scholarly journals Single nucleotide polymorphism (SNP) characterization of drought-responsive genes to estimate genetic variation of Populus tremula var. davidiana and eight other Populus species

2018 ◽  
Vol 48 (6) ◽  
pp. 689-696 ◽  
Author(s):  
Yong-Yul Kim ◽  
Soon-Ho Kwon ◽  
Aruna Jo ◽  
Yang-Gil Kim ◽  
Jei-Wan Lee ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Genetic Variation ◽  
Expectation Maximization Algorithm ◽  
Snp Genotyping ◽  
Populus Tremula ◽  
Taqman Probe ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genetic Mechanisms ◽  
Populus Species

To reveal the genetic mechanisms behind drought tolerance, we attempted to identify the drought-responsive genes in Populus tremula var. davidiana (Dode) C.K. Schneid. and eight other species of Populus. Nine drought-responsive genes were assayed by single nucleotide polymorphism (SNP) genotyping using TaqMan probe-based real-time PCR. A total of 346 SNPs were found from the 101 sequences of the nine genes. Among them, 57 primers were selected for SNP genotyping and haplotype determination. For the SNP genotyping, 56 assays were applicable to section Leuce Duby, 53 to section Aigeiros Duby, 50 to Populus maximowiczii Henry, and 52 to Populus simonii Carrière. The expectation maximization algorithm was implemented to determine haplotypes among species and sections. A total of 78 haploid types were estimated from nine drought-responsive gene loci, and the average number of haploid types per locus was 8.67. The analysis of genetic diversity revealed that P. tremula var. davidiana had substantial levels of genetic variation for the nine drought-responsive genes, which was higher than the eight other species. The means of observed number of alleles (NA) and heterozygosity (Ho) were 5.33 and 0.6609, respectively. Analysis of the genetic differentiation of P. tremula var. davidiana showed that 7.52% of genetic variation was among populations and the remaining was within a population.

scholarly journals Single Nucleotide Polymorphism Genotyping Analysis Shows That Vaccination Can Limit the Number and Diversity of Recombinant Progeny of Infectious Laryngotracheitis Viruses from the United States

2018 ◽  
Vol 84 (23) ◽  
Author(s):  
Carlos A. Loncoman ◽  
Carol A. Hartley ◽  
Mauricio J. C. Coppo ◽  
Glenn F. Browning ◽  
Gabriela Beltrán ◽  
...  
Keyword(s):  
United States ◽  
Single Nucleotide Polymorphism ◽  
Viral Replication ◽  
The United States ◽  
Snp Genotyping ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genotyping Assay ◽  
Infectious Laryngotracheitis

ABSTRACT Infectious laryngotracheitis (ILTV; Gallid alphaherpesvirus 1) causes mild to severe respiratory disease in poultry worldwide. Recombination in this virus under natural (field) conditions was first described in 2012 and more recently has been studied under laboratory conditions. Previous studies have revealed that natural recombination is widespread in ILTV and have also demonstrated that recombination between two attenuated ILTV vaccine strains generated highly virulent viruses that produced widespread disease within poultry flocks in Australia. In the United States, natural ILTV recombination has also been detected, but not as frequently as in Australia. To better understand recombination in ILTV strains originating from the United States, we developed a TaqMan single nucleotide polymorphism (SNP) genotyping assay to detect recombination between two virulent U.S. field strains of ILTV (63140 and 1874c5) under experimental in vivo conditions. We also tested the capacity of the Innovax-ILT vaccine (a recombinant vaccine using herpesvirus of turkeys as a vector) and the Trachivax vaccine (a conventionally attenuated chicken embryo origin vaccine) to reduce recombination. The Trachivax vaccine prevented ILTV replication, and therefore recombination, in the trachea after challenge. The Innovax-ILT vaccine allowed the challenge viruses to replicate and to recombine, but at a significantly lower rate than in an unvaccinated group of birds. Our results demonstrate that the TaqMan SNP genotyping assay is a useful tool to study recombination between these ILTV strains and also show that vaccination can limit the number and diversity of recombinant progeny viruses. IMPORTANCE Recombination allows alphaherpesviruses to evolve over time and become more virulent. Historically, characterization of viral vaccines in poultry have mainly focused on limiting clinical disease, rather than limiting virus replication, but such approaches can allow field viruses to persist and evolve in vaccinated populations. In this study, we vaccinated chickens with Gallid alphaherpesvirus 1 vaccines that are commercially available in the United States and then performed coinoculations with two field strains of virus to measure the ability of the vaccines to prevent field strains from replicating and recombining. We found that vaccination reduced viral replication, recombination, and diversity compared to those in unvaccinated chickens, although the extent to which this occurred differed between vaccines. We suggest that characterization of vaccines could include studies to examine the ability of vaccines to reduce viral recombination in order to limit the rise of new virulent field strains due to recombination, especially for those vaccines that are known not to prevent viral replication following challenge.

