scholarly journals Gas Chromatography-Mass Spectrometry and Single Nucleotide Polymorphism-Genotype-By-Sequencing Analyses Reveal the Bean Chemical Profiles and Relatedness of Coffea canephora Genotypes in Nigeria

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 425
Author(s):  
Chinyere F. Anagbogu ◽  
Christopher O. Ilori ◽  
Ranjana Bhattacharjee ◽  
Olufemi O. Olaniyi ◽  
Diane M. Beckles
Keyword(s):  
Gas Chromatography ◽  
Single Nucleotide Polymorphism ◽  
Coffea Canephora ◽  
Gas Chromatography Mass Spectrometry ◽  
P Value ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Chemical Profiles ◽  
Genotype By Sequencing

The flavor and health benefits of coffee (Coffea spp.) are derived from the metabolites that accumulate in the mature bean. However, the chemical profiles of many C. canephora genotypes remain unknown, even as the production of these coffee types increases globally. Therefore, we used Gas Chromatography-Mass Spectrophotometry to determine the chemical composition of C. canephora genotypes in Nigeria—those conserved in germplasm repositories and those cultivated by farmers. GC-MS revealed 340 metabolites in the ripe beans, with 66 metabolites differing (p-value < 0.05) across the represented group. Univariate and multivariate approaches showed that the ‘Niaouli’ genotypes could be clearly distinguished from ‘Kouillou’ and ‘Java’ genotypes, while there was almost no distinction between ‘Kouillou’ and ‘Java,’. Varietal genotyping based on bean metabolite profiling was synchronous with that based on genome-wide Single Nucleotide Polymorphism analysis. Across genotypes, the sucrose-to-caffeine ratio was low, a characteristic indicative of low cup quality. The sucrose-to-caffeine ratio was also highly correlated, indicative of common mechanisms regulating the accumulation of these compounds. Nevertheless, this strong correlative link was broken within the ‘Niaouli’ group, as caffeine and sucrose content were highly variable among these genotypes. These ‘Niaouli’ genotypes could therefore serve as useful germplasm for starting a Nigerian C. canephora quality improvement breeding program.

scholarly journals Whole-Genome Single-Nucleotide-Polymorphism Analysis for Discrimination of Clostridium botulinum Group I Strains

2014 ◽  
Vol 80 (7) ◽  
pp. 2125-2132 ◽  
Author(s):  
Narjol Gonzalez-Escalona ◽  
Ruth Timme ◽  
Brian H. Raphael ◽  
Donald Zink ◽  
Shashi K. Sharma
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Clostridium Botulinum ◽  
Toxin Gene ◽  
Polymorphism Analysis ◽  
Snp Analysis ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type ◽  
Group I

ABSTRACTClostridium botulinumis a genetically diverse Gram-positive bacterium producing extremely potent neurotoxins (botulinum neurotoxins A through G [BoNT/A-G]). The complete genome sequences of three strains harboring only the BoNT/A1 nucleotide sequence are publicly available. Although these strains contain a toxin cluster (HA+OrfX−) associated with hemagglutinin genes, little is known about the genomes of subtype A1 strains (termed HA−OrfX+) that lack hemagglutinin genes in the toxin gene cluster. We sequenced the genomes of three BoNT/A1-producingC. botulinumstrains: two strains with the HA+OrfX−cluster (69A and 32A) and one strain with the HA−OrfX+cluster (CDC297). Whole-genome phylogenic single-nucleotide-polymorphism (SNP) analysis of these strains along with other publicly availableC. botulinumgroup I strains revealed five distinct lineages. Strains 69A and 32A clustered with theC. botulinumtype A1 Hall group, and strain CDC297 clustered with theC. botulinumtype Ba4 strain 657. This study reports the use of whole-genome SNP sequence analysis for discrimination ofC. botulinumgroup I strains and demonstrates the utility of this analysis in quickly differentiatingC. botulinumstrains harboring identical toxin gene subtypes. This analysis further supports previous work showing that strains CDC297 and 657 likely evolved from a common ancestor and independently acquired separate BoNT/A1 toxin gene clusters at distinct genomic locations.

scholarly journals Flow Cytometric Platform for High-Throughput Single Nucleotide Polymorphism Analysis

BioTechniques ◽  
2001 ◽  
Vol 30 (3) ◽  
pp. 661-669 ◽  
Author(s):  
J.D. Taylor ◽  
D. Briley ◽  
Q. Nguyen ◽  
K. Long ◽  
M.A. Iannone ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
High Throughput ◽  
Polymorphism Analysis ◽  
Single Nucleotide Polymorphism Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Flow Cytometric

Single-Nucleotide Polymorphism Analysis by Pyrosequencing

2000 ◽  
Vol 280 (1) ◽  
pp. 103-110 ◽  
Author(s):  
Afshin Ahmadian ◽  
Baback Gharizadeh ◽  
Anna C. Gustafsson ◽  
Fredrik Sterky ◽  
Pål Nyrén ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Polymorphism Analysis ◽  
Single Nucleotide Polymorphism Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Establishment and application of a novel method based on single nucleotide polymorphism analysis for detecting β-globin gene cluster deletions

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Siqi Hu ◽  
Wenli Zhan ◽  
Jicheng Wang ◽  
Jia Xie ◽  
Weiping Zhou ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Gene Cluster ◽  
Predictive Value ◽  
Globin Gene ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Globin Gene Cluster ◽  
Arms Pcr ◽  
Novel Method

Abstract β-Globin gene mutations reduce or terminate the production of beta globin chains, of which approximately 10% are large deletions within the β-globin gene cluster. Because gene deletion leads to loss of heterozygosity at single nucleotide polymorphism (SNP), a novel method for detecting β-globin gene cluster deletions based on SNP heterozygosity analysis was established in this study. The location range of SNPs was selected according to the breakpoint of β-globin gene cluster deletions. SNPs were screened using bioinformatics analysis and population sequencing data. A novel method which enables genotyping of multiplex SNPs based on tetra-primer ARMS-PCR was designed and optimized. Forty clinical samples were tested in parallel by this method and MLPA to verify the performance of this method for detecting β-globin gene cluster deletion. Six informative SNPs were obtained, achieving heterozygote coverage of 93.3% in normal individuals. Genotyping of six SNPs were successfully integrated into two multiplex tetra-primer ARMS-PCR reactions. The sensitivity, specificity, positive predictive value and negative predictive value of the method for detecting β-globin gene cluster deletion were 100%, 96.30%, 92.86%, and 100%, respectively. This is a simple, cost-effective and novel method for detecting β-globin gene cluster deletions, which may be suitable for use in combination with MLPA for thalassemia molecular testing.

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