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Mursyidin DH, Makruf MI, Badruzsaufari, Noor A. Molecular diversity of exotic durian (Durio spp.) germplasm: a case study of Kalimantan, Indonesia. J Genet Eng Biotechnol 2022; 20:39. [PMID: 35230532 PMCID: PMC8888783 DOI: 10.1186/s43141-022-00321-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023]
Abstract
Background Durian of Indonesia, specifically Durio zibethinus, is a potential agricultural commodity for domestic and international markets. However, its quality is still less competitive or significantly lower to fulfill the export market, compared to a similar one from other countries. This study aimed to determine and analyze the genetic diversity and relationship of the exotic durian (Durio spp.) germplasm originally from Kalimantan, Indonesia, using the rbcL marker. Results Based on this marker, the durian germplasm has a low genetic diversity (π%=0.24). It may strongly correspond with the variability sites or mutation present in the region. In this case, the rbcL region of the durian germplasm has generated 23 variable sites with a transition/transversion (Ti/Tv) bias value of 1.00. However, following the phylogenetic and principal component analyses, this germplasm is separated into four main clades and six groups, respectively. In this case, D. zibethinus was very closely related to D. exleyanus. Meanwhile, D. lowianus and D. excelsus were the farthest. In further analysis, 29 durians were very closely related, and the farthest was shown by Durian Burung (D. acutifolius) and Kalih Haliyang (D. kutejensis) as well as Pampaken Burung Kecil (D. kutejensis) and Durian Burung (D. acutifolius) with a divergence coefficient of 0.011. The Pearson correlation analysis confirms that 20 pairs of individual durians have a strong relation, shown by, e.g., Maharawin Hamak and Durian Burung as well as Mantuala Batu Hayam and Durian Burung Besar. Conclusion While the durian has a low genetic diversity, the phylogenetic analyses revealed that this germplasm originally from Kalimantan, Indonesia, shows unique relationships. These findings may provide a beneficial task in supporting the durian genetic conservation and breeding practices in the future, locally and globally.
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Matiz-Ceron L, Reyes A, Anzola J. Taxonomical Evaluation of Plant Chloroplastic Markers by Bayesian Classifier. FRONTIERS IN PLANT SCIENCE 2022; 12:782663. [PMID: 35185949 PMCID: PMC8850773 DOI: 10.3389/fpls.2021.782663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
DNA barcodes are standardized sequences that range between 400 and 800 bp, vary at different taxonomic levels, and make it possible to assign sequences to species that have been previously taxonomically characterized. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as none of them excels above the others in this area. One tool that has been widely used and served as a baseline when evaluating new approaches is Naïve Bayesian Classifiers (NBC). The present study aims at evaluating the classification power of several plant chloroplast genetic markers that have been proposed as barcodes (trnL, rpoB, rbcL, matK, psbA-trnH, and psbK) using an NBC. We performed the classification at different taxonomic levels, and identified problematic genera when resolution was desired. We propose matK and trnL as potential candidate markers with resolution up to genus level. Some problematic genera within certain families could lead to the misclassification no matter which marker is used (i.e., Aegilops, Gueldenstaedtia, Helianthus, Oryza, Shorea, Thysananthus, and Triticum). Finally, we suggest recommendations for the taxonomic identification of plants in samples with potential mixtures.
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Affiliation(s)
- Luisa Matiz-Ceron
- Research Group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
| | - Alejandro Reyes
- Research Group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
| | - Juan Anzola
- Research Group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
- Department of Engineering and Natural Sciences, Universidad Central, Bogotá, Colombia
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3
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Recent techniques for the authentication of the geographical origin of tea leaves from camellia sinensis: A review. Food Chem 2021; 374:131713. [PMID: 34920400 DOI: 10.1016/j.foodchem.2021.131713] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 11/15/2021] [Accepted: 11/26/2021] [Indexed: 01/11/2023]
Abstract
Tea is one of the most important beverages worldwide, is produced in several distinct geographical regions, and is traded on the global market. The ability to determine the geographical origin of tea products helps to ensure authenticity and traceability. This paper reviews the recent research on authentication of tea using a combination of instrumental and chemometric methods. To determine the production region of a tea sample, instrumental methods based on analyzing isotope and mineral element contents are suitable because they are less affected by tea variety and processing methods. Chemometric analysis has proven to be a valuable method to identify tea. Principal component analysis (PCA) and linear discriminant analysis (LDA) are the most preferred methods for processing large amounts of data obtained through instrumental component analysis.
