1
|
Zhang Q, Zhong S, Dong Q, Yang H, Yang H, Tan F, Chen C, Ren T, Shen J, Cao G, Luo P. Identification of Photoperiod- and Phytohormone-Responsive DNA-Binding One Zinc Finger (Dof) Transcription Factors in Akebia trifoliata via Genome-Wide Expression Analysis. Int J Mol Sci 2023; 24:ijms24054973. [PMID: 36902404 PMCID: PMC10002981 DOI: 10.3390/ijms24054973] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
As a kind of plant-specific transcription factor (TF), DNA-Binding One Zinc Finger (Dof) is widely involved in the response to environmental change, and as an evolutionarily important perennial plant species, Akebia trifoliata is ideal for studying environmental adaptation. In this study, a total of 41 AktDofs were identified in the A. trifoliata genome. First, the characteristics, including the length, exon number, and chromosomal distribution of the AktDofs and the isoelectric point (PI), amino acid number, molecular weight (MW), and conserved motifs of their putative proteins, were reported. Second, we found that all AktDofs evolutionarily underwent strong purifying selection, and many (33, 80.5%) of them were generated by whole-genome duplication (WGD). Third, we outlined their expression profiles by the use of available transcriptomic data and RT-qPCR analysis. Finally, we identified four candidate genes (AktDof21, AktDof20, AktDof36, and AktDof17) and three other candidate genes (AktDof26, AktDof16, and AktDof12) that respond to long day (LD) and darkness, respectively, and that are closely associated with phytohormone-regulating pathways. Overall, this research is the first to identify and characterize the AktDofs family and is very helpful for further research on A. trifoliata adaptation to environmental factors, especially photoperiod changes.
Collapse
Affiliation(s)
- Qiuyi Zhang
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Shengfu Zhong
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Qing Dong
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Hao Yang
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Huai Yang
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Feiquan Tan
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Chen Chen
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Tianheng Ren
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Jinliang Shen
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Guoxing Cao
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
- Correspondence:
| |
Collapse
|
2
|
Zheng K, Cai Y, Chen W, Gao Y, Jin J, Wang H, Feng S, Lu J. Development, Identification, and Application of a Germplasm Specific SCAR Marker for Dendrobium officinale Kimura et Migo. FRONTIERS IN PLANT SCIENCE 2021; 12:669458. [PMID: 34054907 PMCID: PMC8160518 DOI: 10.3389/fpls.2021.669458] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/20/2021] [Indexed: 05/27/2023]
Abstract
The stems of Dendrobium officinale have been used as a rare and valuable Chinese tonic medicine, known as "Tiepi Fengdou", since the Qing dynasty. Because of the increased market demand and continued exploitation of this plant, the reserves of wild D. officinale resources have been depleted, and D. officinale products on the market are being increasingly adulterated. Such changes have strongly affected the sustainable utilization of this valuable medicinal plant resource and the development of related industries. In this study, a species-specific DNA marker was developed for the rapid and accurate authentication of D. officinale. In total, 36 start codon-targeted (SCoT) polymorphism primers were screened in 36 definite Dendrobium species, and a distinct species-specific DNA amplicon (SCoT13-215) for D. officinale was obtained. After the sequence was cloned and sequenced, a sequence-characterized amplified region marker was developed (named SHF/SHR) and validated through PCR amplification of all 38 Dendrobium samples. The marker's specificity for D. officinale was confirmed through the consistent amplification of a clear 197-bp band. This SCAR marker can be used to rapidly, effectively, and reliably identify D. officinale among various Dendrobium species and may play an important role in ensuring the quality of medicinal preparations and protecting the germplasm of this important medicinal species.
