Novel Insertion/Deletion Polymorphisms and Genetic Studies of the Shadow of Prion Protein (SPRN) in Raccoon Dogs

Prion diseases, or transmissible spongiform encephalopathies (TSEs), are a group of invariably fatal neurodegenerative disorders. One of the candidate genes involved in prion diseases is the shadow of the prion protein (SPRN) gene. Raccoon dogs, a canid, are considered to be a prion disease-resistant species. To date, the genetic polymorphisms of the SPRN gene and the predicted protein structure of the shadow of prion protein (Sho) have not been explored in raccoon dogs. SPRN was amplified using polymerase chain reaction (PCR). We also investigated the genetic polymorphisms of SPRN by analyzing the frequencies of genotypes, alleles, and haplotypes, as well as the linkage disequilibrium among the identified genetic variations. In addition, in silico analysis with MutPred-Indel was performed to predict the pathogenicity of insertion/deletion polymorphisms. Predicted 3D structures were analyzed by the Alphafold2. We found a total of two novel synonymous single nucleotide polymorphisms and three insertion/deletion polymorphisms. In addition, the 3D structure of the Sho protein in raccoon dogs was predicted to resemble that of the Sho protein in dogs. This is the first study regarding the genetic and structural characteristics of the raccoon dog SPRN gene.

Novel Single-Nucleotide Polymorphisms (SNPs) and Genetic Studies of the Shadow of Prion Protein (SPRN) in Quails

Prion diseases are a group of deadly neurodegenerative disorders caused by the accumulation of the normal prion protein (PrPC) into misfolding pathological conformations (PrPSc). The PrP gene is essential for the development of prion diseases. Another candidate implicated in prion pathogenesis is the shadow of the prion protein (SPRN) gene. To date, genetic polymorphisms of the SPRN gene and the structure of the Sho protein have not been explored in quails. We used polymerase chain reaction (PCR) to amplify the SPRN gene sequence and then conducted Sanger DNA sequencing to identify the genetic polymorphisms in quail SPRN. Furthermore, we examined the genotype, allele, and haplotype frequencies, and assessed the linkage disequilibrium among the genetic polymorphisms of the SPRN gene in quails. Additionally, we used in silico programs such as MutPred2, SIFT, MUpro, AMYCO, and SODA to predict the pathogenicity of non-synonymous single-nucleotide polymorphisms (SNPs). Alphafold2 predicted the 3D structure of the Sho protein in quails. The results showed that a total of 13 novel polymorphisms were found in 106 quails, including 4 non-synonymous SNPs. Using SIFT and MUpro in silico programs, three out of the four non-synonymous SNPs (A68T, L74P, and M105I) were predicted to have deleterious effects on quail Sho. Furthermore, the 3D structure of quail Sho was predicted to be similar to that of chicken Sho. To our knowledge, this is the first report to investigate the genetic and structural properties of the quail SPRN gene.

First Report of Single Nucleotide Polymorphisms (SNPs) of the Leporine Shadow of Prion Protein Gene (SPRN) and Absence of Nonsynonymous SNPs in the Open Reading Frame (ORF) in Rabbits

Prion disorders are fatal infectious diseases that are caused by a buildup of pathogenic prion protein (PrPSc) in susceptible mammals. According to new findings, the shadow of prion protein (Sho) encoded by the shadow of prion protein gene (SPRN) is associated with prion protein (PrP), promoting the progression of prion diseases. Although genetic polymorphisms in SPRN are associated with susceptibility to several prion diseases, genetic polymorphisms in the rabbit SPRN gene have not been investigated in depth. We discovered two novel single nucleotide polymorphisms (SNPs) in the leporine SPRN gene on chromosome 18 and found strong linkage disequilibrium (LD) between them. Additionally, strong LD was not found between the polymorphisms of PRNP and SPRN genes in rabbits. Furthermore, nonsynonymous SNPs that alter the amino acid sequences within the open reading frame (ORF) of SPRN have been observed in prion disease-susceptible animals, but this is the first report in rabbits. As far as we are aware, this study represents the first examination of the genetic features of the rabbit SPRN gene.

