Single nucleotide polymorphisms (SNPs) in the open reading frame (ORF) of prion protein gene (PRNP) in Nigerian livestock species.

BACKGROUND: Prion diseases, also known as transmissible spongiform encephalopathies (TSEs) remain one of the deleterious disorders, which have affected several animal species. Polymorphism of the prion protein (PRNP) gene majorly determines the susceptibility of animals to TSEs. However, only limited studies have examined the variation in PRNP gene in different Nigerian livestock species. Thus, this study aimed to identify the polymorphism of PRNP gene in Nigerian livestock species (including camel, dog, horse, goat, and sheep). We sequenced the open reading frame (ORF) of 65 camels, 31 village dogs and 12 horses from Nigeria and compared with PRNP sequences of 886 individuals retrieved from public databases. RESULTS: All the 994 individuals were assigned into 162 haplotypes. The sheep had the highest number of haplotypes (n = 54), and the camel had the lowest (n = 7). Phylogenetic tree further confirmed clustering of Nigerian individuals into their various species. We detected five non-synonymous SNPs of PRNP comprising of G9A, G10A, C11G, G12C, and T669C shared by all Nigerian livestock species and were in Hardy-Weinberg Equilibrium (HWE). The amino acid changes in these five non-synonymous SNP were all "benign" via Polyphen-2 program. Three SNPs G34C, T699C, and C738G occurred only in Nigerian dogs while C16G, G502A, G503A, and C681A in Nigerian horse. In addition, C50T was detected only in goats and sheep. CONCLUSION: Our study serves as the first to simultaneously investigate the polymorphism of PRNP gene in Nigerian livestock species and provides relevant information that could be adopted in programs targeted at breeding for prion diseases resistance.

Characterization and genetic diversity of MHC class II DRB genes in the Arabian camel (Camelus dromedarius).

This study investigated the MHC DRB genes in the Arabian camel (Camelus dromedarius). The results revealed the presence of - at least - two transcribed DRB-like genes in chromosome 20, designated MhcCadr-DRB1 and MhcCadr-DRB2. These genes are 155 Kb apart, have similar gene structure, and are transcribed in opposite directions. Compared to DRB1, the DRB2 locus contains a deletion of 12 nucleotides in the second exon (270 bp), exhibits lower transcript abundance, and is expressed as two splice variants differing by exon 2 skipping. This gene seems to be of minor functional relevance in the dromedary camel. Conversely, the DRB1 is thought to be the main gene in this species showing higher transcript abundance and polymorphism levels. A total of seven DRB1 exon 2 alleles were identified in the Tunisian dromedary camel resulting from 18 amino acid substitutions. Six full length alleles were characterized at the mRNA level. Although there is no clear evidence for balancing selection (i.e., heterozygote advantage), signals of weak historical positive selection acting on the DRB1 gene were detected, as indicated by the limited number of the sites being positively selected. This trend might be related to the low exposure to pathogens and to the demographic history of the species. Comparative analysis with Bactrian and wild camel genomes suggested occurrence of trans species polymorphism (TSP) in the Camelus genus. The results lay the foundation for the MHC DRB1 genetic diversity analysis in this genus since the developed genotyping protocols are fully applicable in the three Camelus species.

Polymorphism of prion protein gene (PRNP) in Nigerian sheep.

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.

Scrapie-associated polymorphisms of the prion protein gene (PRNP) in Nigerian native goats.