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Avarave S, Thomas J. Biodiversity of South Indian tea clones with detection of plant-based adulterants in tea dust using DNA barcoding. Nat Prod Res 2021; 36:4614-4619. [PMID: 34847786 DOI: 10.1080/14786419.2021.2002325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Tea is by and large a highly penetrated product in south India. Hence the adulteration risk in tea dust gets hiked in the markets. We constructed a standard database using plant plastid markers (rbcL, matK, trnH-psbA, rpoC, rpoB, ycf 1) and nuclear (ITS2) locus from prominent south Indian tea clones representing Assam, China, and Cambod varieties. These barcodes were used as reference algorithm to investigate the authenticity of 10 sampled commercial tea dust by recovering its DNA barcodes using rbcL, matK, and ITS2 loci. PCR amplification success, sequencing efficiency, genetic polymorphisms, BLAST search, and phylogenetic analysis were performed to enhance genotypic information on south tea cultivars and in authenticating the commercial samples of Camellia sinensis. Findings suggest that the chloroplast and nuclear loci can identify tea plant at the genus and varietal level respectively and rbcL as the potential marker for detecting plant-based admixtures coupled with TA cloning after DNA barcoding.
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Affiliation(s)
- Steffi Avarave
- Algae Biomass Research Laboratory, Department of Biotechnology, Karunya Institute of Technology and Sciences (Deemed to be University), Coimbatore, Tamil Nadu, India
| | - Jibu Thomas
- Algae Biomass Research Laboratory, Department of Biotechnology, Karunya Institute of Technology and Sciences (Deemed to be University), Coimbatore, Tamil Nadu, India
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5
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Azizi MMF, Lau HY, Abu-Bakar N. Integration of advanced technologies for plant variety and cultivar identification. J Biosci 2021. [DOI: 10.1007/s12038-021-00214-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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Ho VT, Tran TKP, Vu TTT, Widiarsih S. Comparison of matK and rbcL DNA barcodes for genetic classification of jewel orchid accessions in Vietnam. J Genet Eng Biotechnol 2021; 19:93. [PMID: 34152504 PMCID: PMC8217478 DOI: 10.1186/s43141-021-00188-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/01/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Jewel orchid is the common name of several orchid species which can be alike in morphological characteristics, but variable in medicinal properties. At present, two DNA barcode loci, namely, maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL), are intensively utilized for plant identification. However, the discrimination effectiveness of these loci is variable among plant species. This study was carried out to compare the identifying efficacy of these two loci on jewel orchid population collected throughout Vietnam. RESULTS The results revealed that 21 jewel orchid accessions studied were segregated into four different species with significant variations. The discrimination power of matK and rbcL markers in this jewel orchid study displayed different efficiency level. The rbcL gene has higher distinguishing potential than either matK gene alone or the combination of both genes. CONCLUSION The findings of this project could provide valuable information that is necessary for classification, plant origin identification, breeding, and conservation program of jewel orchid in Vietnam.
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Affiliation(s)
- Viet The Ho
- Ho Chi Minh City University of Food Industry, 140 Le Trong Tan, Tan Phu District, Ho Chi Minh City, Vietnam.