Single-nucleotide polymorphism (SNP) genotyping using cationic conjugated polymers in homogeneous solution

2009 ◽  
Vol 4 (6) ◽  
pp. 984-991 ◽  
Author(s):  
Xinrui Duan ◽  
Wei Yue ◽  
Libing Liu ◽  
Zhengping Li ◽  
Yuliang Li ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Conjugated Polymers ◽  
Homogeneous Solution ◽  
Snp Genotyping ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Single-Nucleotide-Polymorphism Genotyping ofCoxiella burnetiiduring a Q Fever Outbreak in The Netherlands

2011 ◽  
Vol 77 (6) ◽  
pp. 2051-2057 ◽  
Author(s):  
Cornelis J. J. Huijsmans ◽  
Jeroen J. A. Schellekens ◽  
Peter C. Wever ◽  
Rudolf Toman ◽  
Paul H. M. Savelkoul ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
The Netherlands ◽  
Q Fever ◽  
Snp Genotyping ◽  
Cow Milk ◽  
Clinical Samples ◽  
Nucleotide Polymorphism ◽  
Animal Reservoir ◽  
Single Nucleotide ◽  
Outbreak Area

ABSTRACTCoxiella burnetiiis the etiological agent of Q fever. Currently, the Netherlands is facing the largest Q fever epidemic ever, with almost 4,000 notified human cases. Although the presence of a hypervirulent strain is hypothesized, epidemiological evidence, such as the animal reservoir(s) and genotype of theC. burnetiistrain(s) involved, is still lacking. We developed a single-nucleotide-polymorphism (SNP) genotyping assay directly applicable to clinical samples. Ten discriminatory SNPs were carefully selected and detected by real-time PCR. SNP genotyping appeared to be highly suitable for discrimination ofC. burnetiistrains and easy to perform with clinical samples. With this new method, we show that the Dutch outbreak is caused by at least 5 differentC. burnetiigenotypes. SNP typing of 14 human samples from the outbreak revealed the presence of 3 dissimilar genotypes. Two genotypes were also present in livestock at 9 farms in the outbreak area. SNP analyses of bulk milk from 5 other farms, commercial cow milk, and cow colostrum revealed 2 additional genotypes that were not detected in humans. SNP genotyping data from clinical samples clearly demonstrate that at least 5 differentC. burnetiigenotypes are involved in the Dutch outbreak.

scholarly journals Genetic variation and identification of single nucleotide polymorphism of insulin-like growth factor- 1 gene in Tilapia guineensis

2020 ◽  
Vol 21 (11) ◽  
Author(s):  
Esther Ukenye ◽  
IWALEWA MEGBOWON ◽  
OLALEKAN OGUNTADE ◽  
TOPE OKETOKI ◽  
OLUWAFEMI AMUSA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Genetic Variation ◽  
Growth Factor ◽  
Coastal Waters ◽  
Growth Traits ◽  
Selection Marker ◽  
Insulin Like Growth Factor ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Abstract. Ukenye E, Megbowon I, Oguntade O, Oketoki T, Amusa O, Usman A, Sokenu B, Adeleke R, Joseph B, Omatah C. 2020. Genetic variation and identification of single nucleotide polymorphism of insulin-like growth factor- 1 gene in Tilapia guineensis Biodiversitas 21: 5317-5321. Tilapia guineensis is an important cichlid species of West African coastal waters with good nutritional, economic, and aquaculture relevance. The knowledge of the genetic basis of variation in growth traits in Tilapia fish is of great importance to support genetic improvement in the context of aquaculture. In this study, regions of the Tilapia guineensis IGF-1 gene were sequenced, aligned and compared across populations to identify single nucleotide polymorphism and genetic diversity among four populations of T. guineensis in South-west Nigerian coastal waters. A total of thirty-four SNPs were identified across the studied populations and were detected in the forward reaction with twenty-two transversions and twelve transitions. Badagry population showed the highest genetic diversity with the highest molecular diversity indices; number of polymorphic sites, pairwise differences, number of segregating sites and nucleotide diversity while the least diverse population was Pepe. Analysis of molecular variance (AMOVA) revealed that genetic variation was mostly within populations. This finding provides more information regarding variation in insulin growth factor I of T. guineensis and will encourage association study for production traits that will inform useful selection marker for breeding program.

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