Isolation and characterization of 91 single nucleotide polymorphism (SNP) markers for the blue swimming crab (Portunus pelagicus)

2017 ◽  
Vol 9 (4) ◽  
pp. 549-556 ◽  
Author(s):  
Guidong Miao ◽  
Hongyu Ma ◽  
Xiaolong Yang ◽  
Shuqi Wang ◽  
Qingyang Wu ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Snp Markers ◽  
Swimming Crab ◽  
Nucleotide Polymorphism ◽  
Portunus Pelagicus ◽  
Single Nucleotide ◽  
Isolation And Characterization

Molecular Characterization of Cacao (Theobroma cacao) Germplasm from Jamaica Using Single Nucleotide Polymorphism (SNP) Markers

2018 ◽  
Vol 11 (3-4) ◽  
pp. 93-106 ◽  
Author(s):  
Aliza A. Lindo ◽  
Dwight E. Robinson ◽  
Paula F. Tennant ◽  
Lyndel W. Meinhardt ◽  
Dapeng Zhang
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Molecular Characterization ◽  
Theobroma Cacao ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers

2021 ◽  
Vol 19 (1) ◽  
pp. 20-28
Author(s):  
Abush Tesfaye Abebe ◽  
Adesike Oladoyin Kolawole ◽  
Nnanna Unachukwu ◽  
Godfree Chigeza ◽  
Hailu Tefera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Glycine Max ◽  
Snp Markers ◽  
Fixation Index ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Lines ◽  
Soybean Germplasm ◽  
Elite Breeding Lines

AbstractSoybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

A single nucleotide polymorphism-based technique for specific characterization of YO and YN isolates of Potato virus Y (PVY).

2005 ◽  
Vol 125 (1) ◽  
pp. 83-93 ◽  
Author(s):  
Emmanuel Jacquot ◽  
Michel Tribodet ◽  
Flora Croizat ◽  
Valérie Balme-Sinibaldi ◽  
Camille Kerlan
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

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.

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