The First Genetic Characterization of the SPRN Gene in Pekin Ducks (Anas platyrhynchos domesticus)

Prion diseases are fatal neurodegenerative disorders characterized by an accumulation of misfolded prion protein (PrPSc) in brain tissues. The shadow of prion protein (Sho) encoded by the shadow of prion protein gene (SPRN) is involved in prion disease progress. The interaction between Sho and PrP accelerates the PrPSc conversion rate while the SPRN gene polymorphisms have been associated with prion disease susceptibility in several species. Until now, the SPRN gene has not been investigated in ducks. We identified the duck SPRN gene sequence and investigated the genetic polymorphisms of 184 Pekin ducks. We compared the duck SPRN nucleotide sequence and the duck Sho protein amino acid sequence with those of several other species. Finally, we predicted the duck Sho protein structure and the effects of non-synonymous single nucleotide polymorphisms (SNPs) using computational programs. We were the first to report the Pekin duck SPRN gene sequence. The duck Sho protein sequence showed 100% identity compared with the chicken Sho protein sequence. We found 27 novel SNPs in the duck SPRN gene. Four amino acid substitutions were predicted to affect the hydrogen bond distribution in the duck Sho protein structure. Although MutPred2 and SNPs&GO predicted that all non-synonymous polymorphisms were neutral or benign, SIFT predicted that four variants, A22T, G49D, A68T, and M105I, were deleterious. To the best of our knowledge, this is the first report about the genetic and structural characteristics of the duck SPRN gene.

Novel polymorphisms and genetic studies of the shadow of prion protein gene (SPRN) in pheasants

Background

Prion diseases in mammals are caused by the structural conversion of the natural prion protein (PrPC) to a pathogenic isoform, the "scrapie form of prion protein (PrPSc)." Several studies reported that the shadow of prion protein (Sho), encoded by the shadow of prion protein gene (SPRN), is involved in prion disease development by accelerating the conformational conversion of PrPC to PrPSc. Until now, genetic polymorphisms of the SPRN gene and the protein structure of Sho related to fragility to prion disease have not been investigated in pheasants, which are a species of poultry.

Methods

Here, we identified the SPRN gene sequence by polymerase chain reaction (PCR) and compared the SPRN gene and Sho protein sequences among various prion disease-susceptible and -resistant species to identify the distinctive genetic features of pheasant Sho using Clustal Omega. In addition, we investigated genetic polymorphisms of the SPRN gene in pheasants and analyzed genotype, allele, and haplotype frequencies, as well as linkage disequilibrium among the genetic polymorphisms. Furthermore, we used in silico programs, namely Mutpred2, MUpro and AMYCO, to investigate the effect of non-synonymous single nucleotide polymorphisms (SNPs). Finally, the predicted secondary and tertiary structures of Sho proteins from various species were analyzed by Alphafold2.

Results

In the present study, we reported pheasant SPRN gene sequences for the first time and identified a total of 14 novel SNPs, including 7 non-synonymous and 4 synonymous SNPs. In addition, the pheasant Sho protein sequence showed 100% identity with the chicken Sho protein sequence. Furthermore, amino acid substitutions were predicted to affect the hydrogen bond distribution in the 3D structure of the pheasant Sho protein.

Conclusion

To the best of our knowledge, this is the first report of the genetic and structural features of the pheasant SPRN gene.

Screening Indels from the whole genome to identify the candidates and their association with economic traits in several goat breeds

In the present study, the re-sequencing of our previous whole-genome sequencing (WGS) for selected individuals of Dazu-black goat (DBG) and Inner-Mongolia Cashmere goat (IMCG) breeds was used to detect and compare the differentiation in Indels depending on the reference genome of goat. Then, three selected candidate Indels rs668795676, rs657996810, and rs669452874 of the three genes SUFU, SYCP2L and GLIPR1L1, respectively, have been chosen, based on the results of prior GWAS across the genome, and examined for their association with body weight and dimensions (body height, body length, heart girth, chest width, cannon circumference, and chest depth) by kompetitive allele specific PCR assay for 342 goats from the three studied goat breeds (DBG, n = 203; ♂99, ♀104), IMCG (n = 65; 15♂, 50♀), and Hechuan white goat (HWG, n = 74; 34♂, 40♀) breeds. The analysis of 192.747 Gb WGS revealed an average 334,151 Indels in the whole genome of DBG and IMCG breeds. Chromosome 1 had a maximum number of mutations (Indels) of 58,497 and 55,527 for IMCG and DBG, respectively, while chromosome 25 had the least number of mutations of 15,680 and 16,103 for IMCG and DBG, respectively. The majority of Indels were either Ins or Del of short fragments of 1-5 bp, which covered 79.06 and 71.78% of the total number of Indels mutations in IMCG and DBG, respectively. Comparing the differences of Indels between the studied goat breeds revealed 100 and 110 unique Indels for IMCG and DBG, respectively. The Indels loci in the intron region were unique for both studied goat breeds which were related to 30 and 38 candidate genes in IMCG and DBG, respectively, including SUFU, SYCP2L, and GLIPR1L1 genes. Concerning rs669452874 locus, body height and body length of Del/Del genotype in DBG were significantly higher (P < 0.05) than that of Ins/Del genotype, while body height and body length of Del/Del genotype in IMCG were significantly higher (P < 0.01) than those of Ins/Ins genotype, whereas body height and body length and heart girth of Del/Del genotype in HWG were significantly higher (P < 0.01) than those of the Ins/Del and Ins/Ins genotypes. Thus, Del/Del genotype of rs669452874 locus can be used as a candidate molecular marker related to the body dimensions in the studied goat breeds.

