Polymorphism of prion protein gene (PRNP) in Nigerian sheep

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ABSTRACT

Polymorphism of the prion protein gene ( PRNP) gene determines an animal’s susceptibility to scrapie. Three polymorphisms at codons 136, 154, and 171 have been linked to classical scrapie susceptibility, although many variants of PRNP have been reported. However, no study has investigated scrapie susceptibility in Nigerian sheep from the drier agro-climate zones. In this study, we aimed to identify PRNP polymorphism in nucleotide sequences of 126 Nigerian sheep by comparing them with public available studies on scrapie-affected sheep. Further, we deployed Polyphen-2, PROVEAN, and AMYCO analyses to determine the structure changes produced by the non-synonymous SNPs. Nineteen (19) SNPs were found in Nigerian sheep with 14 being non-synonymous. Interestingly, one novel SNP (T718C) was identified. There was a significant difference ( P < 0.05) in the allele frequencies of PRNP codon 154 between sheep in Italy and Nigeria. Based on the prediction by Polyphen-2, R154H was probably damaging while H171Q was benign. Contrarily, all SNPs were neutral via PROVEAN analysis while two haplotypes (HYKK and HDKK) had similar amyloid propensity of PRNP with resistance haplotype in Nigerian sheep. Our study provides valuable information that could be possibly adopted in programs targeted at breeding for scrapie resistance in sheep from tropical regions.

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DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets.

Julio Rozas, Albert Ferrer-Mata, Juan Carlos Sánchez-DelBarrio … (2017)

We present version 6 of the DNA Sequence Polymorphism (DnaSP) software, a new version of the popular tool for performing exhaustive population genetic analyses on multiple sequence alignments. This major upgrade incorporates novel functionalities to analyze large data sets, such as those generated by high-throughput sequencing technologies. Among other features, DnaSP 6 implements: 1) modules for reading and analyzing data from genomic partitioning methods, such as RADseq or hybrid enrichment approaches, 2) faster methods scalable for high-throughput sequencing data, and 3) summary statistics for the analysis of multi-locus population genetics data. Furthermore, DnaSP 6 includes novel modules to perform single- and multi-locus coalescent simulations under a wide range of demographic scenarios. The DnaSP 6 program, with extensive documentation, is freely available at http://www.ub.edu/dnasp.

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Predicting the Functional Effect of Amino Acid Substitutions and Indels

Yongwook Choi, Gregory E. Sims, Sean Murphy … (2012)

As next-generation sequencing projects generate massive genome-wide sequence variation data, bioinformatics tools are being developed to provide computational predictions on the functional effects of sequence variations and narrow down the search of casual variants for disease phenotypes. Different classes of sequence variations at the nucleotide level are involved in human diseases, including substitutions, insertions, deletions, frameshifts, and non-sense mutations. Frameshifts and non-sense mutations are likely to cause a negative effect on protein function. Existing prediction tools primarily focus on studying the deleterious effects of single amino acid substitutions through examining amino acid conservation at the position of interest among related sequences, an approach that is not directly applicable to insertions or deletions. Here, we introduce a versatile alignment-based score as a new metric to predict the damaging effects of variations not limited to single amino acid substitutions but also in-frame insertions, deletions, and multiple amino acid substitutions. This alignment-based score measures the change in sequence similarity of a query sequence to a protein sequence homolog before and after the introduction of an amino acid variation to the query sequence. Our results showed that the scoring scheme performs well in separating disease-associated variants (n = 21,662) from common polymorphisms (n = 37,022) for UniProt human protein variations, and also in separating deleterious variants (n = 15,179) from neutral variants (n = 17,891) for UniProt non-human protein variations. In our approach, the area under the receiver operating characteristic curve (AUC) for the human and non-human protein variation datasets is ∼0.85. We also observed that the alignment-based score correlates with the deleteriousness of a sequence variation. In summary, we have developed a new algorithm, PROVEAN (Protein Variation Effect Analyzer), which provides a generalized approach to predict the functional effects of protein sequence variations including single or multiple amino acid substitutions, and in-frame insertions and deletions. The PROVEAN tool is available online at http://provean.jcvi.org.

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PrP genetics in ruminant transmissible spongiform encephalopathies.

Wilfred Goldmann (2008)

Scrapie, bovine spongiform encephalopathy (BSE), and chronic wasting disease (CWD) are prion diseases in ruminants with considerable impact on animal health and welfare. They can also pose a risk to human health and control is therefore an important issue. Prion protein (PrP) genetics may be used to control and eventually eradicate animal prion diseases. The PrP gene in sheep and other representatives of the order Artiodactyles has many polymorphisms of which several are crucial determinants of susceptibility to prion diseases, also known as transmissible spongiform encephalopathies (TSE). This review will present the current understanding of PrP genetics in ruminants highlighting similarity and difference between the species in the context of TSE.

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Journal

Journal ID (nlm-ta): Prion

Journal ID (iso-abbrev): Prion

Title: Prion

Publisher: Taylor & Francis

ISSN (Print): 1933-6896

ISSN (Electronic): 1933-690X

Publication date (Electronic, pub): 9 March 2023

Publication date (Electronic, collection): 2023

Publication date PMC-release: 9 March 2023

Volume: 17

Issue: 1

Pages: 44-54

Affiliations

[a ]State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences; , Kunming, China

[b ]Sino-Africa Joint Research Center, Chinese Academy of Sciences; , Kunming, China

[c ]Centre for Biotechnology Research, Bayero University; , Kano, Nigeria

[d ]Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University; , Guangzhou, China

[e ]Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, Bayero University; , Kano, Nigeria

[f ]Ministry of Agriculture and Rural Development, Secretariat; , Ibadan, Nigeria

[g ]Taraba State Ministry of Agriculture and Natural Resources; , Jalingo, Nigeria

[h ]Department of Virology, College of Medicine, University of Ibadan; , Ibadan, Nigeria

[i ]Department of Ecology and Evolutionary Biology, Princeton University; , Princeton, NJ, USA

[j ]Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Bayero University; , Kano, Nigeria

[k ]Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan; , Ibadan, Nigeria

[l ]Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Health Sciences, Bayero University; , Kano, Nigeria

[m ]Division of Veterinary Office; , Serti, Nigeria

[n ]Small Ruminant Section, Solomon Kesinton Agro-Allied Limited Iperu-Remo; , Ogun State, Nigeria

[o ]Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi; , Makurdi, Nigeria

[p ]Department of Animal Science, Faculty of Agriculture, National University of Lesotho; , Lesotho, Southern Africa

[q ]Department of Animal Science, Faculty of Agriculture, University of Ibadan; , Ibadan, Nigeria

[r ]Livestock and Wildlife Laboratory, Institut des Régions Arides, Université de Gabes; , Medenine, Tunisia

Author notes

CONTACT Adeniyi C. Adeola chadeola@ 123456mail.kiz.ac.cn Molecular Evolution and Genome Diversity, State Key Laboratory of Genetic Resources & Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; , Kunming, Yunnan 650203, China

[*]

These authors contributed equally to this work.

Article

Publisher ID: 2186767

DOI: 10.1080/19336896.2023.2186767

PMC ID: 10012947

PubMed ID: 36892181

SO-VID: 2529ffd4-cb99-4c33-ab5a-6ec8c281d3eb

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This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Polymorphism of prion protein gene (PRNP) in Nigerian sheep

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Most cited references 77

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets.

Predicting the Functional Effect of Amino Acid Substitutions and Indels

PrP genetics in ruminant transmissible spongiform encephalopathies.

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