivar of wheat, 'ZM1860', and a Cd-sensitive cultivar, 'ZM32', selected from a panel of 442 accessions, exhibited significantly different plant resistance and grain accumulation. We performed an integrated comparative analysis of the morpho-physiological traits, ionomic and phytohormone profiles, genomic variations, transcriptomic landscapes, and gene functionality in order to identify the mechanisms underlying these differences. Under Cd toxicity, 'ZM1860' outperformed 'ZM32', which showed more severe leaf chlorosis, poorer root architecture, higher accumulation of reactive oxygen species, and disordered phytohormone homeostasis. Ionomics showed that 'ZM32' had a higher root-to-shoot translocation coefficient of Cd and accumulated more Cd in the grains than 'ZM1860'. Whole-genome re-sequencing (WGS) and transcriptome sequencing identified numerous DNA variants and differentially expressed genes involved in abiotic stress responses and ion transport between the two genotypes. Combined ionomics, transcriptomics, and functional gene analysis identified the plasma membrane-localized heavy metal ATPase TaHMA2b-7A as a crucial Cd exporter regulating long-distance Cd translocation in wheat. WGS- and PCR-based analysis of sequence polymorphisms revealed a 25-bp InDel site in the promoter region of TaHMA2b-7A, and this was probably responsible for the differential expression. Our multiomics approach thus enabled the identification of a core transporter involved in long-distance Cd translocation in wheat, and it may provide an elite genetic resource for improving plant Cd resistance and reducing grain Cd accumulation in wheat and other cereal crops.
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Affiliation(s)
- Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jun-Fan Chen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Tian-Yu Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Dan-Dan Shen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ying-Na Feng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Pan-Feng Guan
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shao-Min Huang
- Institute of Plant Nutrient and Environmental Resources, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Zheng-Fu Zhou
- Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Jin-Yong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Cai-Peng Yue
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
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14
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Sowa S, Sozoniuk M, Toporowska J, Kowalczyk K, Paczos-Grzęda E. Reference genes expression stability in Avena sativa L. during compatible and incompatible interactions with Puccinia graminis. Sci Rep 2022; 12:18369. [PMID: 36319744 PMCID: PMC9626582 DOI: 10.1038/s41598-022-22993-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/21/2022] [Indexed: 12/31/2022] Open
Abstract
A reliable qPCR experiment requires the selection of reference genes with a stable level of expression in a given experimental system. This study attempts to determine the reference genes (RGs) for the A. sativa-P. graminis experimental setup. We evaluated nine candidate reference genes in A. sativa (oat line Pg4 and the cultivar Kasztan) during compatible and incompatible interactions with different pathotypes of Puccinia graminis 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). We found that the most appropriate combination of RGs for RT-qPCR data normalization were HNR (heterogeneous nuclear ribonucleoprotein 27C) + EF1A (elongation factor 1-alpha) + EIF4A (eukaryotic initiation factor 4A-3). The worst candidates for normalization in this dataset were CYP (cyclophilin) and TUA (alpha tubulin). Identified reference genes are suitable candidates for the standardization of gene expression studies in the A. sativa-P. graminis interaction system and potentially other related pathogens. To date, this is the first report of RGs selection in this pathosystem.
