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Zhang J, He X, Zhou J, Dong Z, Yu H, Tang Q, Yuan L, Peng S, Zhong X, He Y. Selection and Verification of Standardized Reference Genes of Angelica dahurica under Various Abiotic Stresses by Real-Time Quantitative PCR. Genes (Basel) 2024; 15:79. [PMID: 38254968 PMCID: PMC10815136 DOI: 10.3390/genes15010079] [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: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
In traditional Chinese medicine, Angelica dahurica is a valuable herb with numerous therapeutic applications for a range of ailments. There have not yet been any articles on the methodical assessment and choice of the best reference genes for A. dahurica gene expression studies. Real-time quantitative PCR (RT-qPCR) is widely employed as the predominant method for investigating gene expression. In order to ensure the precise determination of target gene expression outcomes in RT-qPCR analysis, it is imperative to employ stable reference genes. In this study, a total of 11 candidate reference genes including SAND family protein (SAND), polypyrimidine tract-binding protein (PTBP), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), TIP41-like protein (TIP41), cyclophilin 2 (CYP2), elongation factor 1 α (EF1α), ubiquitin-protein ligase 9 (UBC9), tubulin β-6 (TUB6), thioredoxin-like protein YLS8 (YLS8), and tubulin-α (TUBA) were selected from the transcriptome of A. dahurica. Subsequently, three statistical algorithms (geNorm, NormFinder, and BestKeeper) were employed to assess the stability of their expression patterns across seven distinct stimulus treatments. The outcomes obtained from these analyses were subsequently amalgamated into a comprehensive ranking using RefFinder. Additionally, one target gene, phenylalanine ammonia-lyase (PAL), was used to confirm the effectiveness of the selected reference genes. According to the findings of this study, the two most stable reference genes for normalizing the expression of genes in A. dahurica are TIP41 and UBC9. Overall, our research has determined the appropriate reference genes for RT-qPCR in A. dahurica and provides a crucial foundation for gene screening and identifying genes associated with the biosynthesis of active ingredients in A. dahurica.
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Affiliation(s)
- Jing Zhang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Xinyi He
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Jun Zhou
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Zhuang Dong
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Han Yu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Qi Tang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Lei Yuan
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Siqing Peng
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Xiaohong Zhong
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Yuedong He
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
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Song C, Zhang Y, Zhang W, Manzoor MA, Deng H, Han B. The potential roles of acid invertase family in Dendrobium huoshanense: Identification, evolution, and expression analyses under abiotic stress. Int J Biol Macromol 2023; 253:127599. [PMID: 37871722 DOI: 10.1016/j.ijbiomac.2023.127599] [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: 08/20/2023] [Revised: 09/22/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
Dendrobium huoshanense, a traditional Chinese medicine prized for its horticultural and medicinal properties, thrives in an unfavorable climate and is exposed to several adverse environmental conditions. Acid invertase (AINV), a widely distributed enzyme that has been demonstrated to play a significant role in response to environmental stresses. However, the identification of the AINV gene family in D. huoshanense, the collinearity between relative species, and the expression pattern under external stress have yet to be resolved. We systematically retrieved the D. huoshanense genome and screened out four DhAINV genes, which were further classified into two subfamilies by the phylogenetic analysis. The evolutionary history of AINV genes in D. huoshanense was uncovered by comparative genomics investigations. The subcellular localization predicted that the DhVINV genes may be located in the vacuole, while the DhCWINV genes may be located in the cell wall. The exon/intron structures and conserved motifs of DhAINV genes were found to be highly conserved in two subclades. The conserved amino acids and catalytic motifs in DhAINV proteins were determined to be critical to their function. Notably, the cis-acting elements in all DhAINV genes were mainly relevant to abiotic stresses and light response. In addition, the expression profile coupled with qRT-PCR revealed the typical expression patterns of DhAINV in response to diverse abiotic stresses. Our findings could be beneficial to the characterization and further investigation of AINV functions in Dendrobium plants.
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Affiliation(s)
- Cheng Song
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, College of Biological and Pharmaceutical Engineering, West Anhui University, Luan 237012, China.
| | - Yingyu Zhang
- Henan Key Laboratory of Rare Diseases, Endocrinology and Metabolism Center, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
| | - Wenwu Zhang
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 201109, China
| | - Hui Deng
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, College of Biological and Pharmaceutical Engineering, West Anhui University, Luan 237012, China
| | - Bangxing Han
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, College of Biological and Pharmaceutical Engineering, West Anhui University, Luan 237012, China.
