scholarly journals Single-Strand Conformation Polymorphism Fingerprint Method for Dictyostelids

2021 ◽  
Vol 12 ◽  
Author(s):  
Phongthana Pasookhush ◽  
Asmatullah Usmani ◽  
Kowit Suwannahong ◽  
Prasit Palittapongarnpim ◽  
Kamolchanok Rukseree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Large Scale ◽  
Single Strand Conformation Polymorphism ◽  
Ssu Rdna ◽  
Single Strand ◽  
Biological Research ◽  
Gene Sequences ◽  
Genetic Diversity Study ◽  
Conformation Polymorphism ◽  
Diversity Study

Dictyostelid social amoebae are a highly diverse group of eukaryotic soil microbes that are valuable resources for biological research. Genetic diversity study of these organisms solely relies on molecular phylogenetics of the SSU rDNA gene, which is not ideal for large-scale genetic diversity study. Here, we designed a set of PCR–single-strand conformation polymorphism (SSCP) primers and optimized the SSCP fingerprint method for the screening of dictyostelids. The optimized SSCP condition required gel purification of the SSCP amplicons followed by electrophoresis using a 9% polyacrylamide gel under 4°C. We also tested the optimized SSCP procedure with 73 Thai isolates of dictyostelid that had the SSU rDNA gene sequences published. The SSCP fingerprint patterns were related to the genus-level taxonomy of dictyostelids, but the fingerprint dendrogram did not reflect the deep phylogeny. This method is rapid, cost-effective, and suitable for large-scale sample screening as compared with the phylogenetic analysis of the SSU rDNA gene sequences.

scholarly journals Detection of Genetic Diversity in Four Candidate Genes by Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) Analysis of Goats in Sri Lanka

2016 ◽  
Vol 4 (1) ◽  
pp. 133-138
Author(s):  
H.B.P.C. Ariyarathne ◽  
LGS Lokugalappatti ◽  
H.B.S. Ariyaratne ◽  
D.M.S. Munasinghe
Keyword(s):  
Genetic Diversity ◽  
Polymerase Chain Reaction ◽  
Candidate Genes ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Sri Lankan ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Phenotypic Groups ◽  
Conformation Polymorphism

Genetic diversity of Sri Lankan goats (Capra hircus) was evaluated using Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) method to detect polymophism in four candidate genes (LALBA, k-CSN3, GnRHR and BMP4) in a sample of 219 goats representing three phenotypic groups. All studied loci were polymorphic, having three morphs for BMP4, LALBA and two morphs for k-CSN3 and GnRHR in the study population. A significant difference between genotypic frequencies for BMP4 and GnRHR genes was found while PIC criterion revealed an intermediate polymorphism for all analyzed phenotypic groups except for k-CSN3 and GnRHR genes. Cross-bred animals for BMP4 gene and nondescript animals for LALBA gene were comparatively more polymorphic according to the effective allele number criterion. This study provides insight into the genetic diversity of Sri Lankan goats, which can be utilized to develop single nucleotide polymorphism markers to be used in association studies, and marker assisted selection.Int J Appl Sci Biotechnol, Vol 4(1): 133-138

scholarly journals Isolation and Characterization of Microsatellite Loci of Clarias macrocephalus and Their Application to Genetic Diversity Study

1999 ◽  
Vol 65 (4) ◽  
pp. 520-526 ◽  
Author(s):  
Uthairat Na-Nakorn ◽  
Nobuhiko Taniguchi ◽  
Estu Nugroho ◽  
Shingo Seki ◽  
Wongpathom Kamonrat
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Isolation And Characterization ◽  
Clarias Macrocephalus ◽  
Genetic Diversity Study ◽  
Diversity Study
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