scholarly journals Allele Frequencies of the Single Nucleotide Polymorphisms Related to the Body Burden of Heavy Metals in the Korean Population and Their Ethnic Differences

2016 ◽  
Vol 32 (3) ◽  
pp. 195-205 ◽  
Author(s):  
Sang-Yong Eom ◽  
Ji-Ae Lim ◽  
Yong-Dae Kim ◽  
Byung-Sun Choi ◽  
Myung Sil Hwang ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Single Nucleotide Polymorphisms ◽  
Ethnic Differences ◽  
Body Burden ◽  
The Body ◽  
Allele Frequencies ◽  
Korean Population ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Rapid Pyrosequencing Method for FMO3 Non-Synonymous Genetic Variant Evaluation in A Korean Population

2021 ◽  
Author(s):  
Jin-woo Park ◽  
In-Hwan Park ◽  
Jong-Min Kim ◽  
Kyoung-Ah Kim ◽  
Ji-Young Park
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Ethnic Differences ◽  
Japanese Population ◽  
Genetic Variant ◽  
Allele Frequencies ◽  
Korean Population ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pyrosequencing Method

Abstract Background: The aim of this study was to develop a feasible pyrosequencing method to detect non-synonymous single nucleotide polymorphisms (SNPs) of the flavin-containing monooxygenase 3 (FMO3) gene and compare the ethnic differences in the frequencies of these alleles. Methods and Results: This pyrosequencing method was used to identify four non-synonymous FMO3 SNPs, including c.855C>T (rs909530), c.441C>T (rs1800822), c.923A>G (rs2266782), and c.472G>A (rs2266782). The allele frequencies of these SNPs in 122 unrelated Korean subjects were analyzed, and were as follows: 44.7% for c.855C>T, 23.4% for c.441C>T, 23.0% for c.923A>G, and 27.1% for c.472G>A. Linkage disequilibrium (LD) analysis showed that c.923A>G and c.472G>A were in strong LD (D′ = 0.8289, r2 = 0.5332). Conclusions: The designed pyrosequencing method was successfully applied to identify the c.855C>T, c.441C>T, c.923A>G, and c.472G>A SNPs. The frequencies were similar to those reported previously in a Japanese population. However, in general, large differences between ethnicities were found.

scholarly journals Positive Association of Obesity with Single Nucleotide Polymorphisms of Syndecan 3 in the Korean Population

2006 ◽  
Vol 91 (12) ◽  
pp. 5095-5099 ◽  
Author(s):  
Eunyoung Ha ◽  
Mi-Ja Kim ◽  
Bong-Keun Choi ◽  
Jung-Jae Rho ◽  
Dong-Jae Oh ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Positive Association ◽  
Korean Population ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Allele frequencies and diversity parameters of 27 single nucleotide polymorphisms within and across goat breeds

2006 ◽  
Vol 6 (4) ◽  
pp. 992-997 ◽  
Author(s):  
I. CAPPUCCIO ◽  
L. PARISET ◽  
P. AJMONE-MARSAN ◽  
S. DUNNER ◽  
O. CORTES ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Allele Frequencies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

Ethnic Differences of two Non-synonymous Single Nucleotide Polymorphisms in CDA Gene

2009 ◽  
Vol 24 (6) ◽  
pp. 553-556 ◽  
Author(s):  
Emiko Sugiyama ◽  
Su-Jun Lee ◽  
Sang Seop Lee ◽  
Woo-Young Kim ◽  
Su-Ryang Kim ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Ethnic Differences ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Genetic characterization of buckwheat accessions through genome-wide allele frequency fingerprints / Genetska karakterizacija vzorcev ajde z odtisi frekvence alelov v genomu

2020 ◽  
Vol 61 (1) ◽  
pp. 17-23
Author(s):  
Michelle M. Nay ◽  
Stephen L. Byrne ◽  
Eduardo A. Pérez ◽  
Achim Walter ◽  
Bruno Studer
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Allele Frequency ◽  
Genotyping By Sequencing ◽  
Allele Frequencies ◽  
Fagopyrum Esculentum ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Fagopyrum Esculentum Moench

Genomics-assisted breeding of buckwheat (Fagopyrum esculentum Moench) depends on robust genotyping methods. Genotyping by sequencing (GBS) has evolved as a flexible and cost-effective technique frequently used in plant breeding. Several GBS pipelines are available to genetically characterize single genotypes but these are not able to represent the genetic diversity of buckwheat accessions that are maintained as genetically heterogeneous, open-pollinating populations. Here we report the development of a GBS pipeline which, rather than reporting the state of bi-allelic single nucleotide polymorphisms (SNPs), resolves allele frequencies within populations on a genome-wide scale. These genome-wide allele frequency fingerprints (GWAFFs) from 100 pooled individual plants per accession were found to be highly reproducible and revealed the genetic similarity of 20 different buckwheat accessions analysed in our study. The GWAFFs cannot only be used as an efficient tool to precisely describe buckwheat breeding material, they also offer new opportunities to investigate the genetic diversity between different buckwheat accessions and establish variant databases for key material. Furthermore, GWAFFs provide the opportunity to associate allele frequencies to phenotypic traits and quality parameters that are most reliably described on population level. This is the key to practically implement powerful genomics-assisted breeding concepts such as marker-assisted selection and genomic selection in future breeding schemes of allogamous buckwheat. Key words: Buckwheat (Fagopyrum esculentum Moench), genotyping by sequencing (GBS), population genomics, genome-wide allele frequency fingerprints (GWAFFs)   Izvleček Genomsko podprto žlahtnjenje ajde (Fagopyrum esculentum Moench) je odvisno od robustnih metod genotipiziranja. Genotipiziranje s spremljanjem sekvenc (genotyping by sequencing, GBS) se je razvilo kot fleksibilna in razmeroma poceni metoda, ki se jo uporablja pri žlahtnjenju rastlin. Uporabnih je več virov GBS za genetsko karakterizacijo posamičnih genotipov, toda te metode niso primerne za predstavitev genetske raznolikosti vzorcev ajde, ki jih vzdržujemo v heterozigotni obliki, kar velja za odprto oplodne populacije. Tu poročamo o razvoju GBS metode, ki, namesto prikazovanja bi-alelnega polimorfizma posameznih nukleotidov (single nucleotide polymorphisms, SNPs), pokaže frekvence alelov v populaciji na nivoju genoma. Ta prikaz frekvence alelov na nivoju genoma (genome-wide allele frequency fingerprints, GWAFFs) z združenimi sto posameznimi rastlinami vsakega vzorca se je pokazal kot visoko ponovljiv in je prikazal genetsko podobnost 20 različnih vzorcev ajde, ki smo jih analizirali v naši raziskavi. Metoda GWAFFs ni uporabna samo kot učinkovito orodje za natančen opis materiala za žlahtnjenje ajde, ponuja tudi možnosti raziskave  genetskih razlik med različnimi vzorci ajde in omogoča zbirke podatkov. Nadalje, metoda GWAFFs omogoča povezovanje frekvenc alelov s fenotipskimi lastnostmi in kvalitativnih parametrov, ki so najbolj zanesljivo opisani na nivoju populacij. To je ključ za praktično uporabo z genomiko podprtega žlahtnjenja, kot je z genskimi markerji podprta selekcija in genomska selekcija z GWAFFs. Ključne besede: ajda (Fagopyrum esculentum Moench), genotipizacija s sekvenciranjem (GBS), populacijska genomika, GWAFFs

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