scholarly journals Genetic diversity and re-classification of coffee (Coffea canephora Pierre ex A. Froehner) from South Western Nigeria through genotyping-by-sequencing-single nucleotide polymorphism analysis

2019 ◽  
Vol 66 (3) ◽  
pp. 685-696 ◽  
Author(s):  
Chinyere F. Anagbogu ◽  
Ranjana Bhattacharjee ◽  
Christopher Ilori ◽  
Pumipat Tongyoo ◽  
Keji E. Dada ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Genotyping By Sequencing ◽  
Coffea Canephora ◽  
Polymorphism Analysis ◽  
Single Nucleotide Polymorphism Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Genetic Diversity of Purple Passion Fruit, Passiflora edulis f. edulis, Based on Single-Nucleotide Polymorphism Markers Discovered through Genotyping by Sequencing

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 144
Author(s):  
Nohra Castillo Rodríguez ◽  
Xingbo Wu ◽  
María Isabel Chacón ◽  
Luz Marina Melgarejo ◽  
Matthew Wohlgemuth Blair
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Genotyping By Sequencing ◽  
Passion Fruit ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Passiflora Edulis ◽  
Tropical Fruit ◽  
Commercial Cultivars ◽  
Purple Passion Fruit

Orphan crops, which include many of the tropical fruit species used in the juice industry, lack genomic resources and breeding efforts. Typical of this dilemma is the lack of commercial cultivars of purple passion fruit, Passiflora edulis f. edulis, and of information on the genetic resources of its substantial semiwild gene pool. In this study, we develop single-nucleotide polymorphism (SNP) markers for the species and show that the genetic diversity of this fruit crop has been reduced because of selection for cultivated genotypes compared to the semiwild landraces in its center of diversity. A specific objective of the present study was to determine the genetic diversity of cultivars, genebank accession, and landraces through genotyping by sequencing (GBS) and to conduct molecular evaluation of a broad collection for the species P. edulis from a source country, Colombia. We included control genotypes of yellow passion fruit, P. edulis f. flavicarpa. The goal was to evaluate differences between fruit types and compare landraces and genebank accessions from in situ accessions collected from farmers. In total, 3820 SNPs were identified as informative for this diversity study. However, the majority distinguished yellow and purple passion fruit, with 966 SNPs useful in purple passion fruits alone. In the population structure analysis, purple passion fruits were very distinct from the yellow ones. The results for purple passion fruits alone showed reduced diversity for the commercial cultivars while highlighting the higher diversity found among landraces from wild or semi-wild conditions. These landraces had higher heterozygosity, polymorphism, and overall genetic diversity. The implications for genetics and breeding as well as evolution and ecology of purple passion fruits based on the extant landrace diversity are discussed with consideration of manual or pollinator-assisted hybridization of this species.

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 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.

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