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Affiliation(s)
- Sylwia Sowa
- grid.411201.70000 0000 8816 7059Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Magdalena Sozoniuk
- grid.411201.70000 0000 8816 7059Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Joanna Toporowska
- grid.411201.70000 0000 8816 7059Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Krzysztof Kowalczyk
- grid.411201.70000 0000 8816 7059Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Edyta Paczos-Grzęda
- grid.411201.70000 0000 8816 7059Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
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15
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Chen JF, Liu Y, Zhang TY, Zhou ZF, Huang JY, Zhou T, Hua YP. Integrated physiological and transcriptional dissection reveals the core genes involving nutrient transport and osmoregulatory substance biosynthesis in allohexaploid wheat seedlings under salt stress. BMC PLANT BIOLOGY 2022; 22:502. [PMID: 36289462 PMCID: PMC9608917 DOI: 10.1186/s12870-022-03887-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Soil salinization has become a global problem restricting the seed yield and quality of crops, including wheat (Triticum aestivum L.). Salinity significantly alters plant morphology and severely disrupts physiological homeostasis. Salt tolerance of wheat has been widely studied whereas core ion transporters responsive to salt stress remain elusive. RESULTS In this study, the wheat seedlings were subjected to salinity toxicity for morpho-physiological and transcriptomic analysis of wheat salt tolerance. There was a inversely proportional relationship between salt concentrations and morpho-physiological parameters. Under the condition of 100 mM NaCl, the H2O2, O2-, MDA content and membrane permeability were significantly increased whereas the chlorophyll content was markedly decreased. Under salt stress, a larger proportion of Na+ was partitioned in the roots than in the shoots, which had a lower Na+/K+ ratio and proline content. Salt stress also obviously affected the homeostasis of other cations. Genome-wide transcriptomic analysis showed that a total of 2,807 and 5,570 differentially expressed genes (DEGs) were identified in the shoots and roots, respectively. Functionality analysis showed that these DEGs were mainly enriched in the KEGG pathways related to carbon metabolism, phenylalanine, and amino acid biosynthesis, and were primarily enriched in the GO terms involving proline metabolism and redox processes. The Na+ transporter genes were upregulated under salt stress, which repressed the gene expression of the K+ transporters. Salt stress also significantly elevated the expression of the genes involved in osmoregulation substances biosynthesis, and obviously affected the expression profiling of other cation transporters. Co-expression network analysis identified TaNHX6-D5/TaNHX4-B7 and TaP5CS2-B3 potentially as core members regulating wheat salt tolerance. CONCLUSIONS These results might help us fully understand the morpho-physiological and molecular responses of wheat seedlings to salt stress, and provide elite genetic resources for the genetic modification of wheat salt tolerance.
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Affiliation(s)
- Jun-fan Chen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 China
| | - Ying Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 China
| | - Tian-yu Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 China
| | - Zheng-fu Zhou
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 China
| | - Jin-yong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 China
| | - Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 China
| | - Ying-peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 China
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16
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Cheng SS, Ku YS, Cheung MY, Lam HM. Identification of stably expressed reference genes for expression studies in Arabidopsis thaliana using mass spectrometry-based label-free quantification. FRONTIERS IN PLANT SCIENCE 2022; 13:1001920. [PMID: 36247637 PMCID: PMC9557097 DOI: 10.3389/fpls.2022.1001920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Arabidopsis thaliana has been used regularly as a model plant in gene expression studies on transcriptional reprogramming upon pathogen infection, such as that by Pseudomonas syringae pv. tomato DC3000 (Pst DC3000), or when subjected to stress hormone treatments including jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA). Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) has been extensively employed to quantitate these gene expression changes. However, the accuracy of the quantitation is largely dependent on the stability of the expressions of reference genes used for normalization. Recently, RNA sequencing (RNA-seq) has been widely used to mine stably expressed genes for use as references in RT-qPCR. However, the amplification step in RNA-seq creates an intrinsic bias against those genes with relatively low expression levels, and therefore does not provide an accurate quantification of all expressed genes. In this study, we employed mass spectrometry-based label-free quantification (LFQ) in proteomic analyses to identify those proteins with abundances unaffected by Pst DC3000 infection. We verified, using RT-qPCR, that the levels of their corresponding mRNAs were also unaffected by Pst DC3000 infection. Compared to commonly used reference genes for expression studies in A. thaliana upon Pst DC3000 infection, the candidate reference genes reported in this study generally have a higher expression stability. In addition, using RT-qPCR, we verified that the mRNAs of the candidate reference genes were stably expressed upon stress hormone treatments including JA, SA, and ABA. Results indicated that the candidate genes identified here had stable expressions upon these stresses and are suitable to be used as reference genes for RT-qPCR. Among the 18 candidate reference genes reported in this study, many of them had greater expression stability than the commonly used reference genes, such as ACT7, in previous studies. Here, besides proposing more appropriate reference genes for Arabidopsis expression studies, we also demonstrated the capacity of mass spectrometry-based LFQ to quantify protein abundance and the possibility to extend protein expression studies to the transcript level.
