Amplified Fragment Length Polymorphism: Applications and Recent Developments

Sheeja, T. E.; Kumar, I. P. Vijesh; Giridhari, Ananduchandra; Divakaran, Minoo; Rajesh, M. K.; Babu, K. Nirmal

doi:10.1007/978-1-0716-0997-2_12

Cited by 14 publications

(6 citation statements)

References 202 publications

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“…Molecular methods for the characterization of microorganisms and of relationships between isolates may be classified into three main groups: PCR-based, restriction enzymes-based, and sequencing-based. PCR-based methods (AFLP, RAPD, VNTR) [ 64 , 65 , 66 ] ( Box 1 ) are commonly used for pathogen typing and as genetic markers for mapping analysis in aquaculture species. The development of PCR-based amplified fragment length polymorphism (AFLP) analysis is a key advancement in simple typing techniques.…”

Section: Pathogen Characterizationmentioning

confidence: 99%

What Can Genetics Do for the Control of Infectious Diseases in Aquaculture?

Sciuto

Colli

Fabris³

et al. 2022

Animals

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Infectious diseases place an economic burden on aquaculture and a limitation to its growth. An innovative approach to mitigate their impact on production is breeding for disease resistance: selection for domestication, family-based selection, marker-assisted selection, and more recently, genomic selection. Advances in genetics and genomics approaches to the control of infectious diseases are key to increasing aquaculture efficiency, profitability, and sustainability and to reducing its environmental footprint. Interaction and co-evolution between a host and pathogen can, however, turn breeding to boost infectious disease resistance into a potential driver of pathogenic change. Parallel molecular characterization of the pathogen and its virulence and antimicrobial resistance genes is therefore essential to understand pathogen evolution over time in response to host immunity, and to apply appropriate mitigation strategies.

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Section: Pathogen Characterizationmentioning

confidence: 99%

What Can Genetics Do for the Control of Infectious Diseases in Aquaculture?

Sciuto

Colli

Fabris³

et al. 2022

Animals

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“…This technique can quickly generate a large number of DNA fragments for any organism, with high degrees of reproducibility and discriminatory power ( Janssen et al., 1996 ; Savelkoul et al., 1999 ; Paun and Schönswetter, 2012 ). Briefly, AFLP is a PCR-based molecular technique that uses selective amplification of a subset of restriction enzyme digested DNA fragments from any source to generate and compare unique electrophoretic patterns among genomes ( Sheeja et al., 2021 ). Thus, AFLP requires limited amounts of materials but combines the advantages of both RFLP and RAPD in terms of reproducibility and resolution ( Janssen et al., 1996 ; Savelkoul et al., 1999 ; Paun and Schönswetter, 2012 ).…”

Section: Amplified Fragment Length Polymorphismmentioning

confidence: 99%

“…Thus, AFLP requires limited amounts of materials but combines the advantages of both RFLP and RAPD in terms of reproducibility and resolution ( Janssen et al., 1996 ; Savelkoul et al., 1999 ; Paun and Schönswetter, 2012 ). In addition, it does not require any prior genome information ( Sheeja et al., 2021 ). Overall, despites its higher labor intensity and higher cost than other methods such as RFLP, RAPD and PCR-fingerprinting, the AFLP technique is generally more discriminatory than other molecular typing methods ( Savelkoul et al., 1999 ; Paun and Schönswetter, 2012 ; Grover and Sharma, 2016 ).…”

Section: Amplified Fragment Length Polymorphismmentioning

confidence: 99%

Molecular Markers Reveal Epidemiological Patterns and Evolutionary Histories of the Human Pathogenic Cryptococcus

Hong

Chen

2021

Front. Cell. Infect. Microbiol.

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The human pathogenic Cryptococcus species are the main agents of fungal meningitis in humans and the causes of other diseases collectively called cryptococcosis. There are at least eight evolutionary divergent lineages among these agents, with different lineages showing different geographic and/or ecological distributions. In this review, we describe the main strain typing methods that have been used to analyze the human pathogenic Cryptococcus and discuss how molecular markers derived from the various strain typing methods have impacted our understanding of not only cryptococcal epidemiology but also its evolutionary histories. These methods include serotyping, multilocus enzyme electrophoresis, electrophoretic karyotyping, random amplified polymorphic DNA, restriction fragment length polymorphism, PCR-fingerprinting, amplified fragment length polymorphism, multilocus microsatellite typing, single locus and multilocus sequence typing, matrix-assisted laser desorption/ionization time of flight mass spectrometry, and whole genome sequencing. The major findings and the advantages and disadvantages of each method are discussed. Together, while controversies remain, these strain typing methods have helped reveal (i) the broad phylogenetic pattern among these agents, (ii) the centers of origins for several lineages and their dispersal patterns, (iii) the distributions of genetic variation among geographic regions and ecological niches, (iv) recent hybridization among several lineages, and (v) specific mutations during infections within individual patients. However, significant challenges remain. Multilocus sequence typing and whole genome sequencing are emerging as the gold standards for continued strain typing and epidemiological investigations of cryptococcosis.

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“…RAPD utilizes random primers to amplify DNA fragments, making it a quick and less expensive technique for genetic diversity analysis [31]. AFLP utilizes restriction enzymes and PCR to create DNA fragments, offering high reproducibility and sensitivity [32].…”

Section: Introductionmentioning

confidence: 99%

Optimization of Plant Growth Regulators for In Vitro Mass Propagation of a Disease-Free ‘Shine Muscat’ Grapevine Cultivar

Kim,

Zebro,

Jang

et al. 2023

CIMB

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This study addresses the propagation challenges faced by ‘Shine Muscat’, a newly introduced premium grapevine cultivar in South Korea, where multiple viral infections pose considerable economic loss. The primary objective was to establish a robust in vitro propagation method for producing disease-free grapes and to identify effective plant growth regulators to facilitate large-scale mass cultivation. After experimentation, 2.0 µM 6-benzyladenine (BA) exhibited superior shoot formation in the Murashige and Skoog medium compared with kinetin and thidiazuron. Conversely, α-naphthaleneacetic acid (NAA) hindered shoot growth and induced callus formation, while indole-3-butyric acid (IBA) and indole-3-acetic acid (IAA) demonstrated favorable root formation, with IBA showing better results overall. Furthermore, inter simple sequence repeat analysis confirmed the genetic stability of in vitro-cultivated seedlings using 2.0 μM BA and 1.0 μM IBA, validating the suitability of the developed propagation method for generating disease-free ‘Shine Muscat’ grapes. These findings offer promising prospects for commercial grape cultivation, ensuring a consistent supply of healthy grapes in the market.

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Amplified Fragment Length Polymorphism: Applications and Recent Developments

Cited by 14 publications

References 202 publications

What Can Genetics Do for the Control of Infectious Diseases in Aquaculture?

What Can Genetics Do for the Control of Infectious Diseases in Aquaculture?

Molecular Markers Reveal Epidemiological Patterns and Evolutionary Histories of the Human Pathogenic Cryptococcus

Optimization of Plant Growth Regulators for In Vitro Mass Propagation of a Disease-Free ‘Shine Muscat’ Grapevine Cultivar

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