Novel insertion/deletion polymorphisms and genetic features of the shadow of prion protein gene (SPRN) in dogs, a prion-resistant animal

Prion diseases are fatal infectious neurodegenerative disorders that are induced by misfolded prion protein (PrP^Sc). Previous studies have reported that the shadow of prion protein (Sho) encoded by the shadow of prion protein gene (SPRN) plays a critical role in stimulating the conversion process of normal PrP (PrP^C) into PrP^Sc, and genetic polymorphisms of the SPRN gene are significantly related to susceptibility to prion diseases. Recent studies have reported that dogs show prion resistance, and there have been several attempts to identify resistance factors to prion diseases in dogs. However, there has been no study of the canine SPRN gene thus far. We investigated genetic polymorphisms of the canine SPRN gene in 201 dogs using amplicon sequencing and compared the number of SPRN polymorphisms among prion-related species. In addition, we performed multiple sequence alignments of the amino acid sequences of Sho among prion-related species by ClustalW and analyzed the 3D structure of Sho using AlphaFold. Furthermore, we assessed the protein–protein interaction of canine PrP with canine Sho carrying wild-type and mutant alleles using HawkDock. We found four novel insertion/deletion polymorphisms of the SPRN gene in 201 dogs and identified a significant difference in the number of SPRN polymorphisms between prion-susceptible and prion-resistant animals. In addition, Sho has two α-helixes linked with the coil. Furthermore, we found different binding complexes and binding free energies between canine Sho and PrP according to SPRN polymorphisms. To the best of our knowledge, this is the first report of canine SPRN polymorphisms.

The First Report of Polymorphisms and Genetic Characteristics of the Shadow of Prion Protein (SPRN) in Prion Disease-Resistant Animal, Chickens

Prion diseases are irreversible neurodegenerative disorders caused by the aggregated form of prion protein (PrPSc) derived from the normal form of prion protein (PrPC). Previous studies have reported that shadow of prion protein (Sho) interacts with prion protein (PrP) and accelerates the conversion of PrPC to PrPSc. In addition, genetic polymorphisms of the shadow of the prion protein gene (SPRN) are related to the vulnerability of prion diseases in various hosts. However, to date, polymorphisms and genetic features of the SPRN gene have not been investigated in chickens, which are prion disease-resistant animals. We investigated genetic polymorphisms of the SPRN gene in 2 breeds of chickens, i.e., Dekalb White and Ross, using amplicon sequencing. We analyzed genotype, allele and haplotype frequencies and linkage disequilibrium (LD) among the genetic polymorphisms. In addition, we compared the amino acid sequences of Sho among several prion-related species to identify the unique genetic features of chicken Sho using ClustalW. Furthermore, we evaluated the N-terminal signal peptide and glycosylphosphatidylinositol (GPI)-anchor using SignalP and PredGPI, respectively. Finally, we compared the number of SPRN polymorphisms between prion disease-resistant and prion disease-susceptible animals. We identified 7 novel single nucleotide polymorphisms (SNPs), including 1 synonymous SNP in the open reading frame (ORF) of the chicken SPRN gene. We also found significantly different genotypes, allele frequencies and haplotypes between the 2 chicken breeds. In addition, we found that the interaction regions between Sho and PrP and the NXT glycosylation motif were conserved among all species. Notably, sequence similarity was extremely low in the N-terminal and C-terminal regions between mammals and chickens. Furthermore, we found that chicken Sho was the longest N-terminal signal peptide, and the amino acids of the cutting site of chicken are different from those of mammals. Last, unlike other species investigated, omega-site and signal sequences of the GPI-anchor were not found in chickens. To the best of our knowledge, this is the first report of genetic polymorphisms of the SPRN gene in chickens.

