DNA TECHNIQUES FOR THE AUTHENTICATION OF CHINESE MEDICINAL MATERIALS
Kevin Chan, Henry Lee in The Way Forward for Chinese Medicine, 2001
AFLP is a newly emerged DNA marker technology based on the selective amplification of restriction fragments (Vos et al. 1995). Total genomic DNA is digested with appropriate restriction enzymes, ligated to synthetic adaptors and amplified using primers complementary to selective sequence on the adaptor. The complexity of the AFLP profiles is dictated by the primers chosen and the composition of the genomic DNA. Results are reproducible as specific primers and high stringent amplification conditions are used. This technique has been widely employed in the analysis of genetic diversity in bacteria (Lin and Kuo 1996; Janssen et al. 1997), fungi (Muller et al. 1996; Leissner et al. 1997), plants (Lu et al. 1996; He and Prakash 1997), insects (Reineke et al. 1998) and human (Latorra and Schanfield 1996), as well as in the studies of genetic relatedness (Travis et al. 1996; Ellis et al. 1997) and gene mapping (Otsen et al. 1996).
Sources of Essential Oils
K. Hüsnü Can Başer, Gerhard Buchbauer in Handbook of Essential Oils, 2020
Besides sequence information–based approaches, multilocus DNA methods (RAPD, amplified fragment length polymorphism, etc.) are complementing in resolving complicated taxa and can become a barcode for the identification of populations and cultivars (Weising et al., 2005). With multilocus DNA methods, it is furthermore possible to tag a specific feature of a plant of which the genetic basis is still unknown. This approach is called molecular markers (in sensu strictu) because they mark the occurrence of a specific trait like a chemotype or flower color. The gene regions visualized, for example, on an agarose gel are not the specific gene responsible for a trait but are located on the genome in the vicinity of this gene and therefore co-occur with the trait and are absent when the trait is absent. An example for such an inexpensive and fast polymerase chain reaction system was developed by Bradbury et al. (2005) to distinguish fragrant from nonfragrant rice cultivars. If markers would be developed for chemotypes in essential oil plants, species identification by DNA and the determination of a chemotype could be performed in one step.
Impact of Integrated Omics Technologies for Identification of Key Genes and Enhanced Artemisinin Production in Artemisia annua L.
Tariq Aftab, M. Naeem, M. Masroor, A. Khan in Artemisia annua, 2017
There has been significant progress in molecular plant breeding techniques using various molecular tools such as DNA markers (e.g., restriction fragment length polymorphism [RFLP], RAPD, amplified fragment length polymorphism [AFLP], SSRs, SNPs, sequence tagged microsatellite sites [STMS], SCAR, etc.) and functional markers (ESTs, microarray, qRT-PCR, etc.), which can be variously used to speed up the selection/recognition of desired genotypes for high-yielding traits at an early stage of development (Figure 10.5). Although these marker-assisted molecular breeding techniques are being applied in various crops, there is relatively little information on molecular marker–based approaches in medicinal plants, in which secondary metabolism is of great importance. One such effort was made in A. annua by CIMAP (India) for developing the high-AN variety CIM‑Arogya through marker-assisted selection breeding. For the production of high-yield varieties of A. annua, a fast-track molecular breeding project, led by CNAP’s Director Dianna Bowles and Deputy Director Ian Graham, was funded by the Bill & Melinda Gates Foundation. With the aim of producing a better non-GM variety of A. annua, about 23,000 parental lines were screened for desired high-yielding traits, and several hybrid crosses were made. After a rigorous selection procedure aided by molecular tools, the two best-performing hybrids, Hyb1209r (Shennong) and Hyb8001r (Zenith), with enhanced AN production have been commercially released.
Genetic diversity, allelic variation and marker trait associations in gamma irradiated mutants of rice (Oryza sativa L.)