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17
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Validation of Appropriate Reference Genes for qRT–PCR Normalization in Oat (Avena sativa L.) under UV-B and High-Light Stresses. Int J Mol Sci 2022; 23:ijms231911187. [PMID: 36232488 PMCID: PMC9570368 DOI: 10.3390/ijms231911187] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
Oat is a food and forage crop species widely cultivated worldwide, and it is also an important forage grass in plateau regions of China, where there is a high level of ultraviolet radiation and sunlight. Screening suitable reference genes for oat under UV-B and high-light stresses is a prerequisite for ensuring the accuracy of real-time quantitative PCR (qRT–PCR) data used in plant adaptation research. In this study, eight candidate reference genes (sulfite oxidase, SUOX; victorin binding protein, VBP; actin-encoding, Actin1; protein PSK SIMULATOR 1-like, PSKS1; TATA-binding protein 2-like, TBP2; ubiquitin-conjugating enzyme E2, UBC2; elongation factor 1-alpha, EF1-α; glyceraldehyde-3-phosphate dehydrogenase 1, GAPDH1;) were selected based on previous studies and our oat transcriptome data. The expression stability of these reference genes in oat roots, stems, and leaves under UV-B and high-light stresses was first calculated using three frequently used statistical software (geNorm, NormFinder, and BestKeeper), and then the comprehensive stability of these genes was evaluated using RefFinder. The results showed that the most stably expressed reference genes in the roots, stems, and leaves of oat under UV-B stress were EF1-α, TBP2, and PSKS1, respectively; the most stably expressed reference genes in the roots, stems, and leaves under high-light stress were PSKS1, UBC2, and PSKS1, respectively. PSKS1 was the most stably expressed reference gene in all the samples. The reliability of the selected reference genes was further validated by analysis of the expression of the phenylalanine ammonia-lyase (PAL) gene. This study highlights reference genes for accurate quantitative analysis of gene expression in different tissues of oat under UV-B and high-light stresses.
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18
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Tian D, Xie Q, Deng Z, Xue J, Li W, Zhang Z, Dai Y, Zheng B, Lu T, De Smet I, Guo Y. Small secreted peptides encoded on the wheat ( triticum aestivum L.) genome and their potential roles in stress responses. FRONTIERS IN PLANT SCIENCE 2022; 13:1000297. [PMID: 36212358 PMCID: PMC9532867 DOI: 10.3389/fpls.2022.1000297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
Small secreted peptides (SSPs) are important signals for cell-to-cell communication in plant, involved in a variety of growth and developmental processes, as well as responses to stresses. While a large number of SSPs have been identified and characterized in various plant species, little is known about SSPs in wheat, one of the most important cereal crops. In this study, 4,981 putative SSPs were identified on the wheat genome, among which 1,790 TaSSPs were grouped into 38 known SSP families. The result also suggested that a large number of the putaitive wheat SSPs, Cys-rich peptides in particular, remained to be characterized. Several TaSSP genes were found to encode multiple SSP domains, including CLE, HEVEIN and HAIRPININ domains, and two potentially novel TaSSP family DYY and CRP8CI were identified manually among unpredicted TaSSPs. Analysis on the transcriptomic data showed that a great proportion of TaSSPs were expressed in response to abiotic stresses. Exogenous application of the TaCEPID peptide encoded by TraesCS1D02G130700 enhanced the tolerance of wheat plants to drought and salinity, suggesting porential roles of SSPs in regulating stress responses in wheat.
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Affiliation(s)
- Dongdong Tian
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qi Xie
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Zhichao Deng
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jin Xue
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wei Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zenglin Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yifei Dai
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Tiegang Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
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19
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Mohr T, Horstman J, Gu YQ, Elarabi NI, Abdallah NA, Thilmony R. CRISPR-Cas9 Gene Editing of the Sal1 Gene Family in Wheat. PLANTS 2022; 11:plants11172259. [PMID: 36079639 PMCID: PMC9460255 DOI: 10.3390/plants11172259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022]
Abstract
The highly conserved Sal1 encodes a bifunctional enzyme with inositol polyphosphate-1-phosphatase and 3′ (2′), 5′-bisphosphate nucleotidase activity and has been shown to alter abiotic stress tolerance in plants when disrupted. Precise gene editing techniques were used to generate Sal1 mutants in hexaploid bread wheat. The CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats) Cas9 system with three guide RNAs (gRNAs) was used to inactivate six Sal1 homologous genes within the Bobwhite wheat genome. The resulting mutant wheat plants with all their Sal1 genes disabled had slimmer stems, had a modest reduction in biomass and senesced more slowly in water limiting conditions, but did not exhibit improved yield under drought conditions. Our results show that multiplexed gRNAs enabled effective targeted gene editing of the Sal1 gene family in hexaploid wheat. These Sal1 mutant wheat plants will be a resource for further research studying the function of this gene family in wheat.