Novel Polymorphisms and Genetic Characteristics of the Shadow of Prion Protein Gene (SPRN) in Cats, Hosts of Feline Spongiform Encephalopathy

Prion diseases are transmissible spongiform encephalopathies (TSEs) caused by pathogenic prion protein (PrP^Sc) originating from normal prion protein (PrP^C) and have been reported in several types of livestock and pets. Recent studies have reported that the shadow of prion protein (Sho) encoded by the shadow of prion protein gene (SPRN) interacts with prion protein (PrP) and accelerates prion diseases. In addition, genetic polymorphisms in the SPRN gene are related to susceptibility to prion diseases. However, genetic polymorphisms in the feline SPRN gene and structural characteristics of the Sho have not been investigated in cats, a major host of feline spongiform encephalopathy (FSE). We performed amplicon sequencing to identify feline SPRN polymorphisms in the 623 bp encompassing the open reading frame (ORF) and a small part of the 3' untranslated region (UTR) of the SPRN gene. We analyzed the impact of feline SPRN polymorphisms on the secondary structure of SPRN mRNA using RNAsnp. In addition, to find feline-specific amino acids, we carried out multiple sequence alignments using ClustalW. Furthermore, we analyzed the N-terminal signal peptide and glycosylphosphatidylinositol (GPI)-anchor using SignalP and PredGPI, respectively. We identified three novel SNPs in the feline SPRN gene and did not find strong linkage disequilibrium (LD) among the three SNPs. We found four major haplotypes of the SPRN polymorphisms. Strong LD was not observed between PRNP and SPRN polymorphisms. In addition, we found alterations in the secondary structure and minimum free energy of the mRNA according to the haplotypes in the SPRN polymorphisms. Furthermore, we found four feline-specific amino acids in the feline Sho using multiple sequence alignments among several species. Lastly, the N-terminal signal sequence and cutting site of the Sho protein of cats showed similarity with those of other species. However, the feline Sho protein exhibited the shortest signal sequence and a unique amino acid in the omega-site of the GPI anchor. To the best of our knowledge, this is the first report on genetic polymorphisms of the feline SPRN gene.

Exploration of Alternative Splicing (AS) Events in MDV-Infected Chicken Spleens

Marek’s disease (MD) was an immunosuppression disease induced by Marek’s disease virus (MDV). MD caused huge economic loss to the global poultry industry, but it also provided an ideal model for studying diseases induced by the oncogenic virus. Alternative splicing (AS) simultaneously produced different isoform transcripts, which are involved in various diseases and individual development. To investigate AS events in MD, RNA-Seq was performed in tumorous spleens (TS), spleens from the survivors (SS) without any lesion after MDV infection, and non-infected chicken spleens (NS). In this study, 32,703 and 25,217 AS events were identified in TS and SS groups with NS group as the control group, and 1198, 1204, and 348 differently expressed (DE) AS events (p-value < 0.05 and FDR < 0.05) were identified in TS vs. NS, TS vs. SS, SS vs. NS, respectively. Additionally, Function enrichment analysis showed that ubiquitin-mediated proteolysis, p53 signaling pathway, and phosphatidylinositol signaling system were significantly enriched (p-value < 0.05). Small structural variations including SNP and indel were analyzed based on RNA-Seq data, and it showed that the TS group possessed more variants on the splice site region than those in SS and NS groups, which might cause more AS events in the TS group. Combined with previous circRNA data, we found that 287 genes could produce both circular and linear RNAs, which suggested these genes were more active in MD lymphoma transformation. This study has expanded the understanding of the MDV infection process and provided new insights for further analysis of resistance/susceptibility mechanisms.

Polymorphisms of the prion-related protein gene are strongly associated with cervids' susceptibility to chronic wasting disease

BACKGROUND

Chronic wasting disease (CWD) is a cervid prion disease that is caused by abnormal prion protein (PrP^Sc ). Recent studies have reported that prion family genes showed a strong association with the susceptibility of several types of prion diseases. To date, an association study of the prion-related protein gene (PRNT) has not been performed in any type of cervid prion disease.

METHODS

In the present study, we investigated PRNT polymorphisms in large deer, including 235 elk, 257 red deer and 150 sika deer. We compared genotype, allele and haplotype frequencies of PRNT polymorphisms between CWD-negative animals and CWD-positive animals to find an association of PRNT polymorphisms with the susceptibility of CWD.

RESULTS

We found a total of five novel single nucleotide polymorphisms (SNPs) in the cervid PRNT gene. Interestingly, we observed significantly different distributions of genotypes and allele frequencies of three PRNT SNPs, including c.108C>T, c.159+30C>T and c.159+32A>C, between CWD-negative and CWD-positive red deer. In addition, significant differences of two haplotype frequencies in red deer were found between the CWD-negative and CWD-positive groups. However, the association identified in the red deer was not found in elk and sika deer.

CONCLUSION

To the best of our knowledge, this report is the first to describe the strong association of PRNT SNPs with the susceptibility of CWD.