Published in International Journal of Radiation Biology, 2022
S. Ramchander, M. T. Andrew Peter Leon, J. Souframanien, M. Arumugam Pillai
Screening of mutants is a laborious task since a majority of the nucleotide variations produce very little or no phenotypic effects to observe. DNA markers are useful tools in such situations due to their hypervariability, high reproducibility, high throughput, and the ability to screen variations regardless of the stage of the crop and no influence by the growing environment. Although a variety of molecular markers such as restriction fragment length polymorphisms (RFLP) (Botstein et al. 1980; Paran and Michelmore 1993; Becker et al. 1995), randomly amplified polymorphic DNA (RAPD) (Williams et al. 1990; Tingey and del Tufo 1993), amplified fragment length polymorphism (AFLP) (Thomas et al. 1995; Vos et al. 1995; Mackill et al. 1996; Zhu et al. 1998), inter simple sequence repeats (ISSRs) (Albani and Wilkinson 1998; Blair et al. 1999), single-nucleotide polymorphisms (SNPs) (Vieux et al. 2002) and diversity array technology (DArT) (Wenzl et al. 2004) are available, simple sequence repeats (SSRs) (Tautz and Renz 1984; Levinson and Gutman 1987) remains one of the favorite choices in rice breeding. SSRs are wellspread in the eukaryote genome (Field and Wills 1996) and are found in mitochondria (Kumar et al. 2014) and chloroplasts (Kapil et al. 2014). This abundance, co-dominant nature, and ease-of-use make SSRs as one of the preferred method in characterizing mutants, for example: rice mutants developed from N-nitroso-N-methyl urea (Tu Anh et al. 2018), Basmati mutants developed from ethyl methane sulfonate (Hameed et al. 2020) and gamma ray induced mutants of rice (Aryanti and Ishak 2018).
Shared detection of Porphyromonas gingivalis in cohabiting family members: a systematic review and meta-analysis
Published in Journal of Oral Microbiology, 2020
Maha Bennani, Hélène Rangé, Vincent Meuric, Francis Mora, Philippe Bouchard, Maria Clotilde Carra
Bacterial sampling was carried out on supra-gingival and/or subgingival plaque, stimulated saliva, or sampled from dorsum of the tongue, buccal mucosa, or tonsillar area. Detection methods included culture in 10 studies (38.4%), and Polymerase Chain Reaction (PCR) in 11 studies (42.3%). DNA restriction enzyme analysis (REA-DNA) was used in 4 studies (15.3%), pulsed field gel electrophoresis (PFGE) in 1 study, arbitrarily primed polymerase chain reaction (AP-PCR) in 2 (7.6%) studies, amplified fragment length polymorphism (AFLP-PCR) in 3, strain-specific identification of P. gingivalis I Isi 1126 PCR in 1, and Fim A genotyping in 3 studies. Serotyping characterization and ribotyping were reported in 2 studies, respectively.
Utility of TRAP markers to determine indel mutation frequencies induced by gamma-ray irradiation of faba bean (Vicia faba L.) seeds
Published in International Journal of Radiation Biology, 2019
Min-Kyu Lee, Jae Il Lyu, Min Jeong Hong, Dong-Gun Kim, Jung Min Kim, Jin-Baek Kim, Seok Hyun Eom, Bo-Keun Ha, Soon-Jae Kwon
Mutation breeding is a useful tool for improving various crop species. Previously, 68.5% of all radiation-induced mutant cultivars have been generated by gamma ray treatment (FAO/IAEA Mutant Variety Database 2016). Gamma rays are superior mutagens than chemicals because different types of DNA mutations can be generated with mutation frequencies that are suitable for breeding commercial cultivars (Datta 2009; Tanaka et al. 2010). Oldach (2011) compiled a list of 19 faba bean mutant cultivars that were developed between 1959 and 2009. The mutations induced abnormal plant characters associated with plant size (dwarfism), disease resistance (i.e. resistance to Orobanche, Sclerotinia blight, Botrytis fabae, and Uromyces fabae), seed protein content (high protein), vicine content (low vicine content), lodging resistance, and maturation (early maturity). Various molecular techniques applicable to mutation breeding have been developed based on genetic diversity, polymorphisms, and mutated gene tagging, including random amplified polymorphic DNA (RAPD) (Williams et al. 1990), amplified fragment length polymorphism (AFLP) (Zabeau and Vos 2000), restriction fragment length polymorphism (Botstein et al. 1980), simple sequence repeat (Tautz 1989), and target region amplification polymorphism (TRAP) (Hu and Vick 2003). Among these marker types, the TRAP system is a relatively new and simple polymerase chain reaction (PCR)-based method, and available DNA sequence information can be used to detect genetic variations (Hu and Vick 2003). The TRAP method uses a fixed primer specific for a known gene sequence and pairs it with arbitrary primers that target intron or exon regions with AT-rich or GC-rich cores to amplify DNA fragments (Li and Quiros 2001).
Related Knowledge Centers
- DNA Ligase
- DNA Profiling
- Genetic Engineering
- Genome
- Polymerase Chain Reaction
- Restriction Enzyme
- Restriction Fragment
- Genetics
- Adapter
- Sticky & Blunt Ends