Genetic diversity and species differentiation of medicinal plant Persian Poppy (Papaver bracteatum L.) using AFLP and ISSR markers

Hadipour, Mahdi; Kazemitabar, Seyed Kamal; Yaghini, Hamid; Dayani, Soleyman

doi:10.1016/j.egg.2020.100058

Cited by 15 publications

(15 citation statements)

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“…The maximum number of effective alleles is always an indispensable parameter for detecting genetic variation since it reveals more genetic variation. The average number of effective alleles in this study was 1.524 SCoT:0.230) higher than reported in other studies [40][41][42][43], and the germplasm in this study appears to have higher diversity. Shannon's information index (I) is a crucial parameter for understanding genetic diversity variation by integrating equality and abundance [44].…”

Section: Genetic Diversity Status Of Turkish Laurel Germplasm Using Icontrasting

confidence: 69%

Genetic Relationships and Diversity Analysis in Turkish Laurel (Laurus Nobilis L.) Germplasm Using ISSR and SCoT Markers

Yılmaz

Çi̇ftçi̇

2021

Preprint

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Laurel (Laurus nobilis L.) has been used in the Mediterranean basin since ancient ages. Nowadays, Turkey, Mexico, Portugal, Italy, Spain, France, Algeria, and Morocco use aromatic leaves for commercial purposes, and Turkey is the largest exporter in the world. In this study, molecular characterization and genetic relationships of 94 Turkish laurel genotypes were determined by ISSR and SCoT markers. The experiment was conducted with 16 ISSR and 10 SCoT markers. While 348 of 373 bands were polymorphic with a 94.04% polymorphism rate, Nei's genetic distances ranged between 0.17 and 0.70 with 0.39 mean in ISSR. In SCoT, 175 of 227 bands were polymorphic with 76.07% polymorphism rate, and Nei's distances varied between 0.12 and 0.51. Sufficient genetic diversity determined with diversity parameters consisting the average Shannon's information index (ISSR:0.46, SCoT:0.35), the overall gene diversity (ISSR:0.19, SCoT:0.18), and the effective number of alleles (ISSR:1.52, SCoT:1.38). AMOVA (Analysis of molecular variance) revealed most of the variation was within genotypes (%96). Neighbor-joining algorithms, principal coordinate analysis (PCoA), and model-based structure resulted in harmony and clustered according to the geographical regions and provinces they collected. Genotypes were divided into two groups in ISSR and SCoT with UPGMA clustering resulting in a similar polymorphism distribution. The correlation coefficient (r) determined by marker systems' Nei's genetic distance matrices was 0.88. The results of the study put forward resources for advanced breeding techniques, and contribute to the preservation of genetic diversity, and management of genetic resources for the breeders.

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Section: Genetic Diversity Status Of Turkish Laurel Germplasm Using Icontrasting

confidence: 69%

Genetic Relationships and Diversity Analysis in Turkish Laurel (Laurus Nobilis L.) Germplasm Using ISSR and SCoT Markers

Yılmaz

Çi̇ftçi̇

2021

Preprint

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“…Charged molecules such as nucleic acids and metabolites can be well separated using these techniques to obtain fingerprints ( Shen et al, 2019 ; Gong et al, 2021 ). Gel electrophoresis using agarose or polyacrylamide gel is often employed to quickly confirm the presence of certain amplification products or perform sequencing in DNA barcoding and fingerprinting ( Shen et al, 2019 ; Hadipour et al, 2020 ). Capillary electrophoresis (CE) has also been extensively explored in chemical fingerprinting for the standardization and quality control of herbal medicines ( Johnson and Lunte, 2016 ; Gong et al, 2021 ).…”

Section: Applications Of Fingerprinting Methodsmentioning

confidence: 99%

“…AFLP uses selective amplification of digested DNA fragments to generate unique DNA fingerprints, while ISSRs are DNA fragments (100–3,000 bp) located between two adjacent, oppositely oriented microsatellite regions. Hadipour et al investigated the genetic variation of wild Papaver bracteatum L. from 9 different populations in Iran using AFLP and ISSR markers ( Hadipour et al, 2020 ). The genetic diversities were 52% and 48% among different populations; 38% and 41% within the populations for ISSR and AFLP, respectively.…”

Section: Applications Of Fingerprinting Methodsmentioning

confidence: 99%

“…The successful application of DNA barcoding/fingerprinting relies on the quality of DNA, primer affinity, amplification, and amplicon sequencing. Intact plant DNA can typically be extracted from fresh or dried materials using standard DNA extraction methods ( Shen et al, 2019 ; Hadipour et al, 2020 ). However, significant degradation of DNA can occur during the manufacturing process of herbal products ( de Boer et al, 2015 ).…”

Section: Applications Of Fingerprinting Methodsmentioning

confidence: 99%

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Advances in Fingerprint Analysis for Standardization and Quality Control of Herbal Medicines