The First Report of Genetic Polymorphisms of the Equine SPRN Gene in Outbred Horses, Jeju and Halla Horses

Simple Summary

Prion disease is a fatal neurodegenerative disease caused by the accumulation of pathogenic prion protein (PrP^Sc) in various mammalian hosts. However, to date, prion disease has not been reported in horses. Since the Sho protein encoded by the shadow of the prion protein gene (SPRN) plays an essential role in the progression of prion diseases, we investigated the genetic characteristics of the equine SPRN gene in horses. We found four single nucleotide polymorphisms (SNPs) of the equine SPRN gene and significant different distributions among three horse breeds including Jeju, Halla and Thoroughbred horses. Although the polymorphisms affect the property of mRNA of the equine SPRN gene, it did not affect the sequence and structure of Sho protein. Since several non-synonymous SNPs of the SPRN gene have been reported in prion diseases-susceptible animals, the absence of non-synonymous SNP of the equine SPRN gene in the horses is noticeable.

Abstract

Prion disease is a fatal infectious disease caused by the accumulation of pathogenic prion protein (PrP^Sc) in several mammals. However, to date, prion disease has not been reported in horses. The Sho protein encoded by the shadow of the prion protein gene (SPRN) plays an essential role in the pathomechanism of prion diseases. To date, the only genetic study of the equine SPRN gene has been reported in the inbred horse, Thoroughbred horse. We first discovered four SPRN single nucleotide polymorphisms (SNPs) in 141 Jeju and 88 Halla horses by direct DNA sequencing. In addition, we found that the genotype, allele and haplotype frequencies of these SNPs of Jeju horses were significantly different from those of Halla and Thoroughbred horses, this latter breed is also included in this study. Furthermore, we observed that the minimum free energy and mRNA secondary structure were significantly different according to haplotypes of equine SPRN polymorphisms by the RNAsnp program. Finally, we compared the SNPs in the coding sequence (CDS) of the SPRN gene between horses and prion disease-susceptible species. Notably, prion disease-susceptible animals had polymorphisms that cause amino acid changes in the open reading frame (ORF) of the SPRN gene, while these polymorphisms were not found in horses.

Polymorphisms of shadow of prion protein gene (SPRN) in Korean native cattle (Hanwoo) and Holstein cattle

Bovine spongiform encephalopathy (BSE) is a fatal infectious neurodegenerative disease caused by the accumulation of pathogenic prion protein (PrP^Sc) in the central nervous system (CNS), particularly in the brain. In a recent study, the shadow of prion protein (Sho), encoded by the shadow of prion protein (SPRN) gene, accelerates the progression of prion diseases, and a 12-bp insertion/deletion polymorphism in the coding region of the SPRN gene is associated with susceptibility to atypical BSE-affected Polish cattle. To date, the genetic study of the SPRN gene in Korean cattle has not been performed. In this study, we investigated the genotype and allele frequencies of SPRN polymorphisms in 235 Hanwoo and 212 Holstein cattle and analyzed the linkage disequilibrium (LD) and haplotypes of SPRN polymorphisms. In addition, we compared the distribution of the 12-bp insertion/deletion polymorphism between atypical BSE-diagnosed Polish cattle and Korean cattle to evaluate the susceptibility of atypical BSE. Furthermore, we estimated a deleterious effect of polymorphisms on the Sho protein using PROVEAN. We found a total of seven polymorphisms, including one novel single nucleotide polymorphism (SNP), c.231G>A. We also found significantly different distributions of genotype, allele and haplotype frequencies of seven polymorphisms between Hanwoo and Korean Holstein cattle. In addition, all polymorphisms showed strong LDs among the seven polymorphisms. Interestingly, Hanwoo cattle showed more potential susceptible distribution in the genotype and allele frequencies of the 12-bp insertion/deletion polymorphisms of the SPRN gene than Holstein cattle. Finally, using PROVEAN, we found one novel deleterious nonsynonymous SNP to Sho protein, c.110G>C (G37A). To the best of our knowledge, this is the first study of the SPRN gene in Korean cattle.

Polymorphic variants of bovine ADCY5 gene identified in GWAS analysis were significantly associated with ovarian morphological related traits

