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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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Liu J, Yang C, Bai M, Yan F, Qin H, Wang R, Wan Y, Li G. Selection and validation of reference genes for RT-qPCR analysis of different organs at various development stages in Caragana intermedia. Open Life Sci 2022; 17:1155-1164. [PMID: 36185405 PMCID: PMC9483831 DOI: 10.1515/biol-2022-0463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/28/2022] [Accepted: 06/14/2022] [Indexed: 11/15/2022] Open
Abstract
Reverse transcription quantitative PCR (RT-qPCR) is a technique widely used to investigate the expression of genes. An appropriate reference gene (RG) is essential for RT-qPCR analysis to obtain accurate and reliable results. Caragana intermedia plays an important role in afforestation as a bush. However, due to the lack of appropriate RGs, the research on development-related genes is limited. In this study, the selection for suitable RGs of different organs at various development stages to normalize the results of RT-qPCR about development-related genes was performed. To test the expression stability across all samples, we used the software algorithms such as geNorm, NormFinder, BestKeeper, and RefFinder to evaluate all the candidate RGs. Our results showed that CiEF1α was the most stable RG with little fluctuation among all samples. In addition, CiGAPDH in roots, CiSKIP1 in stems and leaves, and CiEF1α in different organs were selected as the most stable RGs. To confirm the applicability of the most stable RGs, the relative expression of CiWRKY17 was normalized using different candidate RGs. Taken together, our research laid a foundation for the study of development-related genes in C. intermedia.
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Affiliation(s)
- Jinhua Liu
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Chuang Yang
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Mingzhu Bai
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Feng Yan
- Ordos Forestry and Grassland Development Center, Ordos 017010, P.R. China
| | - Haiying Qin
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Ruigang Wang
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China.,Inner Mongolia Enterprise Key Laboratory of Tree Breeding, Mengshu Ecological Construction Group Co., Ltd., Hohhot 011517, P.R. China.,Inner Mongolia Engineering Research Center for Plant Gene Resources Mining and Molecular Breeding, Inner Mongolia Agricultural University, Hohhot 010021, P.R. China
| | - Yongqing Wan
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Guojing Li
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
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Yang J, Han F, Yang L, Wang J, Jin F, Luo A, Zhao F. Identification of Reference Genes for RT-qPCR Analysis in Gleditsia microphylla under Abiotic Stress and Hormone Treatment. Genes (Basel) 2022; 13:genes13071227. [PMID: 35886010 PMCID: PMC9315665 DOI: 10.3390/genes13071227] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/25/2022] Open
Abstract
Gleditsia microphylla is an important galactomannan gums source plant with characteristics of drought resistance, barren tolerance, and good adaptability. However, the underlying molecular mechanisms of the biological process are not yet fully understood. Real-time quantitative PCR (RT-qPCR) is an accurate and convenient method to quantify the gene expression level and transcription abundance of suitable reference genes. This study aimed to screen the best internal reference genes in G. microphylla under abiotic stresses, hormone treatments, and different tissues. Based on the transcriptome data, twelve candidate reference genes were selected, and ultimately, nine of them were further evaluated by the geNorm, NormFinder, BestKeeper, and RefFinder algorithms. These results show that TATA-binding protein 1 (TBP1)and Eukaryotic translation initiation factor 4A1 (EIF4A1)were the two most stable reference genes, and glyceraldehyde-3-phosphate dehydrogenase A subunit, chloroplastic (GAPA)and glyceraldehyde-3-phosphate dehydrogenase B subunit, chloroplastic (GAPB)were the two most unstable reference genes across all samples under the given experimental conditions. Meanwhile, the most stable reference genes varied among the different groups and tissues. Therefore, this study suggests that it is better to use a specific reference gene for a particular case rather than using a common reference gene.
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Zhao G, Wang M, Gan Y, Gong H, Li J, Zheng X, Liu X, Zhao S, Luo J, Wu H. Identification of suitable reference genes for quantitative reverse transcription PCR in Luffa ( Luffa cylindrica). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:737-747. [PMID: 35592479 PMCID: PMC9110621 DOI: 10.1007/s12298-022-01182-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED Reverse transcription real-time quantitative PCR is widely used to quantify gene expression. Reference genes are usually used as internal controls to measure the target gene expression level. To date, there is no consensus on the use of systematically validated reference genes in different tissues of Luffa. This study evaluated the expression stability of 11 candidate reference genes in different tissues using five algorithms (BestKeeper, comparative delta-Ct method, GeNorm, NormFinder, and RefFinder). Protein phosphatase 2A was the most stable gene, while alpha Tubulin was the least stable. The relative expression of ethylene-related genes in different tissues was also analyzed to reveal their role in sex determination. This study provides the basis for using suitable reference genes to evaluate targeted gene expression. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01182-8.
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Affiliation(s)
- Gangjun Zhao
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640 China
| | - Meng Wang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640 China
| | - Yaqin Gan
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640 China
| | - Hao Gong
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Junxing Li
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Xiaoming Zheng
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Xiaoxi Liu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Siying Zhao
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640 China
| | - Jianning Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Haibin Wu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642 China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640 China
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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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