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Affiliation(s)
- Toni Mohr
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
| | - James Horstman
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
| | - Yong Q. Gu
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
| | - Nagwa I. Elarabi
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Naglaa A. Abdallah
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Roger Thilmony
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
- Correspondence: ; Tel.: +1-(510)-559-5761
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20
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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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Li L, Li H, Wu L, Qi H. Sulfur dioxide improves drought tolerance through activating Ca 2+ signaling pathways in wheat seedlings. ECOTOXICOLOGY (LONDON, ENGLAND) 2022; 31:852-859. [PMID: 35538264 DOI: 10.1007/s10646-022-02547-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Sulfur dioxide (SO2) and drought are two important co-occurring abiotic stresses affecting the growth and productivity of plants. Here, we will investigate the role of Ca2+ in regulating antioxidant defense during drought or SO2/drought stress, and the effect of SO2 pretreatment on the physiological response of wheat seedlings to drought stress. The results showed that exogenous Ca2+ increased the activities of SOD, CAT and POD, and reduced the contents of H2O2 and MDA in drought-treated wheat seedlings, suggesting Ca2+ could improve drought tolerance by promoting antioxidant defense in plants. Moreover, exogenous Ca2+ up-regulated the expression of two stress-responsive transcription factor (TF) genes, ERF1 and MYB30, to cope with drought stress. Exposure of wheat seedlings to 10 mg m-3 SO2 significantly enhanced the activities of SOD, CAT and POD. The contents of H2O2 and MDA remained at control levels, showing that SO2 at this concentration led to an activation of the antioxidant defense system and did not cause oxidative damage to the seedlings. Furthermore, 10 mg m-3 SO2 pretreatment increased the expression of CCaMK and CPK10, enhanced the activities of SOD and POD, and reduced the accumulation of H2O2 and MDA in drought-treated wheat seedlings, showing a role of SO2 in protection of plants against drought stress. However, with removal of Ca2+ by spraying EGTA on the SO2-pretreated wheat seedlings, the expression of transcription factor genes and activities of antioxidant enzymes were decreased, and the contents of H2O2 and MDA enhanced to the level of drought treatment alone, suggesting a role of Ca2+ in the SO2-induced alleviation of drought stress. Together, these results indicated that exogenous Ca2+ increased defense-related gene expression and enzyme activity in response to drought stress, and that pre-exposure to appropriate levels of SO2 could improve drought tolerance through activation of Ca2+ signaling pathways in plants. This study would provide new strategy for enhancing plant resistance to environmental stress.
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Affiliation(s)
- Lihong Li
- Department of Chemistry and Chemical Engineering, JinzhongUniversity, Yuci, China
| | - Haiyan Li
- Department of Biology, Taiyuan Normal University, Yuci, China
| | - Lihua Wu
- Department of Biology, Taiyuan Normal University, Yuci, China
| | - Hongxue Qi
- Department of Chemistry and Chemical Engineering, JinzhongUniversity, Yuci, China.