Collapse
Affiliation(s)
- Kaixin Zheng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Yuchen Cai
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Weijie Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yadi Gao
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Jingjing Jin
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Shangguo Feng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jiangjie Lu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| |
Collapse
|
3
|
Grazina L, Amaral JS, Mafra I. Botanical origin authentication of dietary supplements by DNA‐based approaches. Compr Rev Food Sci Food Saf 2020; 19:1080-1109. [DOI: 10.1111/1541-4337.12551] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 01/22/2020] [Accepted: 02/06/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Liliana Grazina
- REQUIMTE‐LAQV, Faculdade de FarmáciaUniversidade do Porto Porto Portugal
| | - Joana S. Amaral
- Centro de Investigação de Montanha (CIMO)Instituto Politécnico de Bragança Bragança Portugal
| | - Isabel Mafra
- REQUIMTE‐LAQV, Faculdade de FarmáciaUniversidade do Porto Porto Portugal
| |
Collapse
|
4
|
Esteki M, Shahsavari Z, Simal-Gandara J. Gas Chromatographic Fingerprinting Coupled to Chemometrics for Food Authentication. FOOD REVIEWS INTERNATIONAL 2019. [DOI: 10.1080/87559129.2019.1649691] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- M. Esteki
- Department of Chemistry, University of Zanjan, Zanjan, Iran
| | - Z. Shahsavari
- Department of Chemistry, University of Zanjan, Zanjan, Iran
| | - J. Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo – Ourense Campus, Ourense, Spain
| |
Collapse
|
5
|
Kim WJ, Yang S, Choi G, Moon BC. Peptide Nucleic Acid Based Molecular Authentication for Identification of Four Medicinal Paeonia Species Using Melting Array Analysis of the Internal Transcribed Spacer 2 Region. Molecules 2017; 22:E1922. [PMID: 29112146 PMCID: PMC6150393 DOI: 10.3390/molecules22111922] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/03/2017] [Accepted: 11/03/2017] [Indexed: 11/16/2022] Open
Abstract
Accurate taxonomic identification of plant materials in herbal medicines is important for product quality control. The genus Paeonia (Saxifragales) is the source of the herbal preparations Paeoniae Radix (Paeoniae Radix Alba and Paeoniae Radix Rubra) and Moutan Radicis Cotex. However, confusion has arisen regarding their contents due to linguistic and taxonomic ambiguities, similar morphologies and different definitions of Paeoniae Radix in the Korean and Chinese national pharmacopoeias, leading to the distribution of adulterated products. To develop a method for identifying the four Paeonia species used in these medicines, three fluorescently-labeled peptide nucleic acid (PNA) probes were designed against ITS2 sequences containing single nucleotide polymorphisms (SNPs) and used in a real-time PCR melting curve assay. Each of the four Paeonia species was accurately identified using this analysis. The accuracy and analytical stability of the PNA melting curve assay was confirmed using commercially available samples of the four Paeonia species. This assay is a reliable genetic tool to distinguish between different Paeonia-derived herbal medicines and identify the botanical origins of Paeoniae Radix and Moutan Radicis Cortex. This technique may also contribute to quality control and standardization of herbal medicines by providing a reliable authentication tool and preventing the distribution of inauthentic adulterants.
Collapse
Affiliation(s)
- Wook Jin Kim
- K-herb Research Center, Korea Institute of Oriental Medicine, 1672 Yuseong-daero, Yuseong-gu, Daejeon 305-811, Korea.
| | - Sungyu Yang
- K-herb Research Center, Korea Institute of Oriental Medicine, 1672 Yuseong-daero, Yuseong-gu, Daejeon 305-811, Korea.
| | - Goya Choi
- K-herb Research Center, Korea Institute of Oriental Medicine, 1672 Yuseong-daero, Yuseong-gu, Daejeon 305-811, Korea.
| | - Byeong Cheol Moon
- K-herb Research Center, Korea Institute of Oriental Medicine, 1672 Yuseong-daero, Yuseong-gu, Daejeon 305-811, Korea.
| |
Collapse
|
6
|
Das K, Ganie SH, Mangla Y, Dar TUH, Chaudhary M, Thakur RK, Tandon R, Raina SN, Goel S. ISSR markers for gender identification and genetic diagnosis of Hippophae rhamnoides ssp. turkestanica growing at high altitudes in Ladakh region (Jammu and Kashmir). PROTOPLASMA 2017; 254:1063-1077. [PMID: 27542084 DOI: 10.1007/s00709-016-1013-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/05/2016] [Indexed: 06/06/2023]
Abstract
Hippophae rhamnoides L. ssp. turkestanica (Elaeagnaceae) is a predominantly dioecious and wind-pollinated medicinal plant species. The mature fruits of the species possess antioxidative, anti-inflammatory, antimicrobial, anticancerous, and antistimulatory properties that are believed to improve the immune system. The identification of male and female plants in H. rhamnoides ssp. turkestanica is quite difficult until flowering which usually takes 3-4 years or more. A sex-linked marker can be helpful in establishing the orchards through identification of genders at an early stage of development. Therefore, we studied the genetic diversity of populations in Ladakh with the aim to identify a gender-specific marker using ISSR markers. Fifty-eight ISSR primers were used to characterize the genome of H. rhamnoides ssp. turkestanica, of which eight primers generated 12 sex-specific fragments specific to one or more populations. The ISSR primer (P-45) produced a fragment which faithfully segregates all the males from the female plants across all the three valleys surveyed. This male-specific locus was converted into a SCAR. Forward and reverse primers designed from this fragment amplified a 750-bp sequence in males only, thus specifying it as an informative male-specific sex-linked marker. This SCAR marker was further validated for its capability to differentiate gender on an additional collection of plants, representing three geographically isolated valleys (Nubra, Suru, and Indus) from Ladakh region of India. The results confirmed sex-linked specificity of the marker suggesting that this conserved sequence at the Y chromosome is well preserved through the populations in Ladakh region. At present, there are no reliable markers which can differentiate male from female plants across all the three valleys of Ladakh region at an early stage of plant development. It is therefore envisaged that the developed SCAR marker shall provide a reliable molecular tool for early identification of the sex in this commercial crop. The genetic diversity of populations as surveyed by ISSR primers revealed 85.71 % polymorphism at the population level. The dendrogram obtained divided the genotypes into three different clusters, and the distribution of male and female genotypes in all the clusters was random. The Nei's genetic similarity index was in the range of 0.63-0.96.