2022

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Herbal drugs or herbal medicines (HMs) have a long-standing history as natural remedies for preventing and curing diseases. HMs have garnered greater interest during the past decades due to their broad, synergistic actions on the physiological systems and relatively lower incidence of adverse events, compared to synthetic drugs. However, assuring reproducible quality, efficacy, and safety from herbal drugs remains a challenging task. HMs typically consist of many constituents whose presence and quantity may vary among different sources of materials. Fingerprint analysis has emerged as a very useful technique to assess the quality of herbal drug materials and formulations for establishing standardized herbal products. Rather than using a single or two marker(s), fingerprinting techniques take great consideration of the complexity of herbal drugs by evaluating the whole chemical profile and extracting a common pattern to be set as a criterion for assessing the individual material or formulation. In this review, we described and assessed various fingerprinting techniques reported to date, which are applicable to the standardization and quality control of HMs. We also evaluated the application of multivariate data analysis or chemometrics in assisting the analysis of the complex datasets from the determination of HMs. To ensure that these methods yield reliable results, we reviewed the validation status of the methods and provided perspectives on those. Finally, we concluded by highlighting major accomplishments and presenting a gap analysis between the existing techniques and what is needed to continue moving forward.

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“…DNA barcoding, including random amplification of polymorphic DNA (RAPD) (25) and inter-simple sequence repeats (ISSR) (26), provides a robust evaluation of genome diversity through examination of the presence/absence of more than 20 random fragments of polymorphic DNA at a time. Primer-based approaches amplify random segments of DNA to compare polymorphic variations among species.…”

Section: Geneticsmentioning

confidence: 99%

Chemometric-Guided Approaches for Profiling and Authenticating Botanical Materials

Abraham

Kellogg

2021

Front. Nutr.

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Botanical supplements with broad traditional and medicinal uses represent an area of growing importance for American health management; 25% of U.S. adults use dietary supplements daily and collectively spent over $9. 5 billion in 2019 in herbal and botanical supplements alone. To understand how natural products benefit human health and determine potential safety concerns, careful in vitro, in vivo, and clinical studies are required. However, botanicals are innately complex systems, with complicated compositions that defy many standard analytical approaches and fluctuate based upon a plethora of factors, including genetics, growth conditions, and harvesting/processing procedures. Robust studies rely upon accurate identification of the plant material, and botanicals' increasing economic and health importance demand reproducible sourcing, as well as assessment of contamination or adulteration. These quality control needs for botanical products remain a significant problem plaguing researchers in academia as well as the supplement industry, thus posing a risk to consumers and possibly rendering clinical data irreproducible and/or irrelevant. Chemometric approaches that analyze the small molecule composition of materials provide a reliable and high-throughput avenue for botanical authentication. This review emphasizes the need for consistent material and provides insight into the roles of various modern chemometric analyses in evaluating and authenticating botanicals, focusing on advanced methodologies, including targeted and untargeted metabolite analysis, as well as the role of multivariate statistical modeling and machine learning in phytochemical characterization. Furthermore, we will discuss how chemometric approaches can be integrated with orthogonal techniques to provide a more robust approach to authentication, and provide directions for future research.

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Genetic diversity and species differentiation of medicinal plant Persian Poppy (Papaver bracteatum L.) using AFLP and ISSR markers

Cited by 15 publications

References 31 publications

Genetic Relationships and Diversity Analysis in Turkish Laurel (Laurus Nobilis L.) Germplasm Using ISSR and SCoT Markers

Genetic Relationships and Diversity Analysis in Turkish Laurel (Laurus Nobilis L.) Germplasm Using ISSR and SCoT Markers

Advances in Fingerprint Analysis for Standardization and Quality Control of Herbal Medicines

Chemometric-Guided Approaches for Profiling and Authenticating Botanical Materials

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Genetic diversity and species differentiation of medicinal plant Persian Poppy (Papaver bracteatum L.) using AFLP and ISSR markers

Cited by 15 publications

References 31 publications

Genetic Relationships and Diversity Analysis in Turkish Laurel (Laurus Nobilis L.) Germplasm Using ISSR&nbsp;and SCoT&nbsp;Markers

Genetic Relationships and Diversity Analysis in Turkish Laurel (Laurus Nobilis L.) Germplasm Using ISSR&nbsp;and SCoT&nbsp;Markers

Advances in Fingerprint Analysis for Standardization and Quality Control of Herbal Medicines

Chemometric-Guided Approaches for Profiling and Authenticating Botanical Materials

Contact Info

Product

Resources

About

Genetic Relationships and Diversity Analysis in Turkish Laurel (Laurus Nobilis L.) Germplasm Using ISSR and SCoT Markers

Genetic Relationships and Diversity Analysis in Turkish Laurel (Laurus Nobilis L.) Germplasm Using ISSR and SCoT Markers