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22
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Ptošková K, Szecówka M, Jaworek P, Tarkowská D, Petřík I, Pavlović I, Novák O, Thomas SG, Phillips AL, Hedden P. Changes in the concentrations and transcripts for gibberellins and other hormones in a growing leaf and roots of wheat seedlings in response to water restriction. BMC PLANT BIOLOGY 2022; 22:284. [PMID: 35676624 PMCID: PMC9178827 DOI: 10.1186/s12870-022-03667-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Bread wheat (Triticum aestivum) is a major source of nutrition globally, but yields can be seriously compromised by water limitation. Redistribution of growth between shoots and roots is a common response to drought, promoting plant survival, but reducing yield. Gibberellins (GAs) are necessary for shoot and root elongation, but roots maintain growth at lower GA concentrations compared with shoots, making GA a suitable hormone for mediating this growth redistribution. In this study, the effect of progressive drought on GA content was determined in the base of the 4th leaf and root tips of wheat seedlings, containing the growing regions, as well as in the remaining leaf and root tissues. In addition, the contents of other selected hormones known to be involved in stress responses were determined. Transcriptome analysis was performed on equivalent tissues and drought-associated differential expression was determined for hormone-related genes. RESULTS After 5 days of applying progressive drought to 10-day old seedlings, the length of leaf 4 was reduced by 31% compared with watered seedlings and this was associated with significant decreases in the concentrations of bioactive GA1 and GA4 in the leaf base, as well as of their catabolites and precursors. Root length was unaffected by drought, while GA concentrations were slightly, but significantly higher in the tips of droughted roots compared with watered plants. Transcripts for the GA-inactivating gene TaGA2ox4 were elevated in the droughted leaf, while those for several GA-biosynthesis genes were reduced by drought, but mainly in the non-growing region. In response to drought the concentrations of abscisic acid, cis-zeatin and its riboside increased in all tissues, indole-acetic acid was unchanged, while trans-zeatin and riboside, jasmonate and salicylic acid concentrations were reduced. CONCLUSIONS Reduced leaf elongation and maintained root growth in wheat seedlings subjected to progressive drought were associated with attenuated and increased GA content, respectively, in the growing regions. Despite increased TaGA2ox4 expression, lower GA levels in the leaf base of droughted plants were due to reduced biosynthesis rather than increased catabolism. In contrast to GA, the other hormones analysed responded to drought similarly in the leaf and roots, indicating organ-specific differential regulation of GA metabolism in response to drought.
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Affiliation(s)
- Klára Ptošková
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Marek Szecówka
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Pavel Jaworek
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Ivan Petřík
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Iva Pavlović
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Stephen G Thomas
- Department of Plant Science, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Andrew L Phillips
- Department of Plant Science, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Peter Hedden
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic.
- Department of Plant Science, Rothamsted Research, Harpenden, AL5 2JQ, UK.
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23
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de Oliveira LF, Piovezani AR, Ivanov DA, Yoshida L, Segal Floh EI, Kato MJ. Selection and validation of reference genes for measuring gene expression in Piper species at different life stages using RT-qPCR analysis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 171:201-212. [PMID: 35007951 DOI: 10.1016/j.plaphy.2021.12.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/03/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
The secondary metabolism of Piper species is known to produce a myriad of natural products from various biosynthetic pathways which, represent a rich source of previously uncharacterized chemical compounds. The determination of gene expression profiles in multiple tissue/organ samples could provide valuable clues towards understanding the potential biological functions of chemical changes in these plants. Studies on gene expression by RT-qPCR require particularly careful selection of suitable reference genes as a control for normalization. Here, we provide a study for the identification of reliable reference genes in P. arboreum, P. gaudichaudianum, P. malacophyllum, and P. tuberculatum, at two different life stages: 2-month-old seedlings and adult plants. To do this, annotated sequences were recovered from transcriptome datasets of the above listed Piper spp. These sequences were subjected to expression analysis using RT-qPCR, followed by analysis using the geNorm and NormFinder algorithms. A set of five genes were identified showing stable expression: ACT7 (Actin-7), Cyclophilin (Peptidyl-prolyl cis-trans isomerase), EF1α (Elongation factor 1-alpha), RNABP (RNA-binding protein), and UBCE (Ubiquitin conjugating enzyme). The universality of these genes was then validated using two target genes, ADC (arginine decarboxylase) and SAMDC (S-adenosylmethionine decarboxylase), which are involved in the biosynthesis of polyamines. We showed that normalization genes varied according to Piper spp., and we provide a list of recommended pairs of the best combination for each species. This study provides the first set of suitable candidate genes for gene expression studies in the four Piper spp. assayed, and the findings will facilitate subsequent transcriptomic and functional gene research.