The reproductive performance (e.g. fertility) of dairy cows, which declined over past few decades due to the intense and intensive selection, needs to be improved. Previous genome-wide association study (GWAS) of female Holstein screened the Adenylate cyclase 5 (ADCY5) as the candidate gene for cow fertility. As a member of the adenylyl cyclases family, adenylate cyclase 5 (ADCY5) is famous for regulating extrapyramidal motor system related various neuropsychiatric diseases, and its genetic variant is reported to associate with lower birth and placenta weight which leads to asymmetric fetal growth restriction. It was hypothesized that ADCY5 may affect the fertility of cows by regulating the processes of ovarian development. Herein, genomic DNA from 768 ovaries samples of healthy unrelated Holstein cow were used to screen potential insertion/deletion (indel) mutations using eight pairs of primers, and we found three novel polymorphic indel variants, namely, rs385624978 (P3-D_11-bp), rs433028962 (P5-I_19-bp) and rs382393457 (P8-D_19-bp). The minor allelic frequencies (MAF) of P3-D_11-bp, P5-I_19-bp and P8-D_19-bp loci were 0.188, 0.365 and 0.06, respectively, and there were 7 different haplotypes. Additionally, linkage disequilibrium analysis demonstrated no linkage among them. Importantly, P3-D_11-bp locus was significantly related to both ovarian width (P = 1.0E-6) and corpus luteum diameter (P = 0.015); P5-I_19-bp locus had a significant relation with corpus albicans diameter (P = 0.030) and ovaries with mutational homozygous genotype produced a superior corpus albicans diameter than those with other genotypes. Briefly, three novel indel mutations of bovine ADCY5 gene were identified and two of them were uncovered to be significantly correlated with ovarian phenotypic traits or corpus luteum or albicans traits. These findings contributed to the application of molecular marker-assisted selection (MAS) in improving female fertility in cattle, which could accelerate the development of the cattle industry.

Identification of the prion-related protein gene (PRNT) sequences in various species of the Cervidae family

Chronic wasting disease (CWD) is caused by abnormal deleterious prion protein (PrP^Sc), and transmissible spongiform encephalopathy occurs in the Cervidae family. In recent studies, the susceptibility of prion disease has been affected by polymorphisms of the prion gene family. However, the study of the prion-related protein gene (PRNT) is rare, and the DNA sequence of this gene was not fully reported in all Cervidae families. In the present study, we amplified and first identified PRNT DNA sequences in the Cervidae family, including red deer, elk, sika deer and Korean water deer, using polymerase chain reaction (PCR). We aligned nucleotide sequences of the PRNT gene and the amino acid sequences of prion-related protein (Prt) protein among several species. In addition, we performed phylogenetic analysis to measure the evolutionary relationships of the PRNT gene in the Cervidae family. Furthermore, we performed homology modeling of the Prt protein using SWISS-MODEL and compared the structure of Prt protein between sheep and the Cervidae family using the Swiss-PdbViewer program. We obtained much longer PRNT sequences of red deer compared to the PRNT gene sequence registered in GenBank. Korean water deer denoted more close evolutionary distances with goats and cattle than the Cervidae family. We found 6 Cervidae family-specific amino acids by the alignment of Prt amino acid sequences. There are significantly different distributions of hydrogen bonds and the atomic distance of the N-terminal tail and C-terminal tail between sheep and the Cervidae family. We also detected the mRNA expression of PRNT gene in 3 tissues investigated. To our knowledge, this report is the first genetic study of the PRNT gene in the Cervidae family.

The First Report of Genetic and Structural Diversities in the SPRN Gene in the Horse, an Animal Resistant to Prion Disease

Prion diseases are fatal neurodegenerative diseases and are characterized by the accumulation of abnormal prion protein (PrP^Sc) in the brain. During the outbreak of the bovine spongiform encephalopathy (BSE) epidemic in the United Kingdom, prion diseases in several species were reported; however, horse prion disease has not been reported thus far. In previous studies, the shadow of prion protein (Sho) has contributed to an acceleration of conversion from normal prion protein (PrP^C) to PrP^Sc, and the shadow of prion protein gene (SPRN) polymorphisms have been significantly associated with the susceptibility of prion diseases. We investigated the genotype, allele and haplotype frequencies of the SPRN gene using direct sequencing. In addition, we analyzed linkage disequilibrium (LD) and haplotypes among polymorphisms. We also investigated LD between PRNP and SPRN single nucleotide polymorphisms (SNPs). We compared the amino acid sequences of Sho protein between the horse and several prion disease-susceptible species using ClustalW2. To perform Sho protein modeling, we utilized SWISS-MODEL and Swiss-PdbViewer programs. We found a total of four polymorphisms in the equine SPRN gene; however, we did not observe an in/del polymorphism, which is correlated with the susceptibility of prion disease in prion disease-susceptible animals. The SPRN SNPs showed weak LD value with PRNP SNP. In addition, we found 12 horse-specific amino acids of Sho protein that can induce significantly distributional differences in the secondary structure and hydrogen bonds between the horse and several prion disease-susceptible species. To the best of our knowledge, this is the first report regarding the genetic and structural characteristics of the equine SPRN gene.