| | - Thi Kim Phuong Tran
- Ho Chi Minh City University of Food Industry, 140 Le Trong Tan, Tan Phu District, Ho Chi Minh City, Vietnam
| | - Thi Thanh Tram Vu
- Ho Chi Minh City University of Food Industry, 140 Le Trong Tan, Tan Phu District, Ho Chi Minh City, Vietnam
| | - Sasanti Widiarsih
- Plant Mutation Breeding Division, Centre for Isotopes and Radiation Application, National Nuclear Energy Agency, Jl. Lebakbulus Raya No. 49, South Jakarta, Indonesia
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7
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Shadrin DM. DNA Barcoding: Applications. RUSS J GENET+ 2021. [DOI: 10.1134/s102279542104013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Dhivya S, Ashutosh S, Gowtham I, Baskar V, Harini AB, Mukunthakumar S, Sathishkumar R. Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes. BMC Genomics 2020; 21:659. [PMID: 32972362 PMCID: PMC7513480 DOI: 10.1186/s12864-020-07036-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 08/30/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The banana (Musa sp., AAA) genome is constantly increasing due to high-frequency of somaclonal variations. Due to its large diversity, a conventional numerical and morphological based taxonomic identification of banana cultivars is laborious, difficult and often leads to subject of disagreements. RESULTS Hence, in the present study, we used universal DNA barcode ITS2 region to identify and to find the genetic relationship between the cultivars and varieties of banana. Herein, a total of 16 banana cultivars were PCR amplified using ITS2 primer pair. In addition, 321 sequences which were retrieved from GenBank, USA, were used in this study. The sequences were then aligned using Clustal W and genetic distances were computed using MEGA V5.1. The study showed significant divergence between the intra- and inter-specific genetic distances in ITS2 region. BLAST1 and Distance methods proved that ITS2 DNA barcode region successfully identified and distinguished the cultivar and varieties of banana. CONCLUSION Thus, from the results of the present study, it is clear that ITS2 is not only an efficient DNA barcode to identify the banana species but also a potential candidate for enumerating the phylogenetic relationships between the subspecies and cultivars. This is the first comprehensive study to categorically distinguish the economically important banana subspecies and varieties using DNA barcodes and to understand its evolutionary relationship.
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Affiliation(s)
- S Dhivya
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India
| | - S Ashutosh
- Technologico de Monterrey, Centre of Bioengineering, Epigmenio Gonzalez #500, Fracc. San Pablo, Campus Queretaro, Santiago de Querétaro, Queretaro, Mexico
| | - I Gowtham
- Plant Biofarming Laboratory, DRDO-BU Centre for Life Sciences, Bharathiar University, Coimbatore, 641046, India
| | - V Baskar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India
| | - A Baala Harini
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India
| | - S Mukunthakumar
- Biotechnology and Bioinformatics Division, Jawaharlal Nehru Tropical Botanic Garden & Research Institute, Palode, Thiruvananthapuram, Kerala, 695 562, India
| | - R Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India.
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Braglia L, Gavazzi F, Morello L, Gianì S, Nick P, Breviario D. On the applicability of the Tubulin-Based Polymorphism (TBP) genotyping method: a comprehensive guide illustrated through the application on different genetic resources in the legume family. PLANT METHODS 2020; 16:86. [PMID: 32536963 PMCID: PMC7291473 DOI: 10.1186/s13007-020-00627-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 05/30/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Plant discrimination is of relevance for taxonomic, evolutionary, breeding and nutritional studies. To this purpose, evidence is reported to demonstrate TBP (Tubulin-Based-Polymorphism) as a DNA-based method suitable for assessing plant diversity. RESULTS Exploiting one of the most valuable features of TBP, that is the convenient and immediate application of the assay to groups of individuals that may belong to different taxa, we show that the TBP method can successfully discriminate different agricultural species and their crop wild relatives within the Papilionoideae subfamily. Detection of intraspecific variability is demonstrated by the genotyping of 27 different accessions of Phaseolus vulgaris. CONCLUSIONS These data illustrate TBP as a useful and versatile tool for plant genotyping. Since its potential has not yet been fully appreciated by the scientific community, we carefully report all the experimental details of a successful TBP protocol, while describing different applications, so that the method can be replicated in other laboratories.