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Affiliation(s)
- Leandro Francisco de Oliveira
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua Do Matão, 277, 05508-090, São Paulo, SP, Brazil
| | - Amanda Rusiska Piovezani
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, 05508-900, São Paulo, Brazil; Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua Do Matão, 277, 05508-090, São Paulo, SP, Brazil
| | - Dimitre A Ivanov
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, 05508-900, São Paulo, Brazil; Department of Biology, University of Western Ontario, 1151 Richmond St, London, ON, Canada, N6A 3K7
| | - Leonardo Yoshida
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, 05508-900, São Paulo, Brazil
| | - Eny Iochevet Segal Floh
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua Do Matão, 277, 05508-090, São Paulo, SP, Brazil.
| | - Massuo Jorge Kato
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, 05508-900, São Paulo, Brazil
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Fu Y, Niu F, Jia H, Wang Y, Guo B, Wei Y. Reference gene selection for real-time quantitative PCR assays in different tissues of Huperzia serrata based on full-length transcriptome sequencing. PLANT DIRECT 2021; 5:e362. [PMID: 34849452 PMCID: PMC8611506 DOI: 10.1002/pld3.362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
Huperzia serrata (H. serrata) produces various types of effective lycopodium alkaloids, especially Huperzine A (HupA), which is a promising drug for the treatment of Alzheimer's disease. Numerous studies focused on the chemistry, bioactivities, toxicology, and clinical trials of HupA; however, the public genomic and transcriptomic resources are very limited for H. serrata research, especially for the selection of optimum reference genes. Based on the full-length transcriptome datasets and previous studies, 10 traditional and three new candidate reference genes were selected in different tissue of H. serrata. Then, two optimal reference genes GAPDHB and HisH2A were confirmed by four analysis methods. In order to further verify the accuracy of the two reference genes, they were used to analyze the expression patterns of four HupA-biosynthetic genes (lysine decarboxylas, RS-norcoclaurine 6-O-methyltransferase, cytochrome P45072A1, and copper amine oxidase). The data suggested that the expression pattern of HupA-biosynthetic genes was consistent with them in transcriptome sequencing in different tissue of H. serrata. This study identified that GAPDHB and HisH2A provides the reliable normalization for analyzing the HupA biosynthetic gene expression in different tissues of H. serrata on the transcriptional level.
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Affiliation(s)
- Yanping Fu
- Key Laboratory of Biotechnology of Shannxi Province, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life ScienceNorthwest UniversityXi'anChina
| | - Fei Niu
- Key Laboratory of Biotechnology of Shannxi Province, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life ScienceNorthwest UniversityXi'anChina
| | - Hui Jia
- Key Laboratory of Biotechnology of Shannxi Province, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life ScienceNorthwest UniversityXi'anChina
| | - Yanli Wang
- Key Laboratory of Biotechnology of Shannxi Province, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life ScienceNorthwest UniversityXi'anChina
| | - Bin Guo
- Key Laboratory of Biotechnology of Shannxi Province, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life ScienceNorthwest UniversityXi'anChina
| | - Yahui Wei
- Key Laboratory of Biotechnology of Shannxi Province, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life ScienceNorthwest UniversityXi'anChina
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25
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Selection and Evaluation of Potential Reference Genes for Quantitative Real-Time PCR in Agaricus blazei Based on Transcriptome Sequencing Data. BIOMED RESEARCH INTERNATIONAL 2021. [DOI: 10.1155/2021/6661842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Quantitative real-time PCR (qRT-PCR) is widely used to detect gene expression due to its high sensitivity, high throughput, and convenience. The accurate choice of reference genes is required for normalization of gene expression in qRT-PCR analysis. In order to identify the optimal candidates for gene expression analysis using qRT-PCR in Agaricus blazei, we studied the potential reference genes in this economically important edible fungus. In this study, transcriptome datasets were used as source for identification of candidate reference genes. And 27 potential reference genes including 21 newly stable genes, three classical housekeeping genes, and homologous genes of three ideal reference genes in Volvariella volvacea, were screened based on transcriptome datasets of A. blazei and previous studies. The expression stability of these genes was investigated by qRT-PCR analysis and further evaluated by four software packages, geNorm, NormFinder, BestKeeper, and RefFinder. Among these candidates, α-TUB (Tubulin alpha) and Cox5a (COX5A subunit VA of cytochrome c oxidase) were revealed as the most stable in fruit body, and suitable for 5 different developmental stages. α-TUB and ATP3 (ATP3 gamma subunit of the F1 sector of mitochondrial F1F0 ATP synthase) showed the most stable expression in stipe tissues and, Uqcrc (core subunit of the ubiquinol-cytochrome c reductase complex) and PUP3 (20S proteasome subunit beta 3) performed well in pileus tissues during the process of A. blazei development, while GAPDH (glyceraldehyde-3-phosphate dehydrogenase) was among the least stable genes in all sample sets. Finally, the Ableln3 (homology of eln3 gene of Coprinus cinereus) was adopted to validate the reliability of these stable and unstable reference genes, indicating that the use of unsuitable reference genes as internal controls could change the target gene’s expression pattern. This study can provide guidance for choosing reference genes for analyzing the expression pattern of target genes and facilitate the functional genomic investigation on fruit body formation and development, as well as stipe elongation and pileus expansion in A. blazei.
