Identification of a novel risk factor for chronic wasting disease (CWD) in elk: S100G single nucleotide polymorphism (SNP) of the prion protein gene (PRNP)

Lee, Yu-Ran; Kim, Yongchan; Won, Sae-Young; Jeong, Min-Ju; Park, Kyung-Je; Park, Hoo-Chang; Roh, In-Soon; Kang, Hae‐Eun; Sohn, Hyun‐Joo; Jeong, Byung‐Hoon

doi:10.1186/s13567-023-01177-7

Cited by 3 publications

(4 citation statements)

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“…For this reason, the following sections focus more specifically on the described example cases and how each group selected SNPs, designed primer pools, ran multiplex PCR, and performed sequencing. Variations of these methodologies have been applied in agricultural sciences many times [58][59][60][61][62][63][64]. Below are four different pipelines developed for targeted sequencing genotyping.…”

Section: Next-generation Sequencing Of Snp Genotypingmentioning

confidence: 99%

“…In some situations, it may be more advantageous for some groups to outsource the steps of library preparation and sequencing. A small amount of analysis and bioinformatics would be required in-lab to interpret results [58][59][60][61][62][63][64]. Additional example use-cases of sequencing-based genotyping include the following.…”

Section: Next-generation Sequencing-based Genotyping Conclusionmentioning

confidence: 99%

“…The authors selected 480 different markers which could later be used to select for desirable traits in onions, and [58] report that amplicon sequencing provided cost-effective, reliable, and flexible genotyping [58]. In Lee et al (2023), sequencingbased genotyping was applied in elk to identify SNPs suitable to diagnose a susceptibility to chronic wasting disease [64]. The authors report success in identifying a new SNP marker suitable for this disease [64].…”

Section: Next-generation Sequencing-based Genotyping Conclusionmentioning

confidence: 99%

“…In Lee et al (2023), sequencingbased genotyping was applied in elk to identify SNPs suitable to diagnose a susceptibility to chronic wasting disease [64]. The authors report success in identifying a new SNP marker suitable for this disease [64]. In Gashururu et al (2023), sequencing-based genotyping was applied in Tsetse flies to screen for endosymbionts associated with disease [63].…”

Section: Next-generation Sequencing-based Genotyping Conclusionmentioning

confidence: 99%

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Agrigenomic Diversity Unleashed: Current Single Nucleotide Polymorphism Genotyping Methods for the Agricultural Sciences

Lawrie,

Massey

2023

Applied Biosciences

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Single Nucleotide Polymorphisms (SNPs) are variations that occur at single nucleotides in the genome and are present at an appreciable level in a population. SNPs can be linked to phenotypes of interest, for example diseases, recent adaptations, or species hybridization. They can also be used to study phylogeny and evolutionary history. Technologies that rapidly identify and catalog the presence of SNPs in a DNA sample are known as SNP genotyping panels, and they continue to undergo rapid development. Such methods have great utility across the agricultural sciences in diverse areas such as plant and animal breeding, pathogen and pesticide resistance identification, outbreak tracing, and hybridization detection. Here, we provide an overview of 14 different SNP genotyping technologies and weigh some of the pros and cons associated with each platform. This review is not comprehensive or technical, nor does it aim to be. Rather, the objective is to provide an introduction to the landscape of genotyping technologies for researchers who do not have experience with these methods. Three classes of SNP genotyping methods are Polymerase Chain Reaction (PCR)-based (nine different methods), microarray-based (one method), and Next-Generation Sequencing (NGS)-based (four different methods). We discuss how each genotyping class is suited for different niches; PCR-based has a low SNP count and high sample number, microarray-based has a very high SNP count and a moderate sample number, and Next-Generation Sequencing-based has a moderate SNP count and moderate number of samples. Included are basics about how the methods function and example use cases of each method. Additionally, we introduce and discuss the potential for the MinION sequencer in SNP genotyping. For each technology, we provide insights into cost, equipment needs, labor costs, experimental complexity, data output complexity, and accessibility. These considerations address the feasibility of deploying the technologies in an agricultural science environment.