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Affiliation(s)
- Luca Braglia
- CNR- National Research Council, Institute of Agricultural Biology and Biotechnology-IBBA, Via Alfonso Corti 12, 20133 Milan, Italy
| | - Floriana Gavazzi
- CNR- National Research Council, Institute of Agricultural Biology and Biotechnology-IBBA, Via Alfonso Corti 12, 20133 Milan, Italy
| | - Laura Morello
- CNR- National Research Council, Institute of Agricultural Biology and Biotechnology-IBBA, Via Alfonso Corti 12, 20133 Milan, Italy
| | - Silvia Gianì
- CNR- National Research Council, Institute of Agricultural Biology and Biotechnology-IBBA, Via Alfonso Corti 12, 20133 Milan, Italy
| | - Peter Nick
- Department of Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 4, 76131 Karlsruhe, Baden-Württemberg Germany
| | - Diego Breviario
- CNR- National Research Council, Institute of Agricultural Biology and Biotechnology-IBBA, Via Alfonso Corti 12, 20133 Milan, Italy
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10
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Xia W, Zhang B, Xing D, Li Y, Wu W, Xiao Y, Sun J, Dou Y, Tang W, Zhang J, Huang X, Xu Y, Xie J, Wang J, Huang D. Development of high-resolution DNA barcodes for Dioscorea species discrimination and phylogenetic analysis. Ecol Evol 2019; 9:10843-10853. [PMID: 31624585 PMCID: PMC6787845 DOI: 10.1002/ece3.5605] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 08/04/2019] [Accepted: 08/06/2019] [Indexed: 01/31/2023] Open
Abstract
The genus Dioscorea is widely distributed in tropical and subtropical regions, and is economically important in terms of food supply and pharmaceutical applications. However, DNA barcodes are relatively unsuccessful in discriminating between Dioscorea species, with the highest discrimination rate (23.26%) derived from matK sequences. In this study, we compared genic and intergenic regions of three Dioscorea chloroplast genomes and found that the density of SNPs and indels in intergenic sites was about twice and seven times higher than that of SNPs and indels in the genic regions, respectively. A total of 52 primer pairs covering highly variable regions were designed and seven pairs of primers had 80%-100% PCR success rate. PCR amplicons of 73 Dioscorea individuals and assembled sequences of 47 Dioscorea SRAs were used for estimating intraspecific and interspecific divergence for the seven loci: The rpoB-trnC locus had the highest interspecific divergence. Automatic barcoding gap discovery (ABGD), Poisson tree processes (PTP), and generalized mixed Yule coalescence (GMYC) analysis were applied for species delimitation based on the seven loci and successfully identified the majority of species, except for species in the Enantiophyllum section. Phylogenetic analysis of 51 Dioscorea individuals (28 species) showed that most individuals belonging to the same species tended to cluster in the same group. Our results suggest that the variable loci derived from comparative analysis of plastid genome sequences could be good DNA barcode candidates for taxonomic analysis and species delimitation.
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Affiliation(s)
- Wei Xia
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsHainan UniversityHaikouChina
| | - Bo Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsHainan UniversityHaikouChina
| | - Dan Xing
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsHainan UniversityHaikouChina
| | - Ying Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsHainan UniversityHaikouChina
| | - Wenqiang Wu
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsHainan UniversityHaikouChina
| | - Yong Xiao
- Coconut Research InstituteCATASWenchangChina
| | - Jinhua Sun
- Environment and Plant Protection InstituteCATASHaikouChina
| | - Yajing Dou
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsHainan UniversityHaikouChina
| | - Wenqi Tang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsHainan UniversityHaikouChina
| | - Jinlan Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsHainan UniversityHaikouChina
| | - Xiaolong Huang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsHainan UniversityHaikouChina
| | - Yun Xu
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsHainan UniversityHaikouChina
| | - Jun Xie
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsHainan UniversityHaikouChina
| | - Jihua Wang
- Guangdong Key Laboratory for Crops Genetic ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Dongyi Huang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsHainan UniversityHaikouChina
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Lin CS, Yang CJ, Chen PJ, Liu KW, Lin HP, Lin CC, Lee YC, Cheng WC, Wei CI, Tsai YH. Assessment of Microbiological and Chemical Quality of Bubble Tea Beverages Vended in Taiwan. J Food Prot 2019; 82:1384-1389. [PMID: 31335185 DOI: 10.4315/0362-028x.jfp-18-517] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bubble tea beverages (n = 105) purchased from vendors in Taiwan were tested to determine their microbiological and chemical quality. Nearly half of the tested samples (48.6%, 51 of 105) had aerobic plate counts (APCs) higher than the Taiwan Food and Drug Administration guideline of 4.0 log CFU/mL, and 55 (52.4%) had coliform counts (most probable number [MPN]) higher than the 10 MPN/mL guideline. Escherichia coli, Salmonella, Staphylococcus aureus, sweeteners, preservatives, maleic acid, and coumarin were not detected in any sample. However, catechins were not detected to 188 mg/mL, and caffeine was 10.1 to 457.6 mg/mL. Bubble tea samples obtained from vendors in southern Taiwan had a mean APC of 2.6 log CFU/mL and a mean coliform count of 61.7 MPN/mL; these values were significantly lower (P < 0.05) than those from samples collected from vendors in northern, eastern, or central Taiwan. Samples obtained from southern Taiwan had the highest mean catechin concentrations of 21.3 mg/mL (P < 0.05). About 60% (63 of 105) of the bubble tea samples were not labeled with the origin of the tea leaves, which is in violation of Taiwanese food labeling regulations. In general, the bubble tea beverages tested had satisfactory microbial and chemical qualities.
