High-Resolution Melting Analysis for the Discovery of Novel Single-Nucleotide Polymorphisms in Rainbow and Cutthroat Trout for Species Identification

2010 ◽  
Vol 139 (3) ◽  
pp. 676-684 ◽  
Author(s):  
Molly T. McGlauflin ◽  
Matt J. Smith ◽  
Jonathan T. Wang ◽  
Sewall F. Young ◽  
Neng Chen ◽  
...  
Keyword(s):  
High Resolution ◽  
Single Nucleotide Polymorphisms ◽  
Species Identification ◽  
High Resolution Melting ◽  
Cutthroat Trout ◽  
High Resolution Melting Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Melting Analysis

scholarly journals The Identification of Several Dipterocarpaceae and Fagaceae Trees by Barcode DNA Coupled with High-Resolution Melting Analysis

Forests ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1466
Author(s):  
Maslin Osathanunkul ◽  
Panagiotis Madesis
Keyword(s):  
High Resolution ◽  
Species Identification ◽  
Forest Conservation ◽  
High Resolution Melting ◽  
Economic Problem ◽  
High Resolution Melting Analysis ◽  
Essential Information ◽  
Barcode Dna ◽  
Melting Analysis ◽  
Dipterocarpus Alatus

The loss of forests is a major environmental, social, and economic problem. The disappearance has been occurring to an extreme degree in many parts of Southeast Asia, including Thailand. Logging and clearing of forests for agriculture, cash crops, and food production has destroyed much of the tropical forests in Thailand. Floristic inventory could provide essential information for forest conservation but species identification as a part of inventory creating could be challenging in some cases. Barcode DNA coupled with High Resolution Melting analysis (Bar-HRM) was used here in aiding species identification of plant in Dipterocarpaceae (Dipterocarpus alatus, D. costatu, D. intricatus, D. obtusifolius, Hopea ferrea, H. odorata, Shorea guiso, S. obtuse, S. roxburghii, and S. siamensis) and Fagaceae (Castanopsis echinocarpa, C. inermis, Lithocarpus wallichianus, Quercus aliena and Q. oidocarpa) families. Two main experiments were conducted including: (1) a comparing method for primer design and (2) testing the robustness of the Bar-HRM by trying to identify tree samples that did not have sequences in the GenBank. In experiment 1, the manual design primer pair was found to be the best fit for the work. Of key importance is finding the primers which give the most nucleotide variations within the generated amplicon; this is a parameter that cannot be set in any web-based tools. Next, in experiment 2, Bar-HRM using primers of ITS1 and ITS2 regions were able to discriminate all 10 tested tree species without any problem, even when there were no sequences of the samples to be analysed before performing the HRM. Here, Bar-HRM poses potential to be a game-changer in tropical forest conservation, as it will be useful for species identification.

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