Scrapie susceptibility-associated indel polymorphism of shadow of prion protein gene (SPRN) in Korean native black goats

Prion diseases in sheep and goats are called scrapie and belong to a group of transmissible spongiform encephalopathies (TSEs) caused by the abnormal misfolding of the prion protein encoded by the prion protein gene (PRNP). The shadow of the prion protein gene (SPRN) is the only prion gene family member that shows a protein expression profile similar to that of the PRNP gene in the central nervous system. In addition, genetic susceptibility of the SPRN gene has been reported in variant Creutzfeldt-Jakob disease (CJD), bovine spongiform encephalopathy (BSE) and scrapie. However, genetic studies of the SPRN gene have not been carried out in Korean native black goats. Here, we investigated the genotype and allele frequencies of SPRN polymorphisms in 213 Korean native black goats and compared these polymorphisms with those previously reported for scrapie-affected animals. We found a total of 6 polymorphisms including 1 nonsynonymous single nucleotide polymorphism (SNP) and 1 synonymous SNP in the open reading frame (ORF) region and 3 SNPs and 1 indel polymorphism (c.495_496insCTCCC) in the 3' untranslated region (UTR) by direct DNA sequencing. A significant difference in the allele frequency of the c.495_496insCTCCC indel polymorphism was found between the Italian scrapie-affected goats and the Korean native black goats (P < 0.001). Furthermore, there was a significant difference in the allele frequencies of the c.495_496insCTCCC indel polymorphism between Italian healthy goats and Korean native black goats (P < 0.001). To evaluate the biological impact of the novel nonsynonymous SNP c.416G > A (Arg139Gln), we carried out PROVEAN analysis. PROVEAN predicted the SNP as 'Neutral' with a score of -0.297. To the best of our knowledge, this is the first genetic study of the SPRN gene in Korean native black goats.

Prion-like protein gene (PRND) polymorphisms associated with scrapie susceptibility in Korean native black goats

The polymorphisms of the prion protein (PRNP) gene, which encodes normal prion proteins (PrP), are known to be involved in the susceptibility of prion diseases. The prion-like protein (Doppel) gene (PRND) is the paralog of the PRNP gene and is closely located downstream of the PRNP gene. In addition, the polymorphisms of PRND correlate with disease susceptibility in several animals. We analyzed the genotype and allele frequencies of PRND polymorphisms in 246 Korean native black goats and found a total of six single nucleotide polymorphisms (SNPs) with one novel SNP, c.99C>T. We observed linkage disequilibrium (LD) within and between loci. PRND c.28T>C, c.151A>G, and c.385G>C and PRND c.65C>T and c.286G>A were in perfect LD and we have reported for the first time strong LD between PRND and PRNP or prion-related protein gene (PRNT) loci. Specifically, between the PRND c.28T>C, c.151A>G and c.385G>C and the PRNP codon 143, PRND c.99C>T and the PRNP codon 102 or PRND SNPs (c.28T>C, c.151A>G and c.385G>C) and PRNT SNP (c.321T>C). Furthermore, we confirmed that the genotype distribution of the PRNP p.His143Arg was significantly different according to that of the PRND c.28T>C (P < 0.0001). Finally, using PolyPhen-2 and PROVEAN, we predicted that two non-synonymous SNPs, c.65C>T and c.286G>A, in the PRND gene can have a detrimental effect on Doppel. To the best of our knowledge, this is the first report of genetic characteristics of the PRND gene in Korean native black goats.

Fixed differences in the 3'UTR of buffalo PRNP gene provide binding sites for miRNAs post-transcriptional regulation

Bovine spongiform encephalopathy, a member of transmissible spongiform encephalopathies, has not been reported in buffaloes, Bubalus bubalis. Prion protein (PrP), encoded by the prion protein gene (PRNP), is fundamental in the pathogenesis of transmissible spongiform encephalopathies. We previously showed that buffaloes express more PrP proteins but lower PRNP mRNA than cattle in several pivotal tissues like the obex. Therefore, we sought to establish whether genetic variability in PRNP 3'UTR, mediated by miRNA down-regulation, causes PrP expression differences between cattle and buffaloes. We annotated the 3'UTR of buffalo PRNP gene by 3'RACE experiment. A total of 92 fixed differences in the complete 3'UTR (~ 3 kb) were identified between 13 cattle and 13 buffaloes. Resequencing of UTR-C (g.786-1436) and UTR-B (g.778-1456) fragments confirmed that all mutations except g.1022T in cattle are fixed differences between 147 cattle and 146 buffaloes. In addition, analysis of the variation of ΔG between cattle and buffalo sequences reveals four remarkable differences. Two buffalo-specific insertion sites (a 28-bp insertion and an AG insertion in buffalo 3'UTR of PRNP g.970-997 and g. 1088-1089, respectively) and two mutants (g. 1007-1008 TG→CC) create compatible binding sites for miRNAs in buffalo 3'UTR. This was validated through luciferase reporter assays which demonstrated that miR-125b-5p, miR-132-3p, miR-145-5p, miR-331-3p, and miR-338-3p directly act on the fixed difference sites in buffalo 3'UTR. Additional expressional analyses show that these five miRNAs are coexpressed with PRNP in bovine obex tissues. Our study reveals a miRNAs regulated mechanism explaining the differences in prion expression between cattle and buffalo.