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Section: Next-generation Sequencing Of Snp Genotypingmentioning

confidence: 99%

Section: Next-generation Sequencing-based Genotyping Conclusionmentioning

confidence: 99%

Section: Next-generation Sequencing-based Genotyping Conclusionmentioning

confidence: 99%

Section: Next-generation Sequencing-based Genotyping Conclusionmentioning

confidence: 99%

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Agrigenomic Diversity Unleashed: Current Single Nucleotide Polymorphism Genotyping Methods for the Agricultural Sciences

Lawrie,

Massey

2023

Applied Biosciences

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Prion protein gene (PRNP) variation in German and Danish cervids

Ernst,

Piestrzyńska-Kajtoch,

Gethmann

et al. 2024

Vet Res

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The structure of cellular prion proteins encoded by the prion protein gene (PRNP) impacts susceptibility to transmissible spongiform encephalopathies, including chronic wasting disease (CWD) in deer. The recent emergence of CWD in Northern European reindeer (Rangifer tarandus), moose (Alces alces alces) and red deer (Cervus elaphus), in parallel with the outbreak in North America, gives reason to investigate PRNP variation in European deer, to implement risk assessments and adjust CWD management for deer populations under threat. We here report PRNP-sequence data from 911 samples of German red, roe (Capreolus capreolus), sika (Cervus nippon) and fallow deer (Dama dama) as well as additional data from 26 Danish red deer close to the German border and four zoo species not native to Germany. No PRNP sequence variation was observed in roe and fallow deer, as previously described for populations across Europe. In contrast, a broad PRNP variation was detected in red deer, with non-synonymous polymorphisms at codons 98, 226 and 247 as well as synonymous mutations at codons 21, 78, 136 and 185. Moreover, a novel 24 bp deletion within the octapeptide repeat was detected. In summary, 14 genotypes were seen in red deer with significant differences in their geographical distribution and frequencies, including geographical clustering of certain genotypes, suggesting “PRNP-linages” in this species. Based on data from North American CWD and the genotyping results of the European CWD cases, we would predict that large proportions of wild cervids in Europe might be susceptible to CWD once introduced to naive populations.

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The first report of single nucleotide polymorphisms in the open reading frame of the prion-like protein gene in rabbits

Jeong,

Kim,

Jeong

2024

Front. Vet. Sci.

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BackgroundNatural cases of prion disease have not been reported in rabbits, and prior attempts to identify a prion conversion agent have been unsuccessful. However, recent applications of prion seed amplifying experimental techniques have sparked renewed interest in the potential susceptibility of rabbits to prion disease infections. Among several factors related to prion disease, polymorphisms within the prion-like protein gene (PRND), a member of the prion protein family, have been reported as significantly associated with disease susceptibility in various species. Therefore, our study aimed to investigate polymorphisms in the PRND gene of rabbits and analyze their genetic characteristics.MethodsGenomic DNA was extracted from 207 rabbit samples to investigate leporine PRND polymorphisms. Subsequently, amplicon sequencing targeting the coding region of the leporine PRND gene was conducted. Additionally, linkage disequilibrium (LD) analysis was employed to assess the connection within and between loci. The impact of non-synonymous single nucleotide polymorphisms (SNPs) on the Doppel protein was evaluated using PolyPhen-2.ResultsWe found nine novel SNPs in the leporine PRND gene: c.18A > G, c.76G > C, c.128C > T, c.146C > T, c.315A > G, c.488G > A, c.525G > C, c.544G > A, and c.579A > G. Notably, seven of these PRND SNPs, excluding c.525G > C and c.579A > G, exhibited strong LD values exceeding 0.3. In addition, LD analysis confirmed a robust link between PRNP SNP c.234C > T and PRND SNPs at c.525G > C and c.579A > G. Furthermore, according to PolyPhen-2 and SIFT analyses, the four non-synonymous SNPs were predicted to have deleterious effects on the function or structure of the Doppel protein. However, PANTHER and Missense3D did not indicate such effects.ConclusionIn this paper, we have identified novel SNPs in the rabbit PRND gene and predicted their potential detrimental effects on protein function or structure through four non-synonymous SNPs. Additionally, we observed a genetic linkage between SNPs in the PRND and PRNP genes. These findings may provide insights into understanding the characteristics of rabbits as partially resistant species. To the best of our knowledge, this study is the first to genetically characterize PRND SNPs in rabbits.

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Identification of a novel risk factor for chronic wasting disease (CWD) in elk: S100G single nucleotide polymorphism (SNP) of the prion protein gene (PRNP)

Cited by 3 publications

References 40 publications

Agrigenomic Diversity Unleashed: Current Single Nucleotide Polymorphism Genotyping Methods for the Agricultural Sciences

Agrigenomic Diversity Unleashed: Current Single Nucleotide Polymorphism Genotyping Methods for the Agricultural Sciences

Prion protein gene (PRNP) variation in German and Danish cervids

The first report of single nucleotide polymorphisms in the open reading frame of the prion-like protein gene in rabbits

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