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Affiliation(s)
| | | | | | | | | | - Chih-Cheng Lin
- 1 Department of Food Science.,2 Department of Biotechnology and Pharmaceutical Technology, Yuanpei University of Medical Technology, Hsin-Chu, 300 Taiwan, Republic of China
| | - Yi-Chen Lee
- 3 Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung, 811 Taiwan, Republic of China
| | - Wei-Chih Cheng
- 4 Food and Drug Administration, Ministry of Health and Welfare Taipei, 115 Taiwan, Republic of China
| | - Cheng-I Wei
- 5 International Programs in Agriculture and Natural Resources, College of Agriculture and Natural Resources, University of Maryland, College Park, Maryland 20904, USA
| | - Yung-Hsiang Tsai
- 3 Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung, 811 Taiwan, Republic of China
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Xie Q, Zhang H, Yan F, Yan C, Wei S, Lai J, Wang Y, Zhang B. Morphology and Molecular Identification of Twelve Commercial Varieties of Kiwifruit. Molecules 2019; 24:molecules24050888. [PMID: 30832434 PMCID: PMC6429161 DOI: 10.3390/molecules24050888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/26/2019] [Accepted: 02/28/2019] [Indexed: 11/24/2022] Open
Abstract
The quality and safety of food are important guarantees for the health and legal rights of consumers. As an important special fruitcrop, there are frequently shoddy practices in the kiwifruit (Actinidia chinensis) market, which harms the interests of consumers. However, there is lack of rapid and accurate identification methods for commercial kiwifruit varieties. Here, twelve common commercial varieties of kiwifruit were morphologically discriminated. DNA barcodes of chloroplast regions psbA-trnH, rbcL, matK, rpoB, rpoC1, ycf1b, trnL and rpl32_trnL(UAG), the nuclear region At103 and intergenic region ITS2 were amplified. Divergences and phylogenetic trees were used to analyze the phylogenetic relationship of these twelve commercial kiwifruit varieties. The results showed that matK, ITS2 and rpl32_trnL(UAG) can be utilized as molecular markers to identify CuiYu, JinYan, HuangJinGuo, ChuanHuangJin, HuaYou, YaTe, XuXiang and HongYang. This provides experimental and practical basis to scientifically resolve kiwifruit-related judicial disputes and legal trials.
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Affiliation(s)
- Qiaoli Xie
- School of Forensic Medicine, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an 710061, China.
| | - Hongbo Zhang
- School of Forensic Medicine, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an 710061, China.
| | - Fei Yan
- School of Energy and Power Engineering, Chongqing University, 174 Shapingba Main Street, Chongqing 400030, China.
| | - Chunxia Yan
- School of Forensic Medicine, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an 710061, China.
| | - Shuguang Wei
- School of Forensic Medicine, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an 710061, China.
| | - Jianghua Lai
- School of Forensic Medicine, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an 710061, China.
| | - Yunpeng Wang
- School of Forensic Medicine, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an 710061, China.
| | - Bao Zhang
- School of Forensic Medicine, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an 710061, China.