Scrapie is a fatal prion protein disease stiffly associated with single nucleotide polymorphism (SNPs) of the prion protein gene (PRNP). The prevalence of this deadly disease has been reported in small ruminants, including goats. The Nigerian goats are hardy, trypano-tolerant, and contribute to the protein intake of the increasing population. Although scrapie has been reported in Nigerian goats, there is no study on the polymorphism of the PRNP gene. Herein, we evaluated the genetic and allele distributions of PRNP polymorphism in 132 Nigerian goats and compared them with publicly available studies on scrapie-affected goats. We utilized Polyphen-2, PROVEAN and AMYCO programs to examine structural variations produced by the non-synonymous SNPs. Our study revealed 29 SNPs in Nigerian goats, of which 14 were non-synonymous, and 23 were novel. There were significant differences (P < 0.001) in the allele frequencies of PRNP codons 139, 146, 154 and 193 in Nigerian goats compared with scrapie-affected goats, except for Northern Italian goats at codon 154. Based on the prediction by Polyphen-2, R139S and N146S were 'benign', R154H was 'probably damaging', and T193I was 'possibly damaging'. In contrast, PROVEAN predicted 'neutral' for all non-synonymous SNPs, while AMYCO showed a similar amyloid propensity of PRNP for resistant haplotype and two haplotypes of Nigerian goats. Our study is the first to investigate the polymorphism of scrapie-related genes in Nigerian goats.

Genetic Variation in the Prion Protein Gene (PRNP) of Two Tunisian Goat Populations.

Scrapie is a fatal prion disease. It belongs to transmissible spongiform encephalopathies (TSEs), and occurs in sheep and goats. Similarly, to ovine species, the prion protein gene (PRNP) plays a major role in conferring resistance or susceptibility to TSE in goats. This study assesses the variability of PRNP in native and crossed-breed goat populations raised in the Southeast of Tunisia and provides information on the distribution of PRNP haplotypes and genotypes in these goat populations. A total of 116 unrelated goats including 82 native and 34 crossed-breed goats were screened for PRNP polymorphisms using Sanger sequencing. Sequence analysis revealed 10 non-synonymous polymorphisms (G37V, M137I, R139S, I142M, H143R, N146D, R154H, R211Q, Q222K, and S240P), giving rise to 12 haplotypes and 23 genotypes. Moreover, four silent mutations were detected at codons 30, 42, 138, and 179; the former was reported for the first time in goat (nucleotide 60 c→t). Interestingly, the PrP variants associated with resistance (D146 and K222) or with a prolonged incubation time of goat to scrapie (M142, R143, H154, Q211) were absent or detected with low frequencies except for H154 variant, which is present with high frequency (1%, 1%, 4%, 0%, 88%, and 6%, respectively, for native goats, and 0%, 1%, 0%, 1%, 78%, and 1%, respectively, for crossed goats). The analysis of PRNP polymorphisms of goats raised in other regions of the country will be useful in getting a global view of PRNP genetic variability and the feasibility of goat breeding programs in Tunisia.

Factors affecting milk yield and composition of Tunisian camels (Camelus dromedarius) over complete lactation.

This study aimed to investigate the milk production potential and the impact of nongenetic factors on milk yield and composition of Tunisian dromedary camels. Milk recording and sampling were carried out at monthly intervals over complete lactation for 3 years from 95 camels reared in intensive and semi-intensive systems. The overall means of daily milk yield and fat, protein, total solids, and ash contents were 4.21 ± 1.98 l/day, 2.45 ± 0.9%, 2.67 ± 0.74%, 10.75 ± 1.41%, and 0.85 ± 0.08%, respectively. The total milk yield was 1388.41 ± 575.46 l/lactation for 11 months of lactation. The daily milk yield increased regularly throughout lactation until it reached its peak in the 4th month postpartum and then decreased until the 17th month postpartum. The chemical components, except ash, followed an opposite trend to the milk yield. Their minimum contents were recorded during the 7th and 8th months postpartum, while the maximum levels were observed during the 17th month postpartum. Regarding seasonal variation, the highest daily milk yield was recorded during summer (June), whereas the lowest was found in winter (December). In contrast, the maximum and minimum contents of fat and protein were observed during winter (December) and summer (July), respectively. Similarly, total solids content was maximum in January and minimum in August. Parity had no effect on daily milk yield, while all chemical components were higher in milk from primiparous than multiparous camels. Calf sex and management system did not affect the milk yield and composition. These results are useful in order to develop feeding strategies and breeding programs for improving milk production.