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26
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Li LH, Yi HL, Qi HX. Sulfur dioxide enhance drought tolerance of wheat seedlings through H 2S signaling. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 207:111248. [PMID: 32927156 DOI: 10.1016/j.ecoenv.2020.111248] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/09/2020] [Accepted: 08/24/2020] [Indexed: 06/11/2023]
Abstract
Drought is one of the most common factors that limit plant growth and productivity. Sulfur dioxide (SO2) has recently been found to play a benefical role in protection of plants against environmental stress. In this study, we investigated the effect of SO2 on the physiological and molecular response of wheat seedlings to drought stress. Pretreatment with 10 mg/m3 SO2 significantly increased the survival rate and relative water content (RWC) of wheat seedlings under drought stress, indicating that pre-exposure to appropriate level of SO2 could enhance drought tolerance of plants. These responses were related to the enhanced proline accumulation in the drought-treated wheat seedlings that induced by SO2 pretreatment. Meanwhile, SO2 pretreatment increased the activities of superoxide dismutase (SOD) and peroxidase (POD), and effectively reduced the content of hydrogen peroxide (H2O2) and malondialdehyde (MDA) in drought-treated wheat seedlings, suggesting SO2 could alleviate drought-induced oxidative damage by enhancing antioxidant defense system in plants. Expression analysis of transcription factor genes also showed that SO2 pretreatment decreased the expression of TaNAC69, but the expression of TaERF1 and TaMYB30 changed slightly and maintained at higher levels in wheat seedlings in response to drought stress. Furthermore, SO2 pretreatment triggered marked accumulation of hydrogen sulfide (H2S) in wheat seedlings under drought stress. When scavenged H2S by spraying Hypotaurine (HT), the activities of antioxidant enzymes and the expression of transcription factor genes were decreased, and the content of H2O2 and MDA increased to the level of drought treatment alone, suggesting a regulatory role of SO2-induced H2S in plant adaptation to drought stress. Together, this study indicated that SO2 enhanced drought tolerance of wheat seedlings through H2S signaling, and provided new strategy for enhancing plant tolerance to drought stress.
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Affiliation(s)
- Li-Hong Li
- College of Chemistry and Chemical Engineering, JinzhongUniversity, Yuci, China
| | - Hui-Lan Yi
- School of Life Science, Shanxi University, Taiyuan, China
| | - Hong-Xue Qi
- College of Chemistry and Chemical Engineering, JinzhongUniversity, Yuci, China.
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27
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RNA-Seq Time Series of Vitis vinifera Bud Development Reveals Correlation of Expression Patterns with the Local Temperature Profile. PLANTS 2020; 9:plants9111548. [PMID: 33198137 PMCID: PMC7698159 DOI: 10.3390/plants9111548] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022]
Abstract
Plants display sophisticated mechanisms to tolerate challenging environmental conditions and need to manage their ontogenesis in parallel. Here, we set out to generate an RNA-Seq time series dataset throughout grapevine (Vitis vinifera) early bud development. The expression of the developmental regulator VviAP1 served as an indicator of the progression of development. We investigated the impact of changing temperatures on gene expression levels during the time series and detected a correlation between increased temperatures and a high expression level of genes encoding heat-shock proteins. The dataset also allowed the exemplary investigation of expression patterns of genes from three transcription factor (TF) gene families, namely MADS-box, WRKY, and R2R3-MYB genes. Inspection of the expression profiles from all three TF gene families indicated that a switch in the developmental program takes place in July which coincides with increased expression of the bud dormancy marker gene VviDRM1.
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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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