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13
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Environmental Impact and Carbon Footprint Assessment of Taiwanese Agricultural Products: A Case Study on Taiwanese Dongshan Tea. ENERGIES 2019. [DOI: 10.3390/en12010138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Climate change is an important global environmental threat. Agriculture aggravates climate change by increasing greenhouse gas (GHG) emissions, and in response, climate change reduces agricultural productivity. Consequently, the modern agricultural development mode has progressively transformed into a kind of sustainable development mode. This study aimed to determine the environmental impact and carbon footprint of Dongshan tea from Yilan County. Environmental impact was assessed with use of SimaPro version 8.0.2 and IMPACT2002+. Results showed that climate change has the largest impact upon it in general, followed by human health, natural resources, and ecosystem quality. Furthermore, with use of the IPCC 2007 100a method for carbon footprint of products (CFP), conventional tea was found to have a CFP of 7.035 kgCO2-e, and its main contributors are the raw material (35.15%) and consumer use (45.58%) phases. From this case study, we found that the hotspots of the life cycle of environmental impact of Taiwanese tea mainly come from fertilizer input during the raw material phase, electricity use during manufacturing, and electricity use during water boiling in the consumer use phase (which contributes the largest impact). We propose the ways for consumers to use of highly efficient boiling water facilities and heating preservation, and the government must market the use of organic fertilizers in the national policy subsidies, and farmers have to prudent use of fertilizers and promote the use of local raw fertilizers, and engagement in direct sales for reducing the environmental impacts and costs of agricultural products and thus advancing sustainable agriculture development.
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14
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Bansal S, Thakur S, Mangal M, Mangal AK, Gupta RK. DNA barcoding for specific and sensitive detection of Cuminum cyminum adulteration in Bunium persicum. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2018; 50:178-183. [PMID: 30466976 DOI: 10.1016/j.phymed.2018.04.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/01/2018] [Accepted: 04/08/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Bunium persicum commonly called as Kala zeera, a very high value herbaceous spice used for medicinal purposes is often adulterated with Cuminum cyminum or Safed zeera, a closely related species. Lack of distinctive morphological features makes the identification of genuine kala zeera from its adulterant difficult, the problem is even exaggerated in case of powdered material. METHODOLOGY Genomic DNA was extracted from all the plant materials by using CTAB-SDS method (Möller et al., 1992) with slight modifications. On the basis of reproducibility and high amplification ability, four universal barcoding loci viz. ITS2, rbcL-a, mat K and psbA-trnH and a specific locus Cum were used in the present study. The amplified PCR products were sequenced bidirectionally and assembled to obtain contigs. The sequences thus obtained were aligned using MUSCLE algorithm (Edgar, 2004) and information pertaining to conserved/ variable/ parsimony informative sites, number of transitions, transversions and Indels was obtained after analyzing the sequences. RESULTS AND CONCLUSION Among the tested barcoding loci, psbA-trnH has proven to be best barcode in authentication of kala zeera as its amplification and sequencing success was high and it showed the presence of polymorphic sites to detect interspecific variation. This barcode could differentiate between safed zeera and kala zeera in a single reaction, simultaneously.
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Affiliation(s)
- Sangita Bansal
- ICAR-Central Institute of Post-Harvest Engineering & Technology, Ludhiana, Punjab, India.
| | - Sujata Thakur
- ICAR-Central Institute of Post-Harvest Engineering & Technology, Ludhiana, Punjab, India
| | - Manisha Mangal
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anupam K Mangal
- Central Council for Research in Ayurvedic Sciences (CCRAS), New Delhi, India
| | - R K Gupta
- ICAR-Central Institute of Post-Harvest Engineering & Technology, Ludhiana, Punjab, India
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15
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Lee MS, Huang JY, Lien YY, Sheu SC. The rapid and sensitive detection of edible bird's nest (Aerodramus fuciphagus) in processed food by a loop-mediated isothermal amplification (LAMP) assay. J Food Drug Anal 2018; 27:154-163. [PMID: 30648568 PMCID: PMC9298639 DOI: 10.1016/j.jfda.2018.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/02/2018] [Accepted: 08/07/2018] [Indexed: 12/11/2022] Open
Abstract
Edible bird’s nest (EBN) is a well-known and precious traditional Chinese herbal material (CHM). Because of this, preventing the adulteration of EBN efficiently and precisely is crucial to protect consumers’ interests and health. In this study, a loop-mediated isothermal amplification (LAMP) assay was developed for the detection of EBN using specifically designed LAMP primers. The results demonstrated that the identification of EBN by LAMP assay was specific and rapid (within 1 h). It had no cross-reaction with EBN adulterants, including white fungus, egg white and pig skin, in different ratios. The relative detection limit was 0.01% EBN in the adulterants. Moreover, the sensitivity of LAMP in authenticating EBN was 10−8 μg, it showed higher sensitivity than that of conventional PCR with 105 fold. When genomic DNAs extracted from boiled or steamed EBN samples were used as templates, LAMP for EBN detection was not affected and was reproducible after heat processing. In conclusion, the LAMP assay established herein could be applicable for authenticating EBN and for identifying commercial EBN products in herbal markets.