Collapse
Affiliation(s)
- Kamal Das
- Department of Botany, University of Delhi, Delhi, India
| | | | - Yash Mangla
- Department of Botany, University of Delhi, Delhi, India
| | - Tanvir-Ul-Hassan Dar
- Centre for Biodiversity Studies, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, J&K, India
| | - Manju Chaudhary
- Department of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | | | - Rajesh Tandon
- Department of Botany, University of Delhi, Delhi, India
| | - S N Raina
- Department of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | | |
Collapse
|
7
|
Molecular authentication of Tetrastigma hemsleyanum from its adulterant species using ISSR, CAPS, and ITS2 barcode. Mol Biol Rep 2016; 43:785-94. [DOI: 10.1007/s11033-016-4023-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 05/27/2016] [Indexed: 10/21/2022]
|
8
|
Kim WJ, Moon BC, Yang S, Han KS, Choi G, Lee AY. Rapid Authentication of the Herbal Medicine Plant Species Aralia continentalis Kitag. and Angelica biserrata C.Q. Yuan and R.H. Shan Using ITS2 Sequences and Multiplex-SCAR Markers. Molecules 2016; 21:270. [PMID: 26938512 PMCID: PMC6273786 DOI: 10.3390/molecules21030270] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 02/24/2016] [Accepted: 02/24/2016] [Indexed: 11/17/2022] Open
Abstract
Accurate identification of the plant species that are present in herbal medicines is important for quality control. Although the dried roots of Aralia continentalis (Araliae Continentalis Radix) and Angelica biserrata (Angelicae Pubescentis Radix) are used in the same traditional medicine, namely Dok-Hwal in Korean and Du-Huo in Chinese, the medicines are described differently in the national pharmacopeia. Further confusion arises from the distribution of dried Levisticum officinale and Heracleum moellendorffii roots as the same medicine. Medicinal ingredients from all four plants are morphologically similar, and discrimination is difficult using conventional methods. Molecular identification methods offer rapidity and accuracy. The internal transcribed spacer 2 (ITS2) region of the nuclear ribosomal RNA gene (rDNA) was sequenced in all four plant species, and the sequences were used to design species-specific primers. Primers for each species were then combined to allow sample analysis in a single PCR reaction. Commercial herbal medicine samples were obtained from Korea and China and analyzed using the multiplex assay. The assay successfully identified authentic medicines and also identified inauthentic or adulterated samples. The multiplex assay will be a useful tool for identification of authentic Araliae Continentalis Radix and/or Angelicae Pubescentis Radix preparations in Korea and China.
Collapse
Affiliation(s)
- Wook Jin Kim
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon 305-811, Korea.
| | - Byeong Cheol Moon
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon 305-811, Korea.
| | - Sungyu Yang
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon 305-811, Korea.
| | - Kyeong Suk Han
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon 305-811, Korea.
| | - Goya Choi
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon 305-811, Korea.
| | - A Yeong Lee
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon 305-811, Korea.
| |
Collapse
|
9
|
Ganie SH, Upadhyay P, Das S, Prasad Sharma M. Authentication of medicinal plants by DNA markers. PLANT GENE 2015; 4:83-99. [PMID: 32289060 PMCID: PMC7103949 DOI: 10.1016/j.plgene.2015.10.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/01/2015] [Accepted: 10/07/2015] [Indexed: 11/21/2022]
Abstract
Medicinal plants have been used worldwide for centuries to maintain health and to treat diseases, more so chronic diseases. However, adulteration and use of spurious materials as substitutes have become a major concern for users and industry for reasons of safety and efficacy. Therefore, authentication of medicinal plants is of utmost importance. Morphological, anatomical, chemical and DNA markers solve the problem by differentiating the genuine material from the adulterants, substitutes and spurious drugs. DNA markers use nucleotide sequences to identify species; it takes preference over the other two markers being not age dependent, tissue specific and having a higher discriminating power. Therefore, characterization of plants with such markers is an ideal approach for identification of medicinal plant species and populations/varieties of the same species. Availability of certified taxonomic specimens in herbaria is certainly required for unambiguous confirmation through final visual comparison and analysis.
Collapse
Affiliation(s)
| | - Priti Upadhyay
- Dept. of Botany, University of Delhi, Delhi 110007, India
| | - Sandip Das
- Dept. of Botany, University of Delhi, Delhi 110007, India
| | | |
Collapse
|