Genetic effects of PRNP gene insertion/deletion (indel) on phenotypic traits in sheep

Prion protein (PRNP) gene is well known for affecting mammal transmissible spongiform encephalopathies (TSE), and is also reported to regulate phenotypic traits (e.g. growth traits) in healthy ruminants. To identify the insertion/deletion (indel) variations of the PRNP gene and evaluate their effects on growth traits, 768 healthy individuals from five sheep breeds located in China and Mongolia were identified and analyzed. Herein, four novel indel polymorphisms, namely, Intron-1-insertion-7bp (I1-7bp), Intron-2-insertion-15bp (I2-15bp), Intron-2-insertion-19bp (I2-19bp), and 3' UTR-insertion-7bp (3' UTR-7bp), were found in the sheep PRNP gene. In five analyzed breeds, the minor allelic frequencies (MAF) of the above indels were in the range of 0.008 to 0.986 (I1-7bp), 0.113 to 0.336 (I2-15bp), 0.281 to 0.510 (I2-19bp), and 0.040 to 0.238 (3' UTR-7bp). Additionally, there were 15 haplotypes and the haplotype 'I_I2-15bp-D_3'UTR-7bp-D_I2-19bp-D_I1-7bp' had the highest frequency, which varied from 0.464 to 0.629 in five breeds. Moreover, association analysis revealed that all novel indel polymorphisms were significantly associated with 13 different growth traits (P < 0.05). Particularly, the influences of I2-15bp on chest width (P = 0.001) in Small Tail Han sheep (ewe), 3' UTR-7bp on chest circumference (P = 0.003) in Hu sheep, and I2-19bp on tail length (P = 0.001) in Tong sheep, were highly significant (P < 0.01). These findings may be a further step toward the detection of indel-based typing within and across sheep breeds, and of promising target loci for accelerating the progress of marker-assisted selection in sheep breeding.

Classic and atypical scrapie - a genetic perspective

Scrapie was the first prion disease to be recognised and the study of this disease in sheep and goats has provided a wealth of information not only for scrapie but also for the other prion diseases. All prion diseases are under strong genetic control of the prion gene PRNP, independent of whether they are typical or atypical scrapie and which of the different prion strains is causing infection. Decades of studies using experimental disease challenges and field surveys have established disease association models, in which species-specific amino acid variations in the prion or PrP protein, encoded by the PRNP gene, can predict disease susceptibility or resistance. PRNP genetics represents an important and successful basis for implementing scrapie eradication strategies in sheep and goats. In general terms these studies have revealed that there appear to be many more amino acid changes in PrP leading to increased resistance than to higher susceptibility. Most changes are in the globular part of PrP protein and three regions appear to have major influence. This knowledge can be transferred into prion diseases of other species to facilitate genetic control strategies. However, an obstacle remains with the lack of fully understanding the underlying molecular mechanism, impeding our ability to deal with the difference in the genetic control between typical and atypical forms of scrapie or to predict association in newly infected species. This chapter will discuss the advances in both typical and atypical scrapie from a genetic perspective.

Genetic resistance to transmissible spongiform encephalopathies (TSE) in goats

Breeding programmes to promote resistance to classical scrapie, similar to those for sheep in existing transmissible spongiform encephalopathies (TSE) regulations, have not been established in goats. The European Commission requested a scientific opinion from EFSA on the current knowledge of genetic resistance to TSE in goats. An evaluation tool, which considers both the weight of evidence and strength of resistance to classical scrapie of alleles in the goat PRNP gene, was developed and applied to nine selected alleles of interest. Using the tool, the quality and certainty of the field and experimental data are considered robust enough to conclude that the K222, D146 and S146 alleles both confer genetic resistance against classical scrapie strains known to occur naturally in the EU goat population, with which they have been challenged both experimentally and under field conditions. The weight of evidence for K222 is greater than that currently available for the D146 and S146 alleles and for the ARR allele in sheep in 2001. Breeding for resistance can be an effective tool for controlling classical scrapie in goats and it could be an option available to member states, both at herd and population levels. There is insufficient evidence to assess the impact of K222, D146 and S146 alleles on susceptibility to atypical scrapie and bovine spongiform encephalopathy (BSE), or on health and production traits. These alleles are heterogeneously distributed across the EU Member States and goat breeds, but often at low frequencies (< 10%). Given these low frequencies, high selection pressure may have an adverse effect on genetic diversity so any breeding for resistance programmes should be developed at Member States, rather than EU level and their impact monitored, with particular attention to the potential for any negative impact in rare or small population breeds.