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Affiliation(s)
- Meng-Shiou Lee
- China Medical University, Department of Chinese Pharmaceutical Science and Chinese Medicine Resources, Taichung, 40402,
Taiwan
| | - Jhong-Yong Huang
- National Pingtung University of Science and Technology, Department of Food Science, Pingtung, 91201,
Taiwan
| | - Yi-Yang Lien
- National Pingtung University of Science and Technology, Department of Veterinary Medicine, Pingtung, 91201,
Taiwan
| | - Shyang-Chwen Sheu
- National Pingtung University of Science and Technology, Department of Food Science, Pingtung, 91201,
Taiwan
- Corresponding author. E-mail address: (S.-C. Sheu)
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16
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Next generation crop improvement program: Progress and prospect in tea ( Camellia sinensis (L.) O. Kuntze). ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.aasci.2018.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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De Castro O, Comparone M, Di Maio A, Del Guacchio E, Menale B, Troisi J, Aliberti F, Trifuoggi M, Guida M. What is in your cup of tea? DNA Verity Test to characterize black and green commercial teas. PLoS One 2017; 12:e0178262. [PMID: 28542606 PMCID: PMC5441638 DOI: 10.1371/journal.pone.0178262] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/04/2017] [Indexed: 01/10/2023] Open
Abstract
In this study, we used several molecular techniques to develop a fast and reliable protocol (DNA Verity Test, DVT) for the characterization and confirmation of the species or taxa present in herbal infusions. As a model plant for this protocol, Camellia sinensis, a traditional tea plant, was selected due to the following reasons: its historical popularity as a (healthy) beverage, its high selling value, the importation of barely recognizable raw product (i.e., crushed), and the scarcity of studies concerning adulterants or contamination. The DNA Verity Test includes both the sequencing of DNA barcoding markers and genotyping of labeled-PCR DNA barcoding fragments for each sample analyzed. This protocol (DVT) was successively applied to verify the authenticity of 32 commercial teas (simple or admixture), and the main results can be summarized as follows: (1) the DVT protocol is suitable to detect adulteration in tea matrices (contaminations or absence of certified ingredients), and the method can be exported for the study of other similar systems; (2) based on the BLAST analysis of the sequences of rbcL+matK±rps7-trnV(GAC) chloroplast markers, C. sinensis can be taxonomically characterized; (3) rps7-trnV(GAC) can be employed to discriminate C. sinensis from C. pubicosta; (4) ITS2 is not an ideal DNA barcode for tea samples, reflecting potential incomplete lineage sorting and hybridization/introgression phenomena in C. sinensis taxa; (5) the genotyping approach is an easy, inexpensive and rapid pre-screening method to detect anomalies in the tea templates using the trnH(GUG)-psbA barcoding marker; (6) two herbal companies provided no authentic products with a contaminant or without some of the listed ingredients; and (7) the leaf matrices present in some teabags could be constituted using an admixture of different C. sinensis haplotypes and/or allied species (C. pubicosta).
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Affiliation(s)
- Olga De Castro
- Department of Biology, Botanical Garden, University of Naples Federico II, Naples Italy
| | - Maria Comparone
- Department of Biology, Botanical Garden, University of Naples Federico II, Naples Italy
| | - Antonietta Di Maio
- Department of Biology, Botanical Garden, University of Naples Federico II, Naples Italy
| | | | - Bruno Menale
- Department of Biology, Botanical Garden, University of Naples Federico II, Naples Italy
| | - Jacopo Troisi
- Department of Medicine and Surgery and Dentistry, University of Salerno, Salerno, Italy
| | | | - Marco Trifuoggi
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Marco Guida
- Department of Biology, University of Naples Federico II, Naples Italy
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