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Zhang Y, Mu D, Wang L, Wang X, Wilson IW, Chen W, Wang J, Liu Z, Qiu D, Tang Q. Reference Genes Screening and Gene Expression Patterns Analysis Involved in Gelsenicine Biosynthesis under Different Hormone Treatments in Gelsemium elegans. Int J Mol Sci 2023; 24:15973. [PMID: 37958955 PMCID: PMC10648913 DOI: 10.3390/ijms242115973] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/24/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is an accurate method for quantifying gene expression levels. Choosing appropriate reference genes to normalize the data is essential for reducing errors. Gelsemium elegans is a highly poisonous but important medicinal plant used for analgesic and anti-swelling purposes. Gelsenicine is one of the vital active ingredients, and its biosynthesis pathway remains to be determined. In this study, G. elegans leaf tissue with and without the application of one of four hormones (SA, MeJA, ETH, and ABA) known to affect gelsenicine synthesis, was analyzed using ten candidate reference genes. The gene stability was evaluated using GeNorm, NormFinder, BestKeeper, ∆CT, and RefFinder. The results showed that the optimal stable reference genes varied among the different treatments and that at least two reference genes were required for accurate quantification. The expression patterns of 15 genes related to the gelsenicine upstream biosynthesis pathway was determined by RT-qPCR using the relevant reference genes identified. Three genes 8-HGO, LAMT, and STR, were found to have a strong correlation with the amount of gelsenicine measured in the different samples. This research is the first study to examine the reference genes of G. elegans under different hormone treatments and will be useful for future molecular analyses of this medically important plant species.
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Affiliation(s)
- Yao Zhang
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.Z.); (D.M.); (L.W.); (W.C.)
| | - Detian Mu
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.Z.); (D.M.); (L.W.); (W.C.)
| | - Liya Wang
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.Z.); (D.M.); (L.W.); (W.C.)
| | - Xujun Wang
- Hunan Academy of Forestry, Changsha 410018, China
| | - Iain W. Wilson
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Wenqiang Chen
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.Z.); (D.M.); (L.W.); (W.C.)
| | - Jinghan Wang
- College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China;
| | - Zhaoying Liu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China;
| | - Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
| | - Qi Tang
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.Z.); (D.M.); (L.W.); (W.C.)
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Shu W, Shi M, Zhang Q, Xie W, Chu L, Qiu M, Li L, Zeng Z, Han L, Sun Z. Transcriptomic and Metabolomic Analyses Reveal Differences in Flavonoid Pathway Gene Expression Profiles between Two Dendrobium Varieties during Vernalization. Int J Mol Sci 2023; 24:11039. [PMID: 37446217 DOI: 10.3390/ijms241311039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/24/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Dendrobium (Orchidaceae, Epidendoideae) plants have flowers with a wide variety of colors that persist for a long period throughout the year. The yellow coloration of Dendrobium flowers is mainly determined by the flavonol pathway and the flavone pathway, but the relevant biosynthesis mechanisms during vernalization remain unclear. To explore the similarities and differences in flavonoid biosynthesis in different tissues during vernalization, we selected two species of Dendrobium for a flower color study: Dendrobium capillipes Rchb (which has yellow flowers) and Dendrobium nobile Lindl (which has white flowers). We collected a total of 36 samples from six tissue types and both Dendrobium species during vernalization and subjected the samples to metabolic profiling and transcriptome sequencing. A total of 31,504 differentially expressed genes (DEGs) were identified between different tissues of the two Dendrobium species by transcriptomic analysis. However, many differentially accumulated metabolites (DAMs) and DEGs were enriched not only in the general pathway of "flavonoid biosynthesis" but also in multiple subpathways of "flavone and flavonol biosynthesis". According to a combined transcriptome and metabolome analysis, Putrescine hydroxycinnamoyl transferase 1 (LOC110093422) may be the main gene responsible for the differences in flavonoid accumulation during vernalization, which is closely associated with yellow flowers. Taken together, the results of our study preliminarily revealed the metabolites responsible for and the key genes regulating flavonoid biosynthesis during vernalization. These results provide a basis for the further study of the molecular mechanism of flavonoid synthesis during vernalization.
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Affiliation(s)
- Wenbo Shu
- National Key Laboratory for Germplasm Innovation and Utilization Crops, College of Horticulture and Forestry, Huazhong Agriculture University, Wuhan 430070, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Meirong Shi
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Qiqi Zhang
- National Key Laboratory for Germplasm Innovation and Utilization Crops, College of Horticulture and Forestry, Huazhong Agriculture University, Wuhan 430070, China
| | - Wenyu Xie
- National Key Laboratory for Germplasm Innovation and Utilization Crops, College of Horticulture and Forestry, Huazhong Agriculture University, Wuhan 430070, China
| | - Liwei Chu
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Mingxuan Qiu
- National Key Laboratory for Germplasm Innovation and Utilization Crops, College of Horticulture and Forestry, Huazhong Agriculture University, Wuhan 430070, China
| | - Linyan Li
- National Key Laboratory for Germplasm Innovation and Utilization Crops, College of Horticulture and Forestry, Huazhong Agriculture University, Wuhan 430070, China
| | - Zhixin Zeng
- National Key Laboratory for Germplasm Innovation and Utilization Crops, College of Horticulture and Forestry, Huazhong Agriculture University, Wuhan 430070, China
| | - Lei Han
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Zhenyuan Sun
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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Lu L, Tang Y, Xu H, Qian Y, Tao J, Zhao D. Selection and verification of reliable internal reference genes in stem development of herbaceous peony ( Paeonia lactiflora Pall.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:773-782. [PMID: 37520813 PMCID: PMC10382430 DOI: 10.1007/s12298-023-01325-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 08/01/2023]
Abstract
Herbaceous peony (Paeonia lactiflora Pall.) has emerged in the cut flower market due to its beautiful appearance. The bending flower stems caused by a lack of mechanical strength is the main problem restricting the development of the cut P. lactiflora industry. So it is of great worth to reveal the basis of stem development changes in P. lactiflora to improve its cut flower quality. Quantitative research on gene expression characteristics can provide clues for understanding their biological functions, and the screening of relatively stable expression genes is a prerequisite for the quantitative study of gene expression characteristics. Thus, it is necessary to find appropriate genes during stem development so as to analyze the qRT‒PCR results. In this study, 10 genes were screened, and these genes expressed stably in stems of different stem strengths at three different developmental stages. Then, their expressions were evaluated by RefFinder, BestKeeper, NormFinder, and GeNorm programs. The results demonstrated that γ-tubulin (γ-TUB) was the most suitable gene, followed by α-tubulin (α-TUB) and β-D-glucosidase (β-GUS), whereas histone H3 (His) was the least suitable gene. Besides, the temporal and spatial expression characteristics of PlCOMT1, the key gene concerned with the synthesis of cell wall fillers in P. lactiflora, were also used to evaluate the suitability of genes. Consequently, γ-TUB and α-TUB are the two best combinations during stem development, and their combination can be used for the stem development of P. lactiflora. These findings will provide a reference for the selection of genes related to stem development and the study of molecular mechanisms related to stem development in P. lactiflora. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01325-5.
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Affiliation(s)
- Lili Lu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yuhan Tang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Huajie Xu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yi Qian
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Jun Tao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Daqiu Zhao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
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Wang Q, Guo C, Yang S, Zhong Q, Tian J. Screening and Verification of Reference Genes for Analysis of Gene Expression in Garlic ( Allium sativum L.) under Cold and Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:763. [PMID: 36840111 PMCID: PMC9963267 DOI: 10.3390/plants12040763] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The principal objective of this study was to screen and verify reference genes appropriate for gene expression evaluation during plant growth and development under distinct growth conditions. Nine candidate reference genes were screened based on garlic transcriptome sequence data. RT-qPCR was used to detect the expression levels of the aforementioned reference genes in specific tissues under drought and cold stress. Then, geNorm, NormFinder, BestKeeper, and ReFinder were used to consider the consistency of the expression levels of candidate reference genes. Finally, the stress-responsive gene expression of ascorbate peroxidase (APX) was quantitatively evaluated to confirm the chosen reference genes. Our results indicated that there were variations in the abundance and stability of nine reference gene transcripts underneath cold and drought stress, among which ACT and UBC-E2 had the highest transcript abundance, and 18S rRNA and HIS3 had the lowest transcript abundance. UBC and UBC-E2 were the most stably expressed genes throughout all samples; UBC and UBC-E2 were the most stably expressed genes during cold stress, and ACT and UBC were the most stably expressed genes under drought stress. The most stably expressed genes in roots, pseudostems, leaves, and cloves were EF1, ACT, HIS3, UBC, and UBC-E2, respectively, while GAPDH was the most unstable gene during drought and cold stress conditions and in exclusive tissues. Taking the steady reference genes UBC-E2, UBC, and ACT as references during drought and cold stress, the reliability of the expression levels was further demonstrated by detecting the expression of AsAPX. Our work thereby offers a theoretical reference for the evaluation of gene expression in garlic in various tissues and under stress conditions.
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Affiliation(s)
- Qizhang Wang
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Chunqian Guo
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Shipeng Yang
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Qiwen Zhong
